http://2010.igem.org/wiki/index.php?title=Special:Contributions/Stjahns&feed=atom&limit=50&target=Stjahns&year=&month=2010.igem.org - User contributions [en]2024-03-28T08:32:23ZFrom 2010.igem.orgMediaWiki 1.16.5http://2010.igem.org/Team:Alberta/mediaTeam:Alberta/media2010-11-20T20:08:07Z<p>Stjahns: Replacing page with '{{Team:Alberta/Head}}
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==Genomikon in the Media==<br />
<div id="horiz-line"></div><br />
<p><br />
Coming soon...<br />
</p><br />
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{{Team:Alberta/endMainContent}}</div>Stjahnshttp://2010.igem.org/Team:Alberta/mediaTeam:Alberta/media2010-11-20T20:06:45Z<p>Stjahns: New page: {{Team:Alberta/Head}} {{Team:Alberta/navbar|overview=selected}} {{Team:Alberta/beginLeftSideBar}} {{Team:Alberta/endLeftSideBar}} {{Team:Alberta/beginRightSideBar}} {{Team:Alberta/end...</p>
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==BioBytes 2.0==<br />
<div id="horiz-line"></div><br />
<p><br />
The first major accomplishment of our project was the design and optimization of the [[Team:Alberta/biobyte2|BioBytes 2.0]] standard for parts. Using the BioByte 2.0 system as a standard for our parts we created an assembly method that allows the construction of useful transformable constructs from BioBytes. This was done very early on, but was essential for the progression and success of the remainder of the project.<br />
</p><br />
<br />
==DNA Attachment==<br />
<div id="horiz-line"></div><br />
<p><br />
The next major step in the development of GENOMIKON was to successfully attach the BioBytes 2.0 anchor to poly-T iron micro beads. This was demonstrated by attaching a 1kbp anchor-AB KanR to the iron micro beads, then eluting it off of the beads.</p><br />
[[Image:Alberta Elution Gel.jpg|center]]<br />
<p><br />
As we can see, all of the 1kbp anchor-AB KanR is removed in the initial elution and none remains attached to the beads in the subsequent wash step. This is also true of the two BioBytes 2.0 construct seen on the right that is a 2kbp piece added to a 1kbp piece.<br />
</p><br />
<br />
==Octamer Construction==<br />
<div id="horiz-line"></div><br />
[[Image:Team-alberta-modeling-octomer-gel.png|thumb|left|x300px|Gel showing octamer formation (Lane 3)]]<br />
<p><br />
Our next major accomplishment was the assembly of a 12kbp construct made of 8 pieces of DNA using the BioBytes 2.0 assembly method. The octamer was assembled on an iron micro bead, starting with the anchor, and adding alternating 1kbp pieces and 2kbp pieces until the full 12kbp construct was achieved. This is seen in the third lane. A tetramer of the same construction is seen in the second lane.<br />
</p><br />
<p><br />
It can be observed that the the major product of both the octamer and tetramer constructs was the complete construct. This was an exciting gel, as the octamer was constructed in under 3 hours - a feat that would have taken more than an entire summer using the BioBrick method.<br />
</p><p><br />
With our octamer in hand we pushed forward to create plasmids using the BioBytes 2.0 assembly method to create functional plasmids to transform into ''E. coli''<br />
</p><br />
<br />
<div style="clear:both"></div><br />
<br />
==Transformation of <em>''E. coli''</em> with a Constructed Plasmid==<br />
<div id="horiz-line"></div><br />
<p><br />
The octamer demonstrated that we could create long constructs out of pieces of DNA, so the next step was to construct a fully functional plasmid and test drive it in a cell. [[Image:Alberta Tformplasmid.jpg|right|250px]] To do this, we started with a short construct that contained all the required parts of a plasmid: an Ori, a selectable marker, and RFP so complete assemblies could be easily screened for. This also allowed us to test out the parts we had made specifically for this purpose and test BioBytes 2.0 in a more applicable environment.<br />
</p><br />
<br />
<p><br />
This plasmid is seen on the right and contains everything needed to function in vivo. It was constructed on an iron micro bead starting from the anchor and was finished with the cap.<br />
</p><br />
[[Image:Alberta_Rfpkan.jpg|left|250px|thumb|This shows the cells that were transformed using constructs created using BIoBytes 2.0 fluorescing red and a negative control.]]<br />
As we can see in the figure on the left the transformations were successful. This was a huge step for our team as it shows unambiguously that BioBytes 2.0 can create working plasmids that can be transformed into ''E. coli''.<br />
<br />
<br />
<div style="clear:both"></div><br />
<br />
==High School Student Assemblies==<br />
<div id="horiz-line"></div><br />
<p><br />
Once we had transformed <em>''E. coli''</em> with constructs we made using BioBytes 2.0, we wanted to test the educational value of the project. To do this, we completed the same experiment with five high school students using precision droppers. [[Image:Studentplate.jpg|right|280px|thumb|Cells transformed with plasmids created by high school students]] Each group of students ended up with red fluorescent colonies on their plates. Using the BioBytes 2.0 assembly method, high school students are able, with limited technology, to successfully construct their own plasmids. A more in depth look what was done with the high school students can be found on our [[Team:Alberta/human_practices/HighSchool|High School]] page.<br />
</p><br />
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{{Team:Alberta/endMainContent}}</div>Stjahnshttp://2010.igem.org/Template:Team:Alberta/navbarTemplate:Team:Alberta/navbar2010-11-20T20:05:44Z<p>Stjahns: </p>
<hr />
<div><html><br />
<div id="navbar"><br />
<ul><br />
<li><a href="https://2010.igem.org/Team:Alberta" class="</html>{{{home|}}}<html> nav-home" >HOME</a></li><br />
<li><a href="https://2010.igem.org/Team:Alberta/Tour/start" class="</html>{{{tour|}}}<html> nav-software">AT A GLANCE</a></li><br />
<li class="headlink"><a href="https://2010.igem.org/Team:Alberta/project" class="</html>{{{project|}}}<html> nav-project" >PROJECT </a><br />
<ul><br />
<li><a href="https://2010.igem.org/Team:Alberta/project">Overview</a></li><br />
<hr><br />
<li><a href="https://2010.igem.org/Team:Alberta/biobyte2">BioBytes 2.0</a></li><br />
<hr><br />
<li><a href="https://2010.igem.org/Team:Alberta/Software">Software</a></li><br />
<hr><br />
<li><a href="https://2010.igem.org/Team:Alberta/modelling">Modelling</a></li><br />
<hr><br />
<li><a href="https://2010.igem.org/Team:Alberta/Kit">The Kit</a></li><br />
<hr><br />
<li><a href="https://2010.igem.org/Team:Alberta/Kit_components">Kit Components</a></li><br />
</ul><br />
</li><br />
<li class="headlink" ><a href="https://2010.igem.org/Team:Alberta/Achievements/Overview" class="</html>{{{achievments|}}}<html> nav-practices" >ACHIEVEMENTS </a><br />
<ul><br />
<li><a href="https://2010.igem.org/Team:Alberta/Achievements/Overview">Overview</a></li><br />
<hr><br />
<li><a href="https://2010.igem.org/Team:Alberta/Achievements">Medal Requirements </a></li><br />
</ul><br />
</li><br />
<li class="headlink"><a href="https://2010.igem.org/Team:Alberta/human_practices" class="</html>{{{practices|}}}<html> nav-practices" >HUMAN PRACTICES</a><br />
<ul><br />
<li><a href="https://2010.igem.org/Team:Alberta/human_practices">Overview</a></li><br />
<hr><br />
<li><a href="https://2010.igem.org/Team:Alberta/human_practices/distribution_analysis">Distribution Analysis</a></li><br />
<hr><br />
<li><a href="https://2010.igem.org/Team:Alberta/human_practices/HighSchool">High School</a></li><br />
<hr><br />
<li><a href="https://2010.igem.org/Team:Alberta/human_practices/DiscoverElle">DiscoverElle Visit</a></li><br />
<hr><br />
<li><a href="https://2010.igem.org/Team:Alberta/human_practices/safety">Safety</a></li><br />
</ul><br />
</li><br />
<li><a href="https://2010.igem.org/Team:Alberta/parts"class="</html>{{{parts|}}}<html> nav-parts">PARTS</a></li><br />
<li class="headlink"><a href="https://2010.igem.org/Team:Alberta/Notebook" class="</html>{{{notebook|}}}<html> nav-notebook">TIMELINE & PROTOCOLS</a><br />
<ul><br />
<li><a href="https://2010.igem.org/Team:Alberta/Notebook">Overview</a></li><br />
<hr><br />
<li><a href="https://2010.igem.org/Team:Alberta/Notebook/protocols">General Protocols</a></li><br />
<hr><br />
<li><a href="https://2010.igem.org/Team:Alberta/Notebook/ReusablePlates">Reusable Plates</a></li><br />
<hr><br />
<li><a href="https://2010.igem.org/Team:Alberta/Notebook/BasePlasmids">Base Plasmids</a></li><br />
<hr><br />
<li><a href="https://2010.igem.org/Team:Alberta/Notebook/CreatingParts">Creating Parts</a></li><br />
<hr><br />
<li><a href="https://2010.igem.org/Team:Alberta/Notebook/TransformingCells">Transforming Cells</a></li><br />
<hr><br />
<li><a href="https://2010.igem.org/Team:Alberta/Notebook/Anchor">Anchor</a></li><br />
<hr><br />
<li><a href="https://2010.igem.org/Team:Alberta/Notebook/Beads">Beads</a></li><br />
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<li><a href="https://2010.igem.org/Team:Alberta/Notebook/Optimizations">Optimizations</a></li><br />
<hr><br />
<li><a href="https://2010.igem.org/Team:Alberta/Notebook/Software">Software</a></li><br />
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<li><a href="https://2010.igem.org/Team:Alberta/team" class="</html>{{{team|}}}<html> nav-team" >TEAM</a></li><br />
<li><a href="https://2010.igem.org/Team:Alberta/media" class="</html>{{{team|}}}<html> nav-team" >MEDIA</a></li> <br />
<ul><br />
</div><br />
</html></div>Stjahnshttp://2010.igem.org/Team:Alberta/Tour/softwareTeam:Alberta/Tour/software2010-10-28T03:36:59Z<p>Stjahns: </p>
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[[Image:Alberta-Screen1.png|right|thumb|280px|The part designer software interface.]]<br />
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[[Image:Alberta-Screen2.png|left|thumb|280px|A page out of the lab manual.]]<br />
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==Online Companion Software==<br />
<div id="horiz-line"></div><br />
<br />
Complimenting the physical GENOMIKON kit is an online software suite. Packaged together at [http://genomikon.ca GENOMIKON.ca] is:<br />
*An electronic lab manual that guides users through experiments packaged with the kit, with the capacity for users to design their own experiments.<br />
*An ''in silico'' plasmid design tool, where users can piece together plasmids by simply dragging parts together, while the software automatically generates a protocol for constructing that same plasmid with the kit.<br />
*Informational materials including an encyclopedia and glossary of terms for molecular biology related topics.<br />
*An online student and DYIbio community, where users can share and collaborate on experiments, while teachers can monitor their students' activities and progress.<br />
The aim of the software suite is to empower students to go beyond the traditional "cookbook recipe" model of the high school science lab. Students are encouraged to experiment on their own, trying any number of possible plasmid construction combinations and genetic circuits in their own unique experiments.<br />
<br />
{{Team:Alberta/endMainContent}}</div>Stjahnshttp://2010.igem.org/Team:Alberta/Notebook/protocols/invitro_biobyte_assemblyTeam:Alberta/Notebook/protocols/invitro biobyte assembly2010-10-28T03:13:08Z<p>Stjahns: </p>
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==General Protocols==<br />
-----------------------------<br />
*[[Team:Alberta/Notebook/protocols/invitro_biobyte_assembly | In Vitro BioByte Assembly]]<br />
-----------------------------<br />
*[[Team:Alberta/Notebook/protocols/LB | LB Plates and Broth]]<br />
<br />
*[[Team:Alberta/Notebook/protocols/transformations |Transformations]]<br />
<br />
*[[Team:Alberta/Notebook/protocols/overnight |5mL Overnight ]]<br />
<br />
*[[Team:Alberta/Notebook/protocols/glycerol | Glycerol Stock ]]<br />
-----------------------------<br />
*[[Team:Alberta/Notebook/protocols/miniprep | Plasmid Miniprep ]]<br />
<br />
*[[Team:Alberta/Notebook/protocols/digest | Restriction Digest ]]<br />
<br />
*[[Team:Alberta/Notebook/protocols/vector_dephos | Vector Dephosphorylation]]<br />
<br />
*[[Team:Alberta/Notebook/protocols/ligation | Ligation ]]<br />
-----------------------------<br />
*[[Team:Alberta/Notebook/protocols/agarose_gel | Agarose Gel Electrophoresis ]]<br />
<br />
*[[Team:Alberta/Notebook/protocols/gel_extraction | Gel Extraction ]]<br />
-----------------------------<br />
*[[Team:Alberta/Notebook/protocols/pcr | PCR]]<br />
<br />
*[[Team:Alberta/Notebook/protocols/colony_pcr | Colony PCR ]]<br />
<br />
*[[Team:Alberta/Notebook/protocols/pcr_purification | PCR Purification ]]<br />
-----------------------------<br />
*[[Team:Alberta/Notebook/protocols/labelling | Sample Labelling Conventions]]<br />
<br />
*[[Team:Alberta/Notebook/protocols/sequencing | Fluorescent Sequencing Reaction]]<br />
<br />
*[[Team:Alberta/Notebook/protocols/primer_design | Primer Design]]<br />
-----------------------------<br />
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==In Vitro BioBytes Assembly 2.0==<br />
<br />
<br><br />
<br />
===Reagents:===<br />
<br />
* 1.5mL Eppendorf tubes<br />
* Magnet<br />
* Wash/binding buffer (10mM Tris 1mM EDTA pH8.0)<br />
* Elution buffer ?<br />
* 5x ligase buffer<br />
* Ligase<br />
* PCR cleanup kit<br />
* Para magnetic beads (oligo-dT25mer NEB# S1419S)<br />
* A18_AB anchor stock solution (0.1pM; 67ng/uL in TE)<br />
* AB KanR byte @ 40 ng/uL (0.06 pM/uL; gel purified in E buffer; 0.9 kbp)<br />
* BA Byte (0.1pM; 67ng/uL in TE)<br />
<br />
<br />
===Procedure:===<br />
<br />
Preparing AB byte Anchor:<br />
*Add in a reaction:<br />
{|<br />
|KanR AB Byte (2.2ug; 4pM) || 5uL<br />
|-<br />
|Anchor (900 ng; 50pM) || 4uL<br />
|-<br />
|Q-Ligase buffer (x2) || 20uL<br />
|-<br />
|Q-ligase || 1uL<br />
|-<br />
|Total || 40uL<br />
|}<br />
*5 minutes @ R/T followed by heat inactivation @65<sup>o</sup>C for 10 minutes.<br />
<br />
<br />
===Binding:===<br />
<br />
* Mix beads with a couple of shakes followed by 10 minutes slow rotation.<br />
* Wash x2 with 50uL TE buffer<br />
* Add anchor byte ((0.4pM;0.27ug) and top to 20uL with TE.<br />
* 30 minutes of repeated flicking and inversion<br />
* 2x Wash as above<br />
<br />
<br />
===Ligation:===<br />
<br />
* Add:<br />
{|<br />
|MilliQ water || 6uL<br />
|-<br />
|BA Byte (0.4pM;0.27ug total) || 4uL<br />
|-<br />
|2x Q-ligase buffer || 10uL<br />
|-<br />
|Q-ligase || 1uL<br />
|-<br />
|Total || 20uL<br />
|}<br />
* 5 minutes @ R/T with gentle mixing.<br />
* 2x Wash as above<br />
<br />
<br />
===Elution:===<br />
<br />
* Add 20uL of elution buffer @70<sup>o</sup>C.<br />
* Mix and remove rapidly.<br />
<br />
<br />
<br />
{{Team:Alberta/endMainContent}}</div>Stjahnshttp://2010.igem.org/Team:Alberta/KitTeam:Alberta/Kit2010-10-27T05:03:33Z<p>Stjahns: </p>
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==GENOMIKON - Kit Design==<br />
<div id="horiz-line"></div><br />
<br />
====The Idea====<br />
<p><br />
GENOMIKON evolved from a team objective to bring synthetic biology to high school students. High schools have limitations that don't apply to university research labs and thus we had to over come many design challenges. [[Image:Alberta_Jill1.jpg|160px|right|thumb|One of the many students that can benefit from GENOMIKON.]]</p> <br />
<p>To work GENOMIKON must be:<br />
*Require very little expensive equipment (autoclaves, centrifuges, -70C freezers)<br />
*Fast<br />
*Efficient<br />
*Easily shipped<br />
*Inexpensive<br />
</p><br />
<br />
====The Innovation====<br />
<p><br />
[[Team:Alberta/biobyte2 |BioBytes 2.0]] solved most of these problems.</p><p>BioBytes 2.0 is:<br />
*Fast: Parts can be added to a growing construct in 7 minutes.<br />
*Efficient: It has been modeled to be 95% efficient. We have also used BioBytes 2.0 to create plasmids that have been transformed successfully into ''E. coli''.<br />
*Equipment: It does not require centrifugation or any other expensive equipment inherently.<br />
<br />
</p><br />
====The Kit====<br />
<p><br />
The other limitations were solved by using innovative protocols and products:<br />
*Equipment: Expensive micropipetters are replaced with precision droppers, which can accurately dispense small volumes of solutions.<br />
*Easily Shipped: We will utilize lyophilized competent cells so that cold temperatures are not necessary.<br />
*Inexpensive: Based on our [[Team:Alberta/human_practices/distribution_analysis|distribution analysis]], the kit will be inexpensive to produce and can be sold at costs that are lower than currently used high school biology labs.</p><br />
The full contents of the kit can be found on the [[Team:Alberta/Kit_components|kit components]] page.<br />
<p><br />
[[Image:Alberta Partial kit.jpg|center|550px|thumb|This picture shows the precision pipettes, the buffers, and the magnet racks among other kit items.]]<br />
</p><br />
====Safety====<br />
<p><br />
GENOMIKON was designed with safety in mind and as such it has many safety features built in.<br />
*A common lab strain of ''E. coli'' DH5&alpha; is used. This strain has been used safely in labs around the world and was designed to be safe.<br />
*Proper safety equipment is not required, but will be recommended to further decrease the risks of contamination.<br />
*The kit will teach safety education to the students.<br />
</p><br />
<br />
====Reception====<br />
<p><br />
When we tested our kit with high school students from the Edmonton area, it had a warm reception. They had great things to say about the educational aspect and the scientific aspect of the kit. They did give us some useful feedback. An in-depth look at this component can be seen on [[Team:Alberta/human_practices#Real_World_Trials|real world trials]].<br />
<br />
</p><br />
{{Team:Alberta/endMainContent}}</div>Stjahnshttp://2010.igem.org/Team:Alberta/KitTeam:Alberta/Kit2010-10-27T05:01:51Z<p>Stjahns: </p>
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<br />
==GENOMIKON - Kit Design==<br />
<div id="horiz-line"></div><br />
<br />
====The Idea====<br />
<p><br />
GENOMIKON evolved from a team objective to bring synthetic biology to high school students. High schools have limitations that don't apply to university research labs and thus we had to over come many design challenges. [[Image:Alberta_Jill1.jpg|160px|right|thumb|One of the many students that can benefit from GENOMIKON.]]</p> <br />
<p>To work GENOMIKON must be:<br />
*Require very little expensive equipment (autoclaves, centrifuges, -70C freezers)<br />
*Fast<br />
*Efficient<br />
*Easily shipped<br />
*Inexpensive<br />
</p><br />
<br />
====The Innovation====<br />
<p><br />
[[Team:Alberta/biobyte2 |BioBytes 2.0]] solved most of these problems.</p><p>BioBytes 2.0 is:<br />
*Fast: Parts can be added to a growing construct in 7 minutes.<br />
*Efficient: It has been modeled to be 95% efficient. We have also used BioBytes 2.0 to create plasmids that have been transformed successfully into ''E. coli''.<br />
*Equipment: It does not require centrifugation or any other expensive equipment inherently.<br />
<br />
</p><br />
====The Kit====<br />
<p><br />
The other limitations were solved by using innovative protocols and products:<br />
*Equipment: Expensive micropipetters are replaced with precision droppers, which can accurately dispense small volumes of solutions.<br />
*Easily Shipped: We will utilize lyophilized competent cells so that cold temperatures are not necessary.<br />
*Inexpensive: Based on our [[Team:Alberta/human_practices/distribution_analysis|distribution analysis]], the kit will be inexpensive to produce and can be sold at costs that are lower than currently used high school biology labs.</p><br />
The full contents of the kit can be found on the [[Team:Alberta/Kit_components|kit components]] page.<br />
<p><br />
[[Image:Alberta Partial kit.jpg|center|550px|thumb|This picture shows the precision pipettes, the buffers, and the magnet racks among other kit items.]]<br />
</p><br />
====Safety====<br />
<p><br />
GENOMIKON was designed with safety in mind and as such it has many safety features built in.<br />
*A common lab strain of ''E. coli'' DH5&alpha; is used. This strain has been used safely in labs around the world and was designed to be safe.<br />
*Proper safety equipment is not required, but will be recommended to further decrease the risks of contamination.<br />
*The kit will teach safety education to the students.<br />
</p><br />
<br />
====Reception====<br />
<p><br />
When we tested our kit with high school students from the Edmonton area, it had a warm reception. They had great things to say about the educational aspect and the scientific aspect of the kit. They did give us some useful feedback. An in-depth look at this component can be seen on [[Team:Alberta/human_practices#Real_World_Trials|real world trials]].<br />
<br />
</p><br />
{{Team:Alberta/endMainContent}}</div>Stjahnshttp://2010.igem.org/Team:Alberta/KitTeam:Alberta/Kit2010-10-27T05:00:41Z<p>Stjahns: /* GENOMIKON - Kit Design */</p>
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==GENOMIKON - Kit Design==<br />
<div id="horiz-line"></div><br />
<br />
===The Idea===<br />
<p><br />
GENOMIKON evolved from a team objective to bring synthetic biology to high school students. High schools have limitations that don't apply to university research labs and thus we had to over come many design challenges. [[Image:Alberta_Jill1.jpg|160px|right|thumb|One of the many students that can benefit from GENOMIKON.]]</p> <br />
<p>To work GENOMIKON must be:<br />
*Require very little expensive equipment (autoclaves, centrifuges, -70C freezers)<br />
*Fast<br />
*Efficient<br />
*Easily shipped<br />
*Inexpensive<br />
</p><br />
<br />
===The Innovation===<br />
<p><br />
[[Team:Alberta/biobyte2 |BioBytes 2.0]] solved most of these problems.</p><p>BioBytes 2.0 is:<br />
*Fast: Parts can be added to a growing construct in 7 minutes.<br />
*Efficient: It has been modeled to be 95% efficient. We have also used BioBytes 2.0 to create plasmids that have been transformed successfully into ''E. coli''.<br />
*Equipment: It does not require centrifugation or any other expensive equipment inherently.<br />
<br />
</p><br />
===The Kit===<br />
<p><br />
The other limitations were solved by using innovative protocols and products:<br />
*Equipment: Expensive micropipetters are replaced with precision droppers, which can accurately dispense small volumes of solutions.<br />
*Easily Shipped: We will utilize lyophilized competent cells so that cold temperatures are not necessary.<br />
*Inexpensive: Based on our [[Team:Alberta/human_practices/distribution_analysis|distribution analysis]], the kit will be inexpensive to produce and can be sold at costs that are lower than currently used high school biology labs.</p><br />
The full contents of the kit can be found on the [[Team:Alberta/Kit_components|kit components]] page.<br />
<p><br />
[[Image:Alberta Partial kit.jpg|center|550px|thumb|This picture shows the precision pipettes, the buffers, and the magnet racks among other kit items.]]<br />
</p><br />
===Safety===<br />
<p><br />
GENOMIKON was designed with safety in mind and as such it has many safety features built in.<br />
*A common lab strain of ''E. coli'' DH5&alpha; is used. This strain has been used safely in labs around the world and was designed to be safe.<br />
*Proper safety equipment is not required, but will be recommended to further decrease the risks of contamination.<br />
*The kit will teach safety education to the students.<br />
</p><br />
<br />
===Reception===<br />
<p><br />
When we tested our kit with high school students from the Edmonton area, it had a warm reception. They had great things to say about the educational aspect and the scientific aspect of the kit. They did give us some useful feedback. An in-depth look at this component can be seen on [[Team:Alberta/human_practices#Real_World_Trials|real world trials]].<br />
<br />
</p><br />
{{Team:Alberta/endMainContent}}</div>Stjahnshttp://2010.igem.org/Team:Alberta/Notebook/SoftwareTeam:Alberta/Notebook/Software2010-10-27T04:53:03Z<p>Stjahns: /* Software Notebook */</p>
<hr />
<div>{{Team:Alberta/Head}}<br />
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{{Team:Alberta/navbar|notebook=selected}}<br />
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{{Team:Alberta/beginLeftSideBar|toc=NO}}<br />
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==Software Notebook==<br />
<div id="horiz-line"></div><br />
<br />
See [http://github.com/stjahns/Alberta-IGEM/network github commit network] for more detailed progress.<br />
<br />
== 16/10/2010 ==<br />
<br />
=== Steve ===<br />
* restyling genomikon.ca to match wiki<br />
<br />
== 14/10/2010 ==<br />
<br />
=== Steve ===<br />
* added crude iphone/ipad support, needs work<br />
<br />
== 02/09/2010 ==<br />
* added plasmid construction sandbox<br />
<br />
== 26/08/2010 ==<br />
* prettied up plasmid editor<br />
* added biobyte categories<br />
* rewrote sequence display<br />
<br />
== 17/08/2010 ==<br />
* added 'print to pdf' plugin<br />
* cleaned up routes, added validation to users and groups<br />
<br />
== 09/08/2010 ==<br />
* added part sequence validation perl script<br />
* added part spec sheets<br />
<br />
== 29/07/2010 ==<br />
* added ownership permissions<br />
* added sequence annotations<br />
<br />
== 19/07/2010 ==<br />
* added RBAC role/permission models<br />
<br />
== 01/07/2010 ==<br />
* styled experiment pages<br />
<br />
== 15/06/2010 ==<br />
=== Mike ===<br />
* added associations between users and experiments<br />
* added code for changing views based on ownership<br />
* added user profile page<br />
<br />
Todo:<br />
* add publish experiment checkbox to profile page<br />
* move javascript for experiment view to its own file<br />
* fix weird bug that reappeared in form on Experiment view <br />
* add user "notes" to steps<br />
* add image caching to FlexImage stuff<br />
<br />
== 14/06/2010 ==<br />
<br />
=== Mike ===<br />
* fixed up step model code<br />
* improved javascript on experiment page<br />
<br />
<br />
== 11/06/2010 ==<br />
<br />
=== Mike ===<br />
* synced up with Steve<br />
* added ordering functionality to steps<br />
* added ability to insert steps between other steps<br />
<br />
== 10/06/2010 ==<br />
<br />
=== Mike ===<br />
* Fixed all bugs with image uploading, cleaned up routing for lab book<br />
* added inline upload forms to experiment view<br />
<br />
<br />
== 09/06/2010 ==<br />
<br />
=== Mike ===<br />
* Added FlexImage plugin and integrated with lab book<br />
<br />
<br />
== 08/06/2010 ==<br />
<br />
=== Steve ===<br />
* Integrating construct designer with mike's electronic lab book back-end<br />
* Created a StepGenerator that generates a crude protocol based on the contents of an experiments associated constructs<br />
<br />
== 07/06/2010 ==<br />
<br />
=== Steve ===<br />
[[Image: constructdesignerdev3.png|none|thumb|Screenshot]]<br />
* Added more complicated custom sequence annotation<br />
* Integrating Jacqueline's login stuff with construct & biobyte owner/admin permissions and junk<br />
<br />
== 02/06/2010 ==<br />
<br />
=== Steve ===<br />
<div><br />
[[Image: constructdesignerdev2.png|none|thumb|Screenshot]]<br />
* Added simple construct validation<br />
* Added simple sequence annotation<br />
* Added reverse strand display<br />
</div><br />
<br />
=== Mike ===<br />
<div><br />
* Got inline forms to work, and ajax to work<br />
</div><br />
<br />
== 31/05/2010 ==<br />
===Steve===<br />
<br />
[[Image: partdesignerdev1.png|none|thumb|Early screenshot]]<br />
* Working on parts designer javascript applet<br />
** Functioning drag and drop<br />
** Working on adding more features like sequence annotation<br />
<br />
<br />
===Jacqueline===<br />
<br />
*added user authentication<br />
*added glossary entry form<br />
*working on encyclopedia entry form<br />
<br />
<br />
===Mike===<br />
* working on lab book<br />
* so far have working forms for adding new steps and experiments and navigation of experiments<br />
* today was working on inline editing features and added some styles to the layout<br />
* things to work on: get inline editing to working state, add images to experiment views and possibly image uploading<br />
<br />
{{Team:Alberta/endMainContent}}</div>Stjahnshttp://2010.igem.org/Team:Alberta/Notebook/SoftwareTeam:Alberta/Notebook/Software2010-10-27T04:52:33Z<p>Stjahns: /* Software Notebook */</p>
<hr />
<div>{{Team:Alberta/Head}}<br />
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{{Team:Alberta/navbar|notebook=selected}}<br />
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{{Team:Alberta/beginLeftSideBar|toc=NO}}<br />
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{{Team:Alberta/beginMainContent}}<br />
==Software Notebook==<br />
<div id="horiz-line"></div><br />
<br />
See [http://github.com/stjahns/Alberta-IGEM/network github] for more detailed progress.<br />
<br />
== 16/10/2010 ==<br />
<br />
=== Steve ===<br />
* restyling genomikon.ca to match wiki<br />
<br />
== 14/10/2010 ==<br />
<br />
=== Steve ===<br />
* added crude iphone/ipad support, needs work<br />
<br />
== 02/09/2010 ==<br />
* added plasmid construction sandbox<br />
<br />
== 26/08/2010 ==<br />
* prettied up plasmid editor<br />
* added biobyte categories<br />
* rewrote sequence display<br />
<br />
== 17/08/2010 ==<br />
* added 'print to pdf' plugin<br />
* cleaned up routes, added validation to users and groups<br />
<br />
== 09/08/2010 ==<br />
* added part sequence validation perl script<br />
* added part spec sheets<br />
<br />
== 29/07/2010 ==<br />
* added ownership permissions<br />
* added sequence annotations<br />
<br />
== 19/07/2010 ==<br />
* added RBAC role/permission models<br />
<br />
== 01/07/2010 ==<br />
* styled experiment pages<br />
<br />
== 15/06/2010 ==<br />
=== Mike ===<br />
* added associations between users and experiments<br />
* added code for changing views based on ownership<br />
* added user profile page<br />
<br />
Todo:<br />
* add publish experiment checkbox to profile page<br />
* move javascript for experiment view to its own file<br />
* fix weird bug that reappeared in form on Experiment view <br />
* add user "notes" to steps<br />
* add image caching to FlexImage stuff<br />
<br />
== 14/06/2010 ==<br />
<br />
=== Mike ===<br />
* fixed up step model code<br />
* improved javascript on experiment page<br />
<br />
<br />
== 11/06/2010 ==<br />
<br />
=== Mike ===<br />
* synced up with Steve<br />
* added ordering functionality to steps<br />
* added ability to insert steps between other steps<br />
<br />
== 10/06/2010 ==<br />
<br />
=== Mike ===<br />
* Fixed all bugs with image uploading, cleaned up routing for lab book<br />
* added inline upload forms to experiment view<br />
<br />
<br />
== 09/06/2010 ==<br />
<br />
=== Mike ===<br />
* Added FlexImage plugin and integrated with lab book<br />
<br />
<br />
== 08/06/2010 ==<br />
<br />
=== Steve ===<br />
* Integrating construct designer with mike's electronic lab book back-end<br />
* Created a StepGenerator that generates a crude protocol based on the contents of an experiments associated constructs<br />
<br />
== 07/06/2010 ==<br />
<br />
=== Steve ===<br />
[[Image: constructdesignerdev3.png|none|thumb|Screenshot]]<br />
* Added more complicated custom sequence annotation<br />
* Integrating Jacqueline's login stuff with construct & biobyte owner/admin permissions and junk<br />
<br />
== 02/06/2010 ==<br />
<br />
=== Steve ===<br />
<div><br />
[[Image: constructdesignerdev2.png|none|thumb|Screenshot]]<br />
* Added simple construct validation<br />
* Added simple sequence annotation<br />
* Added reverse strand display<br />
</div><br />
<br />
=== Mike ===<br />
<div><br />
* Got inline forms to work, and ajax to work<br />
</div><br />
<br />
== 31/05/2010 ==<br />
===Steve===<br />
<br />
[[Image: partdesignerdev1.png|none|thumb|Early screenshot]]<br />
* Working on parts designer javascript applet<br />
** Functioning drag and drop<br />
** Working on adding more features like sequence annotation<br />
<br />
<br />
===Jacqueline===<br />
<br />
*added user authentication<br />
*added glossary entry form<br />
*working on encyclopedia entry form<br />
<br />
<br />
===Mike===<br />
* working on lab book<br />
* so far have working forms for adding new steps and experiments and navigation of experiments<br />
* today was working on inline editing features and added some styles to the layout<br />
* things to work on: get inline editing to working state, add images to experiment views and possibly image uploading<br />
<br />
{{Team:Alberta/endMainContent}}</div>Stjahnshttp://2010.igem.org/Team:Alberta/Notebook/SoftwareTeam:Alberta/Notebook/Software2010-10-27T04:51:37Z<p>Stjahns: /* SOFTWARE NOTEBOOK */</p>
<hr />
<div>{{Team:Alberta/Head}}<br />
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{{Team:Alberta/navbar|notebook=selected}}<br />
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{{Team:Alberta/beginLeftSideBar|toc=NO}}<br />
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{{Team:Alberta/beginMainContent}}<br />
==Software Notebook==<br />
<div id="horiz-line"></div><br />
<br />
== 16/10/2010 ==<br />
<br />
=== Steve ===<br />
* restyling genomikon.ca to match wiki<br />
<br />
== 14/10/2010 ==<br />
<br />
=== Steve ===<br />
* added crude iphone/ipad support, needs work<br />
<br />
== 02/09/2010 ==<br />
* added plasmid construction sandbox<br />
<br />
== 26/08/2010 ==<br />
* prettied up plasmid editor<br />
* added biobyte categories<br />
* rewrote sequence display<br />
<br />
== 17/08/2010 ==<br />
* added 'print to pdf' plugin<br />
* cleaned up routes, added validation to users and groups<br />
<br />
== 09/08/2010 ==<br />
* added part sequence validation perl script<br />
* added part spec sheets<br />
<br />
== 29/07/2010 ==<br />
* added ownership permissions<br />
* added sequence annotations<br />
<br />
== 19/07/2010 ==<br />
* added RBAC role/permission models<br />
<br />
== 01/07/2010 ==<br />
* styled experiment pages<br />
<br />
== 15/06/2010 ==<br />
=== Mike ===<br />
* added associations between users and experiments<br />
* added code for changing views based on ownership<br />
* added user profile page<br />
<br />
Todo:<br />
* add publish experiment checkbox to profile page<br />
* move javascript for experiment view to its own file<br />
* fix weird bug that reappeared in form on Experiment view <br />
* add user "notes" to steps<br />
* add image caching to FlexImage stuff<br />
<br />
== 14/06/2010 ==<br />
<br />
=== Mike ===<br />
* fixed up step model code<br />
* improved javascript on experiment page<br />
<br />
<br />
== 11/06/2010 ==<br />
<br />
=== Mike ===<br />
* synced up with Steve<br />
* added ordering functionality to steps<br />
* added ability to insert steps between other steps<br />
<br />
== 10/06/2010 ==<br />
<br />
=== Mike ===<br />
* Fixed all bugs with image uploading, cleaned up routing for lab book<br />
* added inline upload forms to experiment view<br />
<br />
<br />
== 09/06/2010 ==<br />
<br />
=== Mike ===<br />
* Added FlexImage plugin and integrated with lab book<br />
<br />
<br />
== 08/06/2010 ==<br />
<br />
=== Steve ===<br />
* Integrating construct designer with mike's electronic lab book back-end<br />
* Created a StepGenerator that generates a crude protocol based on the contents of an experiments associated constructs<br />
<br />
== 07/06/2010 ==<br />
<br />
=== Steve ===<br />
[[Image: constructdesignerdev3.png|none|thumb|Screenshot]]<br />
* Added more complicated custom sequence annotation<br />
* Integrating Jacqueline's login stuff with construct & biobyte owner/admin permissions and junk<br />
<br />
== 02/06/2010 ==<br />
<br />
=== Steve ===<br />
<div><br />
[[Image: constructdesignerdev2.png|none|thumb|Screenshot]]<br />
* Added simple construct validation<br />
* Added simple sequence annotation<br />
* Added reverse strand display<br />
</div><br />
<br />
=== Mike ===<br />
<div><br />
* Got inline forms to work, and ajax to work<br />
</div><br />
<br />
== 31/05/2010 ==<br />
===Steve===<br />
<br />
[[Image: partdesignerdev1.png|none|thumb|Early screenshot]]<br />
* Working on parts designer javascript applet<br />
** Functioning drag and drop<br />
** Working on adding more features like sequence annotation<br />
<br />
<br />
===Jacqueline===<br />
<br />
*added user authentication<br />
*added glossary entry form<br />
*working on encyclopedia entry form<br />
<br />
<br />
===Mike===<br />
* working on lab book<br />
* so far have working forms for adding new steps and experiments and navigation of experiments<br />
* today was working on inline editing features and added some styles to the layout<br />
* things to work on: get inline editing to working state, add images to experiment views and possibly image uploading<br />
<br />
{{Team:Alberta/endMainContent}}</div>Stjahnshttp://2010.igem.org/Team:Alberta/Notebook/SoftwareTeam:Alberta/Notebook/Software2010-10-27T04:51:04Z<p>Stjahns: </p>
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<div>{{Team:Alberta/Head}}<br />
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{{Team:Alberta/navbar|notebook=selected}}<br />
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{{Team:Alberta/beginLeftSideBar|toc=NO}}<br />
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==SOFTWARE NOTEBOOK==<br />
<div id="horiz-line"></div><br />
<br />
== 16/10/2010 ==<br />
<br />
=== Steve ===<br />
* restyling genomikon.ca to match wiki<br />
<br />
== 14/10/2010 ==<br />
<br />
=== Steve ===<br />
* added crude iphone/ipad support, needs work<br />
<br />
== 02/09/2010 ==<br />
* added plasmid construction sandbox<br />
<br />
== 26/08/2010 ==<br />
* prettied up plasmid editor<br />
* added biobyte categories<br />
* rewrote sequence display<br />
<br />
== 17/08/2010 ==<br />
* added 'print to pdf' plugin<br />
* cleaned up routes, added validation to users and groups<br />
<br />
== 09/08/2010 ==<br />
* added part sequence validation perl script<br />
* added part spec sheets<br />
<br />
== 29/07/2010 ==<br />
* added ownership permissions<br />
* added sequence annotations<br />
<br />
== 19/07/2010 ==<br />
* added RBAC role/permission models<br />
<br />
== 01/07/2010 ==<br />
* styled experiment pages<br />
<br />
== 15/06/2010 ==<br />
=== Mike ===<br />
* added associations between users and experiments<br />
* added code for changing views based on ownership<br />
* added user profile page<br />
<br />
Todo:<br />
* add publish experiment checkbox to profile page<br />
* move javascript for experiment view to its own file<br />
* fix weird bug that reappeared in form on Experiment view <br />
* add user "notes" to steps<br />
* add image caching to FlexImage stuff<br />
<br />
== 14/06/2010 ==<br />
<br />
=== Mike ===<br />
* fixed up step model code<br />
* improved javascript on experiment page<br />
<br />
<br />
== 11/06/2010 ==<br />
<br />
=== Mike ===<br />
* synced up with Steve<br />
* added ordering functionality to steps<br />
* added ability to insert steps between other steps<br />
<br />
== 10/06/2010 ==<br />
<br />
=== Mike ===<br />
* Fixed all bugs with image uploading, cleaned up routing for lab book<br />
* added inline upload forms to experiment view<br />
<br />
<br />
== 09/06/2010 ==<br />
<br />
=== Mike ===<br />
* Added FlexImage plugin and integrated with lab book<br />
<br />
<br />
== 08/06/2010 ==<br />
<br />
=== Steve ===<br />
* Integrating construct designer with mike's electronic lab book back-end<br />
* Created a StepGenerator that generates a crude protocol based on the contents of an experiments associated constructs<br />
<br />
== 07/06/2010 ==<br />
<br />
=== Steve ===<br />
[[Image: constructdesignerdev3.png|none|thumb|Screenshot]]<br />
* Added more complicated custom sequence annotation<br />
* Integrating Jacqueline's login stuff with construct & biobyte owner/admin permissions and junk<br />
<br />
== 02/06/2010 ==<br />
<br />
=== Steve ===<br />
<div><br />
[[Image: constructdesignerdev2.png|none|thumb|Screenshot]]<br />
* Added simple construct validation<br />
* Added simple sequence annotation<br />
* Added reverse strand display<br />
</div><br />
<br />
=== Mike ===<br />
<div><br />
* Got inline forms to work, and ajax to work<br />
</div><br />
<br />
== 31/05/2010 ==<br />
===Steve===<br />
<br />
[[Image: partdesignerdev1.png|none|thumb|Early screenshot]]<br />
* Working on parts designer javascript applet<br />
** Functioning drag and drop<br />
** Working on adding more features like sequence annotation<br />
<br />
<br />
===Jacqueline===<br />
<br />
*added user authentication<br />
*added glossary entry form<br />
*working on encyclopedia entry form<br />
<br />
<br />
===Mike===<br />
* working on lab book<br />
* so far have working forms for adding new steps and experiments and navigation of experiments<br />
* today was working on inline editing features and added some styles to the layout<br />
* things to work on: get inline editing to working state, add images to experiment views and possibly image uploading<br />
<br />
{{Team:Alberta/endMainContent}}</div>Stjahnshttp://2010.igem.org/Team:AlbertaTeam:Alberta2010-10-27T04:47:07Z<p>Stjahns: </p>
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__NOTOC__<br />
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<div id="main-info-box"><br />
==GENOMIKON: An Educational Toolkit for Rapid Genetic Construction.==<br />
<div id="horiz-line"></div><br />
<div style="margin: 0pt; height: 70px;"><br />
GENOMIKON is a kit designed to bring synthetic biology into the high-school classroom. By integrating the BioByte 2.0 assembly method and our innovative website GENOMIKON.ca, we are making synthetic biology accessible, reliable and easy to use. To learn more, see "GENOMIKON AT A GLANCE", and feel free to explore the rest of the site.<br />
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<div id="tour-link" class="tour-link"><p>GENOMIKON AT A GLANCE</p></div><br />
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</div><br />
<div id="info-box1" class="right-info-box achieve-link"><br />
<br />
==Achievements==<br />
# BioBytes 2.0 plasmid assembly technology.<br />
# Plasmid assembly kit for the high school classroom.<br />
# Online educational lab manual software.<br />
# Demonstrated that high school students can successfully assemble plasmids.<br />
<br />
</div><br />
<div id="info-box2" class="right-info-box software-link"><br />
<br />
==THE SOFTWARE==<br />
Learn how to use the kit then, create and share your own designs!<br />
<html><br />
<!---[[Image:team-alberta-main-page-plasmid-builder.png]]--><br />
<img width="242" height="96" border="0" src="/wiki/images/a/a9/Team-alberta-main-page-plasmid-builder.png" alt="Image:team-alberta-main-page-plasmid-builder.png" style="position: relative; top: 60px; left: -9px;"><br />
</html><br />
</div><br />
<div id="info-box3" class="center-info-box biobytes-link"><br />
<br />
==BioBytes 2.0==<br />
Continually developing the BioByte assembly technology created by the Alberta 2009 team, we were able to make this rapid plasmid assembly method amenable to a high school teaching kit. <br />
</div><br />
<div id="info-box4" class="center-info-box kit-link"><br />
==The kit==<br />
Everything you need to put together a plasmid in an afternoon.<br />
<!--[[Image:team-alberta-closed-kit-image-w264.png||x171px]]--><br />
<html><br />
<img height="171" src="/wiki/images/1/17/Team-alberta-closed-kit-image-w264.png"><br />
</html><br />
</div><br />
<div id="thanks-footer"><br />
<span class="llink1"><br />
==[[Team:Alberta/Sponsors|THANK YOU TO OUR GENEROUS CONTRIBUTORS]]==<br />
</span><br />
</div><br />
{{Team:Alberta/endMainContent}}</div>Stjahnshttp://2010.igem.org/Team:Alberta/genomikon.cssTeam:Alberta/genomikon.css2010-10-27T04:45:33Z<p>Stjahns: </p>
<hr />
<div>/* NOTE This is an edited version of the MediaWiki 'monobook' style sheet <br />
* edited by Team Alberta 2010 for their wiki<br />
*/<br />
<br />
<br />
div#test{<br />
background-color:red;<br />
width:100px;<br />
height:100px;<br />
}<br />
<br />
/* things we want to hide */<br />
#info-box1 h2 .editsection, #info-box2 h2 .editsection, #info-box3 h2 .editsection, #info-box4 h2 .editsection{<br />
display:none;<br />
}<br />
h1.firstHeading {<br />
display:none;<br />
}<br />
<br />
#p-logo{<br />
display:none;<br />
}<br />
<br />
/* rearrange the topsection bar */<br />
#top-section{<br />
height:0;<br />
}<br />
#menubar{<br />
top:0;<br />
}<br />
#search-controls{<br />
top:4px;<br />
left:745px;<br />
width:0;<br />
}<br />
#searchInput{<br />
border:1px solid white;<br />
position:absolute;<br />
}<br />
/*<br />
#mw-searchButton{<br />
color:#FFFFFF;<br />
left:172px;<br />
top:0;<br />
position:absolute;<br />
}<br />
#searchGoButton{<br />
position:absolute;<br />
left:130px;<br />
}<br />
*/<br />
<br />
#searchGoButton{<br />
display:none;<br />
}<br />
#mw-searchButton{<br />
background-color:#282560;<br />
border:1px solid white;<br />
color:transparent;<br />
height:19px;<br />
left:124px;<br />
position:absolute;<br />
top:-1px;<br />
width:24px;<br />
cursor:pointer;<br />
background-image:url("https://static.igem.org/mediawiki/2010/8/83/Team-alberta-search-glass.png");<br />
background-position:center center;<br />
background-repeat:no-repeat;<br />
}<br />
<br />
<br />
<br />
/******** things we added ****************/<br />
#tour-link{<br />
-moz-border-radius:10px 10px 10px 10px; <br />
-webkit-border-radius:10px 10px 10px 10px; <br />
background-color:#282560; <br />
position: absolute;<br />
bottom: 0px;<br />
left: 0px;<br />
padding:28px;<br />
width: 89%;<br />
text-align:center;<br />
z-index: 10;<br />
}<br />
<br />
#tour-link:hover{<br />
background-color:#403B9D;<br />
cursor: pointer;<br />
}<br />
#tour-link p {<br />
margin: 0;<br />
color:#FFFFFF;<br />
font-weight:bold;<br />
font-size:30px;<br />
}<br />
<br />
div#igem-logo-link{<br />
background-color:transparent;<br />
background-image:url("https://static.igem.org/mediawiki/2010/7/74/Team-Alberta-IGEM-logo100x77.png");<br />
height:77px;<br />
margin:0;<br />
position:absolute;<br />
width:100px;<br />
left:870px;<br />
top:33px;<br />
}<br />
<br />
div#igem-logo-link a{<br />
color:transparent;<br />
display:block;<br />
height:77px;<br />
width:100px;<br />
}<br />
<br />
#top-strip{<br />
background-color:#282560;<br />
clear:both;<br />
display:block;<br />
height:170px;<br />
padding-left:50%;<br />
padding-right:54%;<br />
position:absolute;<br />
top:0;<br />
width:0<br />
}<br />
#top-strip h2{<br />
color:#73FF9A;<br />
display:block;<br />
font-size:35px;<br />
font-weight:bold;<br />
left:61px;<br />
line-height:39px;<br />
position:relative;<br />
top:22px;<br />
}<br />
<br />
/*** position the genomikon logo ***/<br />
#top-strip a img{<br />
position:absolute;<br />
top:38px;<br />
left:0;<br />
width:auto;<br />
height:79px;<br />
}<br />
<br />
/*** navbar styling **/<br />
#navbar {<br />
position:absolute;<br />
top:131px;<br />
}<br />
#navbar ul {<br />
list-style:none;<br />
width:100%;<br />
}<br />
#navbar ul li{<br />
float:left;<br />
position:relative;<br />
}<br />
#navbar ul li a:visited,#navbar ul li a:link{<br />
margin-right:30px;<br />
color:#fff;<br />
font-weight:bold;<br />
}<br />
#navbar ul li a:hover,#navbar ul li a.selected {<br />
color:#00F2BC;<br />
text-decoration:none;<br />
}<br />
#navbar li.headlink ul{<br />
display:table;<br />
display:none;<br />
background-color:#282560;<br />
margin:0 10px 0 0;<br />
text-align:left;<br />
padding:10px;<br />
z-index:20;<br />
position:absolute;<br />
left:-10px;<br />
width:100%;<br />
}<br />
#navbar li.headlink ul li{<br />
float:none;<br />
}<br />
<br />
<br />
/* make a content area in center and a sidebar on each side*/<br />
#left-sidebar, #right-sidebar, #center-content, #wide-content{<br />
float:left;<br />
/* leave space for header */<br />
margin-top:170px;<br />
min-height:1em;<br />
}<br />
<br />
#left-sidebar.not-top, #right-sidebar.not-top, #center-content.not-top, #wide-content.not-top{<br />
margin-top:0;<br />
}<br />
<br />
#center-content{<br />
width:550px; <br />
}<br />
/*The centre content for the Timeline needs to be a bit wider*/<br />
#center-content .timeline{<br />
width:800px;<br />
float:none;<br />
}<br />
#wide-content{<br />
width:1075px;<br />
}<br />
<br />
#left-sidebar, #right-sidebar{<br />
width:198px;<br />
}<br />
/*Need Timeline to start at left*/<br />
#left-sidebar .Timeline{<br />
width:0px;<br />
}<br />
#left-sidebar{<br />
margin-right:20px;<br />
}<br />
#right-sidebar{<br />
border:none;<br />
margin-left:20px;<br />
<br />
/* position: absolute;<br />
right: 0px;<br />
width: 190px;<br />
border-left: 3px solid gray;<br />
font-size: 95%;<br />
line-height: 90%;*/<br />
}<br />
<br />
#tourbar-back{<br />
clear:both;<br />
height: 3px;<br />
width: 100%;<br />
background-color: #EEEEEE;<br />
}<br />
/* the tourbar */<br />
#tourbar{<br />
clear:both;<br />
height:5em;<br />
margin:173px auto 4em;<br />
width:788px;<br />
}<br />
#tourbar a{<br />
background:none repeat scroll 0 0 #CCCCCC;<br />
color:black;<br />
display:block;<br />
float:left;<br />
height:1em;<br />
padding:3em 0;<br />
text-align:center;<br />
vertical-align:middle;<br />
font-weight: bold;<br />
width:100px;<br />
margin-right:5px;<br />
margin-left:5px;<br />
-moz-border-radius: 10px;<br />
border-radius: 10px;<br />
<br />
}<br />
<br />
#tourbar a:hover{<br />
text-decoration: none;<br />
filter:progid:DXImageTransform.Microsoft.Alpha(opacity=50);<br />
-moz-opacity: 0.5;<br />
opacity: 0.5;<br />
<br />
}<br />
#tourbar a.selected{<br />
margin-top:1em;<br />
}<br />
#tourbar a.left{<br />
background-color:white;<br />
background-image:url("/wiki/images/d/da/Team-alberta-left-arrow.png");<br />
background-repeat:no-repeat;<br />
width:54px;<br />
}<br />
#tourbar a.right{<br />
background-color:white;<br />
background-image:url("/wiki/images/6/6f/Team-alberta-right-arrow.png");<br />
background-repeat:no-repeat;<br />
width:54px;<br />
}<br />
/* the info boxes on homepage */<br />
#main-info-box,#info-box1,#info-box2,#info-box3,#info-box4{<br />
height:250px;<br />
padding:18px;<br />
z-index:-1;<br />
float:left;<br />
}<br />
#info-box1 ol,#info-box2 ol,#info-box3 ol,#info-box4 ol {<br />
margin-left: 1em;<br />
}<br />
<br />
#main-info-box {<br />
width:550px;<br />
overflow:hidden;<br />
padding:0;<br />
height:286px;<br />
position: relative;<br />
z-index: 10;<br />
}<br />
<br />
#tinted-info-box {<br />
width:100%<br />
overflow:hidden;<br />
padding:10px;<br />
height:286px;<br />
clear:both;<br />
background-color: #00F2BC;<br />
<br />
<br />
}<br />
<br />
#left-gray-box {<br />
width:100%;<br />
padding-left: 10px;<br />
background-color: #e6e6e6;<br />
}<br />
<br />
#info-box1,#info-box2,#info-box3,#info-box4 {<br />
background-color:#00CDD0;<br />
color:#282560;<br />
overflow:hidden;<br />
width:228px;<br />
margin-top: 18px;<br />
cursor: pointer;<br />
-moz-border-radius: 10px;<br />
border-radius: 10px;<br />
<br />
}<br />
#info-box1 h2,#info-box2 h2,#info-box3 h2,#info-box4 h2{<br />
color:#282560;<br />
text-align:center;<br />
text-transform:uppercase;<br />
}<br />
#info-box1 p,#info-box2 p,#info-box3 p,#info-box4 p{<br />
color:#000<br />
}<br />
.right-info-box{<br />
}<br />
.center-info-box{<br />
float:left;<br />
}<br />
/* software */<br />
#tourbar a.software{<br />
background-color:#B5FFEE;<br />
}<br />
#info-box1{<br />
margin-top:0;<br />
/* background-color:#00cdd0;*/<br />
background-color:#B5FFEE;<br />
margin-left:12px;<br />
}<br />
<br />
#info-box1:hover {<br />
background-color: #93DDB4<br />
}<br />
<br />
/* kit box */<br />
#tourbar a.kit {<br />
background-color:#b8fed1;<br />
}<br />
<br />
#info-box2{<br />
/*background-color: # b8fed1;*/<br />
background-color:#D6FFE2;<br />
}<br />
#info-box2:hover {<br />
/*background-color:#9AC2FD;*/<br />
background-color:#A6FFC0;<br />
}<br />
<br />
/* achievments boxes*/<br />
#tourbar a.achievements{<br />
background-color:#B4FFC9;<br />
}<br />
#info-box3{<br />
/* background-color:# 7 3FF9A;*/<br />
background-color:#B4FFC9;<br />
margin-left:17px;<br />
}<br />
#info-box3:hover {<br />
background-color:#93DDb8;<br />
}<br />
<br />
/* biobytes boxes */<br />
#tourbar a.biobytes{<br />
background-color:#BCD7FF;<br />
}<br />
#info-box4 {<br />
/* background-color:#00F2BC;*/<br />
background-color:#BCD7FF;<br />
margin-left:18px;<br />
}<br />
#info-box4:hover {<br />
/* background-color:#33f5f6;*/<br />
background-color:#9AC2FD;<br />
}<br />
<br />
<br />
<br />
/* parts table */<br />
#mytable <br />
{<br />
width: 100%;<br />
padding: 0;<br />
margin: 0;<br />
}<br />
<br />
#mytable th <br />
{<br />
background-color:#282560;<br />
color:#fff;<br />
padding:6px 6px 6px 12px;<br />
text-align:left;<br />
}<br />
<br />
#mytable td <br />
{<br />
background: #ccc;<br />
padding: 0.3em 0.3em 0.3em 0.7em;<br />
color: #282560;<br />
}<br />
<br />
<br />
#mytable td.alt <br />
{<br />
background: #ffffff;<br />
color: #282560;<br />
}<br />
<br />
#mytable th.spec <br />
{<br />
background: #a5a5a5 no-repeat;<br />
font: bold 1em "Trebuchet MS", Times;<br />
color: #ffffff;<br />
}<br />
<br />
#mytable th.specalt <br />
{<br />
background: #ffffff no-repeat;<br />
font: bold 1em "Trebuchet MS", Times;<br />
color: #656565;<br />
}<br />
#mytable a:visited, #mytable a:link, #mytable a:hover{<br />
color:#282560;<br />
text-decoration:underline;<br />
}<br />
#mytable a:hover {<br />
color:#00F2BC;<br />
}<br />
<br />
/********* things we changed ***********/<br />
<br />
<br />
#toctitle, span.tocnumber {<br />
display:none;<br />
}<br />
.toclevel-1{<br />
margin-bottom:1em;<br />
}<br />
.toclevel-2{<br />
display:none;<br />
}<br />
span.toctext {<br />
color: #282560;<br />
font-size:14px;<br />
line-height:14px;<br />
}<br />
<br />
#footer-box{<br />
background-color:#E6E6E6;<br />
border:none;<br />
margin:100px auto 0;<br />
padding:5px;<br />
width:965px;<br />
}<br />
body {<br />
background-color:#FFFFFF;<br />
background-image:url("https://static.igem.org/mediawiki/2010/3/36/Team-Alberta-topStrip.png");<br />
background-repeat:repeat-x;<br />
}<br />
<br />
#thanks-footer{<br />
position: relative;<br />
width: 1032px;<br />
left: 0px;<br />
clear:both;<br />
background-color: #DDDDDD;<br />
top: 12px;<br />
border-radius: 10px;<br />
-moz-border-radius: 10px;<br />
text-align: center;<br />
}<br />
<br />
/* new colors */<br />
<br />
h1, h2, h3, h4, h5, h6 {<br />
color: #9D2063;<br />
border:none;<br />
}<br />
<br />
h2 {<br />
line-height:125%;<br />
}<br />
<br />
h3{<br />
font-size:100%;<br />
font-weight:normal;<br />
position:relative;<br />
top:-1em;<br />
color: #282560;<br />
font-style: italic;<br />
margin-bottom: -0.5em;<br />
}<br />
<br />
span.editsection, span.editsection a{<br />
color:#ccc;<br />
}<br />
body{<br />
background-color:#fff;<br />
}<br />
#content{<br />
border:none;<br />
width:975px;<br />
padding-left:0;<br />
padding-right:0;<br />
}<br />
<br />
#menubar li a, #menubar .selected a, #menubar li a:visited{ <br />
color: #888;<br />
}<br />
#menubar li a:hover{<br />
color: #00F2BC;<br />
}<br />
<br />
<br />
/* table of contents */<br />
#toc{<br />
background-color: #EEEEEE;<br />
border:none;<br />
width:100%;<br />
padding-top: 14px;<br />
-moz-border-radius: 10px;<br />
border-radius: 10px;<br />
}<br />
/*timeline stuff*/<br />
<br />
/*months and their overlaying divs*/<br />
<br />
#May{<br />
background-color: Orange;<br />
height: 500px;<br />
width: 780 px;<br />
<br />
}<br />
<br />
ul.rolodex{<br />
list-style-type: none;<br />
list-style-image: none;<br />
}<br />
<br />
ul.rolodex li{<br />
color: #282560;<br />
}<br />
ul.rolodex li:hover {<br />
color: #00F2BC;<br />
cursor: pointer;<br />
}<br />
<br />
.startimage:hover {<br />
filter:progid:DXImageTransform.Microsoft.Alpha(opacity=50);<br />
-moz-opacity: 0.5;<br />
opacity: 0.5;<br />
}<br />
div#horiz-line {<br />
height: 3px;<br />
width: 100%;<br />
background-color: #282560;<br />
margin-top: -1em;<br />
margin-bottom: 1em;<br />
}<br />
#highschool4 {<br />
position: relative;<br />
top: 468px;<br />
}</div>Stjahnshttp://2010.igem.org/Team:Alberta/Notebook/SoftwareTeam:Alberta/Notebook/Software2010-10-27T04:45:01Z<p>Stjahns: </p>
<hr />
<div>{{Team:Alberta/Head}}<br />
<br />
{{Team:Alberta/navbar|notebook=selected}}<br />
<br />
{{Team:Alberta/beginLeftSideBar|toc=NO}}<br />
{{Team:Alberta/endLeftSideBar}}<br />
<br />
{{Team:Alberta/beginRightSideBar}}<br />
{{Team:Alberta/endRightSideBar}}<br />
<br />
{{Team:Alberta/beginMainContent}}<br />
<br />
== 16/10/2010 ==<br />
<br />
=== Steve ===<br />
* restyling genomikon.ca to match wiki<br />
<br />
== 14/10/2010 ==<br />
<br />
=== Steve ===<br />
* added crude iphone/ipad support, needs work<br />
<br />
== 02/09/2010 ==<br />
* added plasmid construction sandbox<br />
<br />
== 26/08/2010 ==<br />
* prettied up plasmid editor<br />
* added biobyte categories<br />
* rewrote sequence display<br />
<br />
== 17/08/2010 ==<br />
* added 'print to pdf' plugin<br />
* cleaned up routes, added validation to users and groups<br />
<br />
== 09/08/2010 ==<br />
* added part sequence validation perl script<br />
* added part spec sheets<br />
<br />
== 29/07/2010 ==<br />
*<br />
<br />
== 15/06/2010 ==<br />
=== Mike ===<br />
* added associations between users and experiments<br />
* added code for changing views based on ownership<br />
* added user profile page<br />
<br />
Todo:<br />
* add publish experiment checkbox to profile page<br />
* move javascript for experiment view to its own file<br />
* fix weird bug that reappeared in form on Experiment view <br />
* add user "notes" to steps<br />
* add image caching to FlexImage stuff<br />
<br />
== 14/06/2010 ==<br />
<br />
=== Mike ===<br />
* fixed up step model code<br />
* improved javascript on experiment page<br />
<br />
<br />
== 11/06/2010 ==<br />
<br />
=== Mike ===<br />
* synced up with Steve<br />
* added ordering functionality to steps<br />
* added ability to insert steps between other steps<br />
<br />
== 10/06/2010 ==<br />
<br />
=== Mike ===<br />
* Fixed all bugs with image uploading, cleaned up routing for lab book<br />
* added inline upload forms to experiment view<br />
<br />
<br />
== 09/06/2010 ==<br />
<br />
=== Mike ===<br />
* Added FlexImage plugin and integrated with lab book<br />
<br />
<br />
== 08/06/2010 ==<br />
<br />
=== Steve ===<br />
* Integrating construct designer with mike's electronic lab book back-end<br />
* Created a StepGenerator that generates a crude protocol based on the contents of an experiments associated constructs<br />
<br />
== 07/06/2010 ==<br />
<br />
=== Steve ===<br />
[[Image: constructdesignerdev3.png|none|thumb|Screenshot]]<br />
* Added more complicated custom sequence annotation<br />
* Integrating Jacqueline's login stuff with construct & biobyte owner/admin permissions and junk<br />
<br />
== 02/06/2010 ==<br />
<br />
=== Steve ===<br />
<div><br />
[[Image: constructdesignerdev2.png|none|thumb|Screenshot]]<br />
* Added simple construct validation<br />
* Added simple sequence annotation<br />
* Added reverse strand display<br />
</div><br />
<br />
=== Mike ===<br />
<div><br />
* Got inline forms to work, and ajax to work<br />
</div><br />
<br />
== 31/05/2010 ==<br />
===Steve===<br />
<br />
[[Image: partdesignerdev1.png|none|thumb|Early screenshot]]<br />
* Working on parts designer javascript applet<br />
** Functioning drag and drop<br />
** Working on adding more features like sequence annotation<br />
<br />
<br />
===Jacqueline===<br />
<br />
*added user authentication<br />
*added glossary entry form<br />
*working on encyclopedia entry form<br />
<br />
<br />
===Mike===<br />
* working on lab book<br />
* so far have working forms for adding new steps and experiments and navigation of experiments<br />
* today was working on inline editing features and added some styles to the layout<br />
* things to work on: get inline editing to working state, add images to experiment views and possibly image uploading<br />
<br />
{{Team:Alberta/endMainContent}}</div>Stjahnshttp://2010.igem.org/Team:AlbertaTeam:Alberta2010-10-27T04:42:48Z<p>Stjahns: </p>
<hr />
<div>{{Team:Alberta/Head}}<br />
{{Team:Alberta/navbar|home=selected}}<br />
__NOTOC__<br />
{{Team:Alberta/beginWideContent}}<br />
<html><br />
<br />
<object width="190" height="497" style="float:left;margin-right:15px;margin-top:5px;"> <param name="flashvars" value="offsite=true&lang=en-us&page_show_url=%2Fphotos%2F55131217%40N04%2Fsets%2F72157625119525505%2Fshow%2F&page_show_back_url=%2Fphotos%2F55131217%40N04%2Fsets%2F72157625119525505%2F&set_id=72157625119525505&jump_to="></param> <param name="movie" value="http://www.flickr.com/apps/slideshow/show.swf?v=71649"></param> <param name="allowFullScreen" value="true"></param><embed type="application/x-shockwave-flash" src="http://www.flickr.com/apps/slideshow/show.swf?v=71649" allowFullScreen="true" flashvars="offsite=true&lang=en-us&page_show_url=%2Fphotos%2F55131217%40N04%2Fsets%2F72157625119525505%2Fshow%2F&page_show_back_url=%2Fphotos%2F55131217%40N04%2Fsets%2F72157625119525505%2F&set_id=72157625119525505&jump_to=" width="190" height="590"></embed></object><br />
</html><br />
<br />
<div id="main-info-box"><br />
==GENOMIKON: An Educational Toolkit for Rapid Genetic Construction.==<br />
<div id="horiz-line"></div><br />
<div style="margin: 0pt; height: 70px;"><br />
GENOMIKON is a kit designed to bring synthetic biology into the high-school classroom. By integrating the BioByte 2.0 assembly method and our innovative website GENOMIKON.ca, we are making synthetic biology accessible, reliable and easy to use. To learn more, see "GENOMIKON AT A GLANCE", and feel free to explore the rest of the site.<br />
</div><br />
<html><br />
<div id="tour-link" class="tour-link"><p>GENOMIKON AT A GLANCE</p></div><br />
<br />
<!--<br />
<div style="clear: both; text-align: center;"><br />
<a href="https://2010.igem.org/Team:Alberta/Tour/start" "id="tourstart"><br />
<img src="/wiki/images/5/5c/Alberta_Start.png" width=140px class=startimage><br />
</a><br />
</div><br />
--><br />
</html><br />
</div><br />
<div id="info-box1" class="right-info-box achieve-link"><br />
<br />
==Achievements==<br />
# BioBytes 2.0 plasmid assembly technology.<br />
# Plasmid assembly kit for the high school classroom.<br />
# Online educational lab manual software.<br />
# Demonstrated that high school students can successfully assemble plasmids.<br />
<br />
</div><br />
<div id="info-box2" class="right-info-box software-link"><br />
<br />
==THE SOFTWARE==<br />
Learn how to use the kit then, create and share your own designs!<br />
<html><br />
<!---[[Image:team-alberta-main-page-plasmid-builder.png]]--><br />
<img width="242" height="96" border="0" src="/wiki/images/a/a9/Team-alberta-main-page-plasmid-builder.png" alt="Image:team-alberta-main-page-plasmid-builder.png" style="position: relative; top: 60px; left: -9px;"><br />
</html><br />
</div><br />
<div id="info-box3" class="center-info-box biobytes-link"><br />
<br />
==BioBytes 2.0==<br />
Continually developing the BioByte assembly technology created by the Alberta 2009 team, we were able to make this rapid plasmid assembly method amenable to a high school teaching kit. <br />
</div><br />
<div id="info-box4" class="center-info-box kit-link"><br />
==The kit==<br />
Everything you need to put together a plasmid in an afternoon.<br />
<!--[[Image:team-alberta-closed-kit-image-w264.png||x171px]]--><br />
<html><br />
<img height="171" src="/wiki/images/1/17/Team-alberta-closed-kit-image-w264.png"><br />
</html><br />
</div><br />
<div id="thanks-footer"><br />
<span class="llink1"><br />
==[[Team:Alberta/Sponsors|THANK YOU TO OUR GENEROUS CONTRIBUTORS]]==<br />
</span><br />
</div><br />
{{Team:Alberta/endMainContent}}</div>Stjahnshttp://2010.igem.org/Team:AlbertaTeam:Alberta2010-10-27T04:38:34Z<p>Stjahns: </p>
<hr />
<div>{{Team:Alberta/Head}}<br />
{{Team:Alberta/navbar|home=selected}}<br />
__NOTOC__<br />
{{Team:Alberta/beginWideContent}}<br />
<html><br />
<br />
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</html><br />
<br />
<div id="main-info-box"><br />
==GENOMIKON: An Educational Toolkit for Rapid Genetic Construction.==<br />
<div id="horiz-line"></div><br />
<div style="margin: 0pt; height: 70px;"><br />
GENOMIKON is a kit designed to bring synthetic biology into the high-school classroom. By integrating the BioByte 2.0 assembly method and our innovative website GENOMIKON.ca, we are making synthetic biology accessible, reliable and easy to use. To learn more, see "GENOMIKON AT A GLANCE", and feel free to explore the rest of the site.<br />
</div><br />
<html><br />
<div id="tour-link" class="tour-link"><p>GENOMIKON AT A GLANCE</p></div><br />
<br />
<!--<br />
<div style="clear: both; text-align: center;"><br />
<a href="https://2010.igem.org/Team:Alberta/Tour/start" "id="tourstart"><br />
<img src="/wiki/images/5/5c/Alberta_Start.png" width=140px class=startimage><br />
</a><br />
</div><br />
--><br />
</html><br />
</div><br />
<div id="info-box1" class="right-info-box achieve-link"><br />
<br />
==Achievements==<br />
# BioBytes 2.0 plasmid assembly technology.<br />
# Plasmid assembly kit for the high school classroom.<br />
# Online educational lab manual software.<br />
# Demonstrated that high school students can successfully assemble plasmids.<br />
<br />
</div><br />
<div id="info-box2" class="right-info-box software-link"><br />
<br />
==THE SOFTWARE==<br />
Learn how to use the kit then, create and share your own designs!<br />
<html><br />
<!---[[Image:team-alberta-main-page-plasmid-builder.png]]--><br />
<img width="242" height="96" border="0" src="/wiki/images/a/a9/Team-alberta-main-page-plasmid-builder.png" alt="Image:team-alberta-main-page-plasmid-builder.png" style="position: relative; top: 60px; left: -9px;"><br />
</html><br />
</div><br />
<div id="info-box3" class="center-info-box biobytes-link"><br />
<br />
==BioBytes 2.0==<br />
Continually developing the BioByte assembly technology created by the Alberta 2009 team, we were able to make this rapid plasmid assembly method amenable to a high school teaching kit. <br />
</div><br />
<div id="info-box4" class="center-info-box kit-link"><br />
==The kit==<br />
Everything you need to put together a plasmid in an afternoon.<br />
<!--[[Image:team-alberta-closed-kit-image-w264.png||x171px]]--><br />
<html><br />
<img height="171" src="/wiki/images/1/17/Team-alberta-closed-kit-image-w264.png"><br />
</html><br />
</div><br />
<div id="thanks-footer"><br />
<span class="llink1"><br />
==[[Team:Alberta/Sponsors|THANK YOU TO OUR GENEROUS CONTRIBUTORS]]==<br />
</span><br />
</div><br />
{{Team:Alberta/endMainContent}}</div>Stjahnshttp://2010.igem.org/Team:Alberta/Notebook/SoftwareTeam:Alberta/Notebook/Software2010-10-27T04:28:40Z<p>Stjahns: /* WWW.GENOMIKON.COM */</p>
<hr />
<div>{{Team:Alberta/Head}}<br />
<br />
{{Team:Alberta/navbar|notebook=selected}}<br />
<br />
{{Team:Alberta/beginLeftSideBar|toc=NO}}<br />
{{Team:Alberta/endLeftSideBar}}<br />
<br />
{{Team:Alberta/beginRightSideBar}}<br />
{{Team:Alberta/endRightSideBar}}<br />
<br />
{{Team:Alberta/beginMainContent}}<br />
<br />
== 16/10/2010 ==<br />
<br />
=== Steve ===<br />
* restyling genomikon.ca to match wiki<br />
<br />
== 14/10/2010 ==<br />
<br />
=== Steve ===<br />
* added crude iphone/ipad support, needs work<br />
<br />
== 15/06/2010 ==<br />
=== Mike ===<br />
* added associations between users and experiments<br />
* added code for changing views based on ownership<br />
* added user profile page<br />
<br />
Todo:<br />
* add publish experiment checkbox to profile page<br />
* move javascript for experiment view to its own file<br />
* fix weird bug that reappeared in form on Experiment view <br />
* add user "notes" to steps<br />
* add image caching to FlexImage stuff<br />
<br />
== 14/06/2010 ==<br />
<br />
=== Mike ===<br />
* fixed up step model code<br />
* improved javascript on experiment page<br />
<br />
<br />
== 11/06/2010 ==<br />
<br />
=== Mike ===<br />
* synced up with Steve<br />
* added ordering functionality to steps<br />
* added ability to insert steps between other steps<br />
<br />
== 10/06/2010 ==<br />
<br />
=== Mike ===<br />
* Fixed all bugs with image uploading, cleaned up routing for lab book<br />
* added inline upload forms to experiment view<br />
<br />
<br />
== 09/06/2010 ==<br />
<br />
=== Mike ===<br />
* Added FlexImage plugin and integrated with lab book<br />
<br />
<br />
== 08/06/2010 ==<br />
<br />
=== Steve ===<br />
* Integrating construct designer with mike's electronic lab book back-end<br />
* Created a StepGenerator that generates a crude protocol based on the contents of an experiments associated constructs<br />
<br />
== 07/06/2010 ==<br />
<br />
=== Steve ===<br />
[[Image: constructdesignerdev3.png|none|thumb|Screenshot]]<br />
* Added more complicated custom sequence annotation<br />
* Integrating Jacqueline's login stuff with construct & biobyte owner/admin permissions and junk<br />
<br />
== 02/06/2010 ==<br />
<br />
=== Steve ===<br />
<div><br />
[[Image: constructdesignerdev2.png|none|thumb|Screenshot]]<br />
* Added simple construct validation<br />
* Added simple sequence annotation<br />
* Added reverse strand display<br />
</div><br />
<br />
=== Mike ===<br />
<div><br />
* Got inline forms to work, and ajax to work<br />
</div><br />
<br />
== 31/05/2010 ==<br />
===Steve===<br />
<br />
[[Image: partdesignerdev1.png|none|thumb|Early screenshot]]<br />
* Working on parts designer javascript applet<br />
** Functioning drag and drop<br />
** Working on adding more features like sequence annotation<br />
<br />
<br />
===Jacqueline===<br />
<br />
*added user authentication<br />
*added glossary entry form<br />
*working on encyclopedia entry form<br />
<br />
<br />
===Mike===<br />
* working on lab book<br />
* so far have working forms for adding new steps and experiments and navigation of experiments<br />
* today was working on inline editing features and added some styles to the layout<br />
* things to work on: get inline editing to working state, add images to experiment views and possibly image uploading<br />
<br />
{{Team:Alberta/endMainContent}}</div>Stjahnshttp://2010.igem.org/Team:Alberta/Tour/conclusionTeam:Alberta/Tour/conclusion2010-10-27T04:25:01Z<p>Stjahns: /* Conclusion */</p>
<hr />
<div>{{Team:Alberta/Head}}<br />
{{Team:Alberta/navbar|tour=selected}}<br />
__NOTOC__<br />
{{Team:Alberta/tourbar|end=selected|left=achievements|right=start}}<br />
<br />
{{Team:Alberta/beginLeftSideBar|toc=NO|class=not-top}}<br />
[[Image:Alberta_Rfpkan.jpg|right|280px|thumb|Cells transformed with a plasmid created using BioBytes 2.0 and a negative control]]<br />
<br />
<br />
{{Team:Alberta/endLeftSideBar}}<br />
{{Team:Alberta/beginRightSideBar|class=not-top}}<br />
[[Image:Team-alberta-closed-kit-image-w264.png|left|280px|thumb|GENOMIKON: The Kit]]<br />
{{Team:Alberta/endRightSideBar}}<br />
<br />
{{Team:Alberta/beginMainContent|class=not-top}}<br />
==Conclusion==<br />
<div id="horiz-line"></div><br />
<br />
GENOMIKON makes synthetic biology easier and faster than ever before bringing the field closer to a young vibrant high school audience. As you have seen our BioBytes Assembly System 2.0 and our GENOMIKON.ca software tools have been integrated together allowing for students to have most enriched learning experience. It brings synthetic biology to people and places it has never been while pushing the development of synthetic biology in new and exciting directions. <br />
<br />
<b>Still have questions? Please see these links for more detailed information:</b><br />
<br />
[[Team:Alberta/biobyte2| BioBytes 2.0]] details the GENOMIKON assembly method.<br />
<br />
[[Team:Alberta/human_practices/safety|Safety]]: read about lab and GENOMIKON kit safety.<br />
<br />
[[Team:Alberta/Notebook/protocols|Protocols]]: all our lab procedures<br />
<br />
[[Team:Alberta/modelling|Modeling]]: learn about the model that demonstrates the efficiency of our assembly method from our experimental results<br />
<br />
[[Team:Alberta/Achievements|Achievements]]: details our many amazing accomplishments<br />
<br />
[[Team:Alberta/human_practices/distribution_analysis|Human practices]]: Details our research into distributing GENOMIKON and the high school curriculum <br />
<br />
[[Team:Alberta/team |Team]]: Meet the team<br />
<br />
[[Team:Alberta/Software|Software]]: outlines the software tools at [http://genomikon.ca GENOMIKON.ca].<br />
<br />
[[Team:Alberta/Notebook |Notebook]]: is a time line of our summer<br />
<br />
[[Team:Alberta/parts |Parts]]: details the parts we submitted<br />
{{Team:Alberta/endMainContent}}</div>Stjahnshttp://2010.igem.org/Team:Alberta/genomikon.cssTeam:Alberta/genomikon.css2010-10-27T04:19:42Z<p>Stjahns: </p>
<hr />
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<br />
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<br />
}<br />
#info-box1 h2,#info-box2 h2,#info-box3 h2,#info-box4 h2{<br />
color:#282560;<br />
text-align:center;<br />
text-transform:uppercase;<br />
}<br />
#info-box1 p,#info-box2 p,#info-box3 p,#info-box4 p{<br />
color:#000<br />
}<br />
.right-info-box{<br />
}<br />
.center-info-box{<br />
float:left;<br />
}<br />
/* software */<br />
#tourbar a.software{<br />
background-color:#B5FFEE;<br />
}<br />
#info-box1{<br />
margin-top:0;<br />
/* background-color:#00cdd0;*/<br />
background-color:#B5FFEE;<br />
margin-left:12px;<br />
}<br />
<br />
#info-box1:hover {<br />
background-color: #93DDB4<br />
}<br />
<br />
/* kit box */<br />
#tourbar a.kit {<br />
background-color:#b8fed1;<br />
}<br />
<br />
#info-box2{<br />
/*background-color: # b8fed1;*/<br />
background-color:#D6FFE2;<br />
}<br />
#info-box2:hover {<br />
/*background-color:#9AC2FD;*/<br />
background-color:#A6FFC0;<br />
}<br />
<br />
/* achievments boxes*/<br />
#tourbar a.achievements{<br />
background-color:#B4FFC9;<br />
}<br />
#info-box3{<br />
/* background-color:# 7 3FF9A;*/<br />
background-color:#B4FFC9;<br />
margin-left:17px;<br />
}<br />
#info-box3:hover {<br />
background-color:#93DDb8;<br />
}<br />
<br />
/* biobytes boxes */<br />
#tourbar a.biobytes{<br />
background-color:#BCD7FF;<br />
}<br />
#info-box4 {<br />
/* background-color:#00F2BC;*/<br />
background-color:#BCD7FF;<br />
margin-left:18px;<br />
}<br />
#info-box4:hover {<br />
/* background-color:#33f5f6;*/<br />
background-color:#9AC2FD;<br />
}<br />
<br />
<br />
<br />
/* parts table */<br />
#mytable <br />
{<br />
width: 100%;<br />
padding: 0;<br />
margin: 0;<br />
}<br />
<br />
#mytable th <br />
{<br />
background-color:#282560;<br />
color:#fff;<br />
padding:6px 6px 6px 12px;<br />
text-align:left;<br />
}<br />
<br />
#mytable td <br />
{<br />
background: #ccc;<br />
padding: 0.3em 0.3em 0.3em 0.7em;<br />
color: #282560;<br />
}<br />
<br />
<br />
#mytable td.alt <br />
{<br />
background: #ffffff;<br />
color: #282560;<br />
}<br />
<br />
#mytable th.spec <br />
{<br />
background: #a5a5a5 no-repeat;<br />
font: bold 1em "Trebuchet MS", Times;<br />
color: #ffffff;<br />
}<br />
<br />
#mytable th.specalt <br />
{<br />
background: #ffffff no-repeat;<br />
font: bold 1em "Trebuchet MS", Times;<br />
color: #656565;<br />
}<br />
#mytable a:visited, #mytable a:link, #mytable a:hover{<br />
color:#282560;<br />
text-decoration:underline;<br />
}<br />
#mytable a:hover {<br />
color:#00F2BC;<br />
}<br />
<br />
/********* things we changed ***********/<br />
<br />
<br />
#toctitle, span.tocnumber {<br />
display:none;<br />
}<br />
.toclevel-1{<br />
margin-bottom:1em;<br />
}<br />
.toclevel-2{<br />
display:none;<br />
}<br />
span.toctext {<br />
color: #282560;<br />
font-size:14px;<br />
line-height:14px;<br />
}<br />
<br />
#footer-box{<br />
background-color:#E6E6E6;<br />
border:none;<br />
margin:100px auto 0;<br />
padding:5px;<br />
width:965px;<br />
}<br />
body {<br />
background-color:#FFFFFF;<br />
background-image:url("https://static.igem.org/mediawiki/2010/3/36/Team-Alberta-topStrip.png");<br />
background-repeat:repeat-x;<br />
}<br />
<br />
#thanks-footer{<br />
position: relative;<br />
width: 1032px;<br />
left: -15px;<br />
clear:both;<br />
background-color: #DDDDDD;<br />
top: 12px;<br />
border-radius: 10px;<br />
-moz-border-radius: 10px;<br />
text-align: center;<br />
}<br />
<br />
/* new colors */<br />
<br />
h1, h2, h3, h4, h5, h6 {<br />
color: #9D2063;<br />
border:none;<br />
}<br />
<br />
h2 {<br />
line-height:125%;<br />
}<br />
<br />
h3{<br />
font-size:100%;<br />
font-weight:normal;<br />
position:relative;<br />
top:-1em;<br />
color: #282560;<br />
font-style: italic;<br />
margin-bottom: -0.5em;<br />
}<br />
<br />
span.editsection, span.editsection a{<br />
color:#ccc;<br />
}<br />
body{<br />
background-color:#fff;<br />
}<br />
#content{<br />
border:none;<br />
width:975px;<br />
padding-left:0;<br />
padding-right:0;<br />
}<br />
<br />
#menubar li a, #menubar .selected a, #menubar li a:visited{ <br />
color: #888;<br />
}<br />
#menubar li a:hover{<br />
color: #00F2BC;<br />
}<br />
<br />
<br />
/* table of contents */<br />
#toc{<br />
background-color: #EEEEEE;<br />
border:none;<br />
width:100%;<br />
padding-top: 14px;<br />
-moz-border-radius: 10px;<br />
border-radius: 10px;<br />
}<br />
/*timeline stuff*/<br />
<br />
/*months and their overlaying divs*/<br />
<br />
#May{<br />
background-color: Orange;<br />
height: 500px;<br />
width: 780 px;<br />
<br />
}<br />
<br />
ul.rolodex{<br />
list-style-type: none;<br />
list-style-image: none;<br />
}<br />
<br />
ul.rolodex li{<br />
color: #282560;<br />
}<br />
ul.rolodex li:hover {<br />
color: #00F2BC;<br />
cursor: pointer;<br />
}<br />
<br />
.startimage:hover {<br />
filter:progid:DXImageTransform.Microsoft.Alpha(opacity=50);<br />
-moz-opacity: 0.5;<br />
opacity: 0.5;<br />
}<br />
div#horiz-line {<br />
height: 3px;<br />
width: 100%;<br />
background-color: #282560;<br />
margin-top: -1em;<br />
margin-bottom: 1em;<br />
}<br />
#highschool4 {<br />
position: relative;<br />
top: 468px;<br />
}</div>Stjahnshttp://2010.igem.org/Team:Alberta/genomikon.cssTeam:Alberta/genomikon.css2010-10-27T04:18:29Z<p>Stjahns: </p>
<hr />
<div><br />
/* NOTE This is an edited version of the MediaWiki 'monobook' style sheet <br />
* edited by Team Alberta 2010 for their wiki<br />
*/<br />
<br />
<br />
div#test{<br />
background-color:red;<br />
width:100px;<br />
height:100px;<br />
}<br />
<br />
/* things we want to hide */<br />
#info-box1 h2 .editsection, #info-box2 h2 .editsection, #info-box3 h2 .editsection, #info-box4 h2 .editsection{<br />
display:none;<br />
}<br />
h1.firstHeading {<br />
display:none;<br />
}<br />
<br />
#p-logo{<br />
display:none;<br />
}<br />
<br />
/* rearrange the topsection bar */<br />
#top-section{<br />
height:0;<br />
}<br />
#menubar{<br />
top:0;<br />
}<br />
#search-controls{<br />
top:4px;<br />
left:745px;<br />
width:0;<br />
}<br />
#searchInput{<br />
border:1px solid white;<br />
position:absolute;<br />
}<br />
/*<br />
#mw-searchButton{<br />
color:#FFFFFF;<br />
left:172px;<br />
top:0;<br />
position:absolute;<br />
}<br />
#searchGoButton{<br />
position:absolute;<br />
left:130px;<br />
}<br />
*/<br />
<br />
#searchGoButton{<br />
display:none;<br />
}<br />
#mw-searchButton{<br />
background-color:#282560;<br />
border:1px solid white;<br />
color:transparent;<br />
height:19px;<br />
left:124px;<br />
position:absolute;<br />
top:-1px;<br />
width:24px;<br />
cursor:pointer;<br />
background-image:url("https://static.igem.org/mediawiki/2010/8/83/Team-alberta-search-glass.png");<br />
background-position:center center;<br />
background-repeat:no-repeat;<br />
}<br />
<br />
<br />
<br />
/******** things we added ****************/<br />
#tour-link{<br />
-moz-border-radius:10px 10px 10px 10px; <br />
-webkit-border-radius:10px 10px 10px 10px; <br />
background-color:#282560; <br />
position: absolute;<br />
bottom: 0px;<br />
left: 0px;<br />
padding:28px;<br />
width: 89%;<br />
text-align:center;<br />
z-index: 10;<br />
}<br />
<br />
#tour-link:hover{<br />
background-color:#403B9D;<br />
cursor: pointer;<br />
}<br />
#tour-link p {<br />
margin: 0;<br />
color:#FFFFFF;<br />
font-weight:bold;<br />
font-size:30px;<br />
}<br />
<br />
div#igem-logo-link{<br />
background-color:transparent;<br />
background-image:url("https://static.igem.org/mediawiki/2010/7/74/Team-Alberta-IGEM-logo100x77.png");<br />
height:77px;<br />
margin:0;<br />
position:absolute;<br />
width:100px;<br />
left:870px;<br />
top:33px;<br />
}<br />
<br />
div#igem-logo-link a{<br />
color:transparent;<br />
display:block;<br />
height:77px;<br />
width:100px;<br />
}<br />
<br />
#top-strip{<br />
background-color:#282560;<br />
clear:both;<br />
display:block;<br />
height:170px;<br />
padding-left:50%;<br />
padding-right:54%;<br />
position:absolute;<br />
top:0;<br />
width:0<br />
}<br />
#top-strip h2{<br />
color:#73FF9A;<br />
display:block;<br />
font-size:35px;<br />
font-weight:bold;<br />
left:61px;<br />
line-height:39px;<br />
position:relative;<br />
top:22px;<br />
}<br />
<br />
/*** position the genomikon logo ***/<br />
#top-strip a img{<br />
position:absolute;<br />
top:38px;<br />
left:0;<br />
width:auto;<br />
height:79px;<br />
}<br />
<br />
/*** navbar styling **/<br />
#navbar {<br />
position:absolute;<br />
top:131px;<br />
}<br />
#navbar ul {<br />
list-style:none;<br />
width:100%;<br />
}<br />
#navbar ul li{<br />
float:left;<br />
position:relative;<br />
}<br />
#navbar ul li a:visited,#navbar ul li a:link{<br />
margin-right:30px;<br />
color:#fff;<br />
font-weight:bold;<br />
}<br />
#navbar ul li a:hover,#navbar ul li a.selected {<br />
color:#00F2BC;<br />
text-decoration:none;<br />
}<br />
#navbar li.headlink ul{<br />
display:table;<br />
display:none;<br />
background-color:#282560;<br />
margin:0 10px 0 0;<br />
text-align:left;<br />
padding:10px;<br />
z-index:20;<br />
position:absolute;<br />
left:-10px;<br />
width:100%;<br />
}<br />
#navbar li.headlink ul li{<br />
float:none;<br />
}<br />
<br />
<br />
/* make a content area in center and a sidebar on each side*/<br />
#left-sidebar, #right-sidebar, #center-content, #wide-content{<br />
float:left;<br />
/* leave space for header */<br />
margin-top:170px;<br />
min-height:1em;<br />
}<br />
<br />
#left-sidebar.not-top, #right-sidebar.not-top, #center-content.not-top, #wide-content.not-top{<br />
margin-top:0;<br />
}<br />
<br />
#center-content{<br />
width:550px; <br />
}<br />
/*The centre content for the Timeline needs to be a bit wider*/<br />
#center-content .timeline{<br />
width:800px;<br />
float:none;<br />
}<br />
#wide-content{<br />
width:1075px;<br />
}<br />
<br />
#left-sidebar, #right-sidebar{<br />
width:198px;<br />
}<br />
/*Need Timeline to start at left*/<br />
#left-sidebar .Timeline{<br />
width:0px;<br />
}<br />
#left-sidebar{<br />
margin-right:20px;<br />
}<br />
#right-sidebar{<br />
border:none;<br />
margin-left:20px;<br />
<br />
/* position: absolute;<br />
right: 0px;<br />
width: 190px;<br />
border-left: 3px solid gray;<br />
font-size: 95%;<br />
line-height: 90%;*/<br />
}<br />
<br />
#tourbar-back{<br />
clear:both;<br />
height: 3px;<br />
width: 100%;<br />
background-color: #EEEEEE;<br />
}<br />
/* the tourbar */<br />
#tourbar{<br />
clear:both;<br />
height:5em;<br />
margin:173px auto 4em;<br />
width:788px;<br />
}<br />
#tourbar a{<br />
background:none repeat scroll 0 0 #CCCCCC;<br />
color:black;<br />
display:block;<br />
float:left;<br />
height:1em;<br />
padding:3em 0;<br />
text-align:center;<br />
vertical-align:middle;<br />
font-weight: bold;<br />
width:100px;<br />
margin-right:5px;<br />
margin-left:5px;<br />
-moz-border-radius: 10px;<br />
border-radius: 10px;<br />
<br />
}<br />
<br />
#tourbar a:hover{<br />
text-decoration: none;<br />
filter:progid:DXImageTransform.Microsoft.Alpha(opacity=50);<br />
-moz-opacity: 0.5;<br />
opacity: 0.5;<br />
<br />
}<br />
#tourbar a.selected{<br />
margin-top:1em;<br />
}<br />
#tourbar a.left{<br />
background-color:white;<br />
background-image:url("/wiki/images/d/da/Team-alberta-left-arrow.png");<br />
background-repeat:no-repeat;<br />
width:54px;<br />
}<br />
#tourbar a.right{<br />
background-color:white;<br />
background-image:url("/wiki/images/6/6f/Team-alberta-right-arrow.png");<br />
background-repeat:no-repeat;<br />
width:54px;<br />
}<br />
/* the info boxes on homepage */<br />
#main-info-box,#info-box1,#info-box2,#info-box3,#info-box4{<br />
height:250px;<br />
padding:18px;<br />
z-index:-1;<br />
float:left;<br />
}<br />
#info-box1 ol,#info-box2 ol,#info-box3 ol,#info-box4 ol {<br />
margin-left: 1em;<br />
}<br />
<br />
#main-info-box {<br />
width:550px;<br />
overflow:hidden;<br />
padding:0;<br />
height:286px;<br />
position: relative;<br />
z-index: 10;<br />
}<br />
<br />
#tinted-info-box {<br />
width:100%<br />
overflow:hidden;<br />
padding:10px;<br />
height:286px;<br />
clear:both;<br />
background-color: #00F2BC;<br />
<br />
<br />
}<br />
<br />
#left-gray-box {<br />
width:100%;<br />
padding-left: 10px;<br />
background-color: #e6e6e6;<br />
}<br />
<br />
#info-box1,#info-box2,#info-box3,#info-box4 {<br />
background-color:#00CDD0;<br />
color:#282560;<br />
overflow:hidden;<br />
width:228px;<br />
margin-top: 18px;<br />
cursor: pointer;<br />
-moz-border-radius: 10px;<br />
border-radius: 10px;<br />
<br />
}<br />
#info-box1 h2,#info-box2 h2,#info-box3 h2,#info-box4 h2{<br />
color:#282560;<br />
text-align:center;<br />
text-transform:uppercase;<br />
}<br />
#info-box1 p,#info-box2 p,#info-box3 p,#info-box4 p{<br />
color:#000<br />
}<br />
.right-info-box{<br />
}<br />
.center-info-box{<br />
float:left;<br />
}<br />
/* software */<br />
#tourbar a.software{<br />
background-color:#B5FFEE;<br />
}<br />
#info-box1{<br />
margin-top:0;<br />
/* background-color:#00cdd0;*/<br />
background-color:#B5FFEE;<br />
margin-left:12px;<br />
}<br />
<br />
#info-box1:hover {<br />
background-color: #93DDB4<br />
}<br />
<br />
/* kit box */<br />
#tourbar a.kit {<br />
background-color:#b8fed1;<br />
}<br />
<br />
#info-box2{<br />
/*background-color: # b8fed1;*/<br />
background-color:#D6FFE2;<br />
}<br />
#info-box2:hover {<br />
/*background-color:#9AC2FD;*/<br />
background-color:#A6FFC0;<br />
}<br />
<br />
/* achievments boxes*/<br />
#tourbar a.achievements{<br />
background-color:#B4FFC9;<br />
}<br />
#info-box3{<br />
/* background-color:# 7 3FF9A;*/<br />
background-color:#B4FFC9;<br />
margin-left:17px;<br />
}<br />
#info-box3:hover {<br />
background-color:#93DDb8;<br />
}<br />
<br />
/* biobytes boxes */<br />
#tourbar a.biobytes{<br />
background-color:#BCD7FF;<br />
}<br />
#info-box4 {<br />
/* background-color:#00F2BC;*/<br />
background-color:#BCD7FF;<br />
margin-left:18px;<br />
}<br />
#info-box4:hover {<br />
/* background-color:#33f5f6;*/<br />
background-color:#9AC2FD;<br />
}<br />
<br />
<br />
<br />
/* parts table */<br />
#mytable <br />
{<br />
width: 100%;<br />
padding: 0;<br />
margin: 0;<br />
}<br />
<br />
#mytable th <br />
{<br />
background-color:#282560;<br />
color:#fff;<br />
padding:6px 6px 6px 12px;<br />
text-align:left;<br />
}<br />
<br />
#mytable td <br />
{<br />
background: #ccc;<br />
padding: 0.3em 0.3em 0.3em 0.7em;<br />
color: #282560;<br />
}<br />
<br />
<br />
#mytable td.alt <br />
{<br />
background: #ffffff;<br />
color: #282560;<br />
}<br />
<br />
#mytable th.spec <br />
{<br />
background: #a5a5a5 no-repeat;<br />
font: bold 1em "Trebuchet MS", Times;<br />
color: #ffffff;<br />
}<br />
<br />
#mytable th.specalt <br />
{<br />
background: #ffffff no-repeat;<br />
font: bold 1em "Trebuchet MS", Times;<br />
color: #656565;<br />
}<br />
#mytable a:visited, #mytable a:link, #mytable a:hover{<br />
color:#282560;<br />
text-decoration:underline;<br />
}<br />
#mytable a:hover {<br />
color:#00F2BC;<br />
}<br />
<br />
/********* things we changed ***********/<br />
<br />
<br />
#toctitle, span.tocnumber {<br />
display:none;<br />
}<br />
.toclevel-1{<br />
margin-bottom:1em;<br />
}<br />
.toclevel-2{<br />
display:none;<br />
}<br />
span.toctext {<br />
color: #282560;<br />
font-size:14px;<br />
line-height:14px;<br />
}<br />
<br />
#footer-box{<br />
background-color:#E6E6E6;<br />
border:none;<br />
margin:100px auto 0;<br />
padding:5px;<br />
width:965px;<br />
}<br />
body {<br />
background-color:#FFFFFF;<br />
background-image:url("https://static.igem.org/mediawiki/2010/3/36/Team-Alberta-topStrip.png");<br />
background-repeat:repeat-x;<br />
}<br />
<br />
#thanks-footer{<br />
position: relative;<br />
width: 1032px;<br />
left: -15px;<br />
clear:both;<br />
background-color: #DDDDDD;<br />
top: 12px;<br />
border-radius: 10px;<br />
-moz-border-radius: 10px;<br />
text-align: center;<br />
}<br />
<br />
/* new colors */<br />
<br />
h1, h2, h3, h4, h5, h6 {<br />
color: #9D2063;<br />
border:none;<br />
}<br />
<br />
h2 {<br />
line-height:125%;<br />
}<br />
<br />
h3{<br />
font-size:100%;<br />
font-weight:normal;<br />
position:relative;<br />
top:-1em;<br />
color: #282560;<br />
font-style: italic;<br />
margin-bottom: -0.5em;<br />
}<br />
<br />
span.editsection, span.editsection a{<br />
color:#ccc;<br />
}<br />
body{<br />
background-color:#fff;<br />
}<br />
#content{<br />
border:none;<br />
width:975px;<br />
padding-left:0;<br />
padding-right:0;<br />
}<br />
<br />
#menubar li a, #menubar .selected a, #menubar li a:visited{ <br />
color: #888;<br />
}<br />
#menubar li a:hover{<br />
color: #00F2BC;<br />
}<br />
<br />
<br />
/* table of contents */<br />
#toc{<br />
background-color: #EEEEEE;<br />
border:none;<br />
width:100%;<br />
padding-top: 14px;<br />
-moz-border-radius: 10px;<br />
border-radius: 10px;<br />
}<br />
/*timeline stuff*/<br />
<br />
/*months and their overlaying divs*/<br />
<br />
#May{<br />
background-color: Orange;<br />
height: 500px;<br />
width: 780 px;<br />
<br />
}<br />
<br />
ul.rolodex{<br />
list-style-type: none;<br />
list-style-image: none;<br />
}<br />
<br />
ul.rolodex li{<br />
color: #282560;<br />
}<br />
ul.rolodex li:hover {<br />
color: #00F2BC;<br />
cursor: pointer;<br />
}<br />
<br />
.startimage:hover {<br />
filter:progid:DXImageTransform.Microsoft.Alpha(opacity=50);<br />
-moz-opacity: 0.5;<br />
opacity: 0.5;<br />
}<br />
div#horiz-line {<br />
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}</div>Stjahnshttp://2010.igem.org/Team:Alberta/human_practices/HighSchoolTeam:Alberta/human practices/HighSchool2010-10-27T04:17:42Z<p>Stjahns: </p>
<hr />
<div>{{Team:Alberta/Head}}<br />
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{{Team:Alberta/navbar|overview=selected}}<br />
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<div id=highschool4><br />
[[Image:Alberta_highschool4.jpg|280px|thumb|right|High school students fucking around with science and shit.]]<br />
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{{Team:Alberta/endLeftSideBar}}<br />
<br />
{{Team:Alberta/beginRightSideBar}}<br />
[[Image:Alberta highschool3.jpg|280px|thumb|left|High School Students using GENOMIKON]]<br />
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<br />
{{Team:Alberta/beginMainContent}}<br />
<br />
<br />
==Real World Trials==<br />
<div id="horiz-line"></div><br />
<br />
<p> Currently, the experiments that can be done at a high school level are greatly limited by a tight budget, a lack of appropriate equipment and space, as well as scheduling issues. Consequently, high school biology experiments have traditionally been centered around dissections. The current experiments neglect many exciting fields in biology, such as synthetic biology. The GENOMIKON kit is meant to change this by being cost-effective, relevant to the high school curriculum, and does not require any expensive reagents or equipment. Not to mention, our experiments fit well within the average high school class period. <br />
<br />
In order to prove the applicability of the GENOMIKON kit, we arranged for five high school students to test it out in our laboratory on Oct. 24, 2010. They built a four-piece DNA construct (AB KanR, BA ori, AB RFP, and cap) using our kit and Biobyte 2.0 assembly protocol in just under two hours. This construct was then transformed into <em> E. coli </em>:. The following day, there were red colonies present on kanamycin plates, demonstrating that their assembly was indeed successful! The students greatly enjoyed this experiment and even gave us some very valuable feedback. <br />
<br />
Here's what the students had to say when asked about what they knew about <em> E. coli </em>:</p><br />
<br />
<p><br />
* 'It's in meat' - Jillian Underwood, 15<br />
* 'It can live in our intestines' - Aymen Saidane, 17 </p><br />
<br />
<p>Not surprisingly, their comments reflect the general public opinions of <em> E. coli </em>. In order to address any misconceptions, the students were educated on the difference between pathogenic <em> E. coli </em> strains (0157:H7), and the harmless strain that we are using in our kit (DH5&alpha;). The students then stated that they were not at all apprehensive about working with the bacteria or DNA used in the experiment. </p><br />
<br />
<p> One of our team members taught the students simple theory, including general information about DNA, our assembly method and the specific BioBytes that they were using. Following this, they were led through the assembly and were also taught how to use the GENOMIKON website. The students agreed that the plasmid designer feature was "cool" and that the glossary and encyclopedia were very useful. <br />
<br />
Interestingly, Aymen Saidane (grade 12), said that he had already learned about molecular biology in his Biology 30 course in high school. However, he had not had the chance to apply his knowledge. The only experiment he had done was 'cut paper DNA sequences with scissors, to represent restriction enzymes, and then matched our pieces with classmates.' This led us to conclude that the GENOMIKON kit is ideal for complementing a grade 12 curriculum.</p><br />
<br />
<p> Here is some more feedback from the students:</p><br />
<br />
<p><br />
* 'The magnetic beads are cool' - Jill Hacking, 15<br />
* 'The plastic pipettes were easy to use and kind of fun' - Bryce Stewart, 15<br />
* They didn't mind the fact that they didn't get to do the transformation since the DNA assembly was the more interesting part.<br />
* 'I don't think I could explain this to my parents, because they wouldn't get it, but if I explained it to a friend, he would understand.' - Alan Ho, 16<br />
* 'I learned the theory already, but I got to apply it today.' - Aymen Saidane, 17 </p><br />
<br />
<br />
<p> This is just the beginning of GENOMIKON in the classroom. In future trials, students can build even more complicated constructs and even design their own experiments. GENOMIKON doubles as an educational tool and as another method to clear up any misconceptions that the public may have about synthetic biology. It will educate students, parents and teachers, first hand, on the many ways synthetic biology can be used to benefit society.<br />
</p><br />
<br />
{{Team:Alberta/endMainContent}}</div>Stjahnshttp://2010.igem.org/Team:Alberta/human_practices/HighSchoolTeam:Alberta/human practices/HighSchool2010-10-27T04:15:31Z<p>Stjahns: </p>
<hr />
<div>{{Team:Alberta/Head}}<br />
<br />
{{Team:Alberta/navbar|overview=selected}}<br />
<br />
{{Team:Alberta/beginLeftSideBar|toc=NO}}<br />
<br />
[[Image:Alberta_highschool4.jpg|280px|thumb|class=highschool4|right|High school students fucking around with science and shit.]]<br />
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{{Team:Alberta/endLeftSideBar}}<br />
<br />
{{Team:Alberta/beginRightSideBar}}<br />
[[Image:Alberta highschool3.jpg|280px|thumb|left|High School Students using GENOMIKON]]<br />
{{Team:Alberta/endRightSideBar}}<br />
<br />
{{Team:Alberta/beginMainContent}}<br />
<br />
<br />
==Real World Trials==<br />
<div id="horiz-line"></div><br />
<br />
<p> Currently, the experiments that can be done at a high school level are greatly limited by a tight budget, a lack of appropriate equipment and space, as well as scheduling issues. Consequently, high school biology experiments have traditionally been centered around dissections. The current experiments neglect many exciting fields in biology, such as synthetic biology. The GENOMIKON kit is meant to change this by being cost-effective, relevant to the high school curriculum, and does not require any expensive reagents or equipment. Not to mention, our experiments fit well within the average high school class period. <br />
<br />
In order to prove the applicability of the GENOMIKON kit, we arranged for five high school students to test it out in our laboratory on Oct. 24, 2010. They built a four-piece DNA construct (AB KanR, BA ori, AB RFP, and cap) using our kit and Biobyte 2.0 assembly protocol in just under two hours. This construct was then transformed into <em> E. coli </em>:. The following day, there were red colonies present on kanamycin plates, demonstrating that their assembly was indeed successful! The students greatly enjoyed this experiment and even gave us some very valuable feedback. <br />
<br />
Here's what the students had to say when asked about what they knew about <em> E. coli </em>:</p><br />
<br />
<p><br />
* 'It's in meat' - Jillian Underwood, 15<br />
* 'It can live in our intestines' - Aymen Saidane, 17 </p><br />
<br />
<p>Not surprisingly, their comments reflect the general public opinions of <em> E. coli </em>. In order to address any misconceptions, the students were educated on the difference between pathogenic <em> E. coli </em> strains (0157:H7), and the harmless strain that we are using in our kit (DH5&alpha;). The students then stated that they were not at all apprehensive about working with the bacteria or DNA used in the experiment. </p><br />
<br />
<p> One of our team members taught the students simple theory, including general information about DNA, our assembly method and the specific BioBytes that they were using. Following this, they were led through the assembly and were also taught how to use the GENOMIKON website. The students agreed that the plasmid designer feature was "cool" and that the glossary and encyclopedia were very useful. <br />
<br />
Interestingly, Aymen Saidane (grade 12), said that he had already learned about molecular biology in his Biology 30 course in high school. However, he had not had the chance to apply his knowledge. The only experiment he had done was 'cut paper DNA sequences with scissors, to represent restriction enzymes, and then matched our pieces with classmates.' This led us to conclude that the GENOMIKON kit is ideal for complementing a grade 12 curriculum.</p><br />
<br />
<p> Here is some more feedback from the students:</p><br />
<br />
<p><br />
* 'The magnetic beads are cool' - Jill Hacking, 15<br />
* 'The plastic pipettes were easy to use and kind of fun' - Bryce Stewart, 15<br />
* They didn't mind the fact that they didn't get to do the transformation since the DNA assembly was the more interesting part.<br />
* 'I don't think I could explain this to my parents, because they wouldn't get it, but if I explained it to a friend, he would understand.' - Alan Ho, 16<br />
* 'I learned the theory already, but I got to apply it today.' - Aymen Saidane, 17 </p><br />
<br />
<br />
<p> This is just the beginning of GENOMIKON in the classroom. In future trials, students can build even more complicated constructs and even design their own experiments. GENOMIKON doubles as an educational tool and as another method to clear up any misconceptions that the public may have about synthetic biology. It will educate students, parents and teachers, first hand, on the many ways synthetic biology can be used to benefit society.<br />
</p><br />
<br />
{{Team:Alberta/endMainContent}}</div>Stjahnshttp://2010.igem.org/Team:Alberta/human_practices/HighSchoolTeam:Alberta/human practices/HighSchool2010-10-27T04:14:57Z<p>Stjahns: </p>
<hr />
<div>{{Team:Alberta/Head}}<br />
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{{Team:Alberta/navbar|overview=selected}}<br />
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[[Image:Alberta_highschool4.jpg|280px|thumb|id=highschool4|right|High school students fucking around with science and shit.]]<br />
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{{Team:Alberta/endLeftSideBar}}<br />
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{{Team:Alberta/beginRightSideBar}}<br />
[[Image:Alberta highschool3.jpg|280px|thumb|left|High School Students using GENOMIKON]]<br />
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<br />
{{Team:Alberta/beginMainContent}}<br />
<br />
<br />
==Real World Trials==<br />
<div id="horiz-line"></div><br />
<br />
<p> Currently, the experiments that can be done at a high school level are greatly limited by a tight budget, a lack of appropriate equipment and space, as well as scheduling issues. Consequently, high school biology experiments have traditionally been centered around dissections. The current experiments neglect many exciting fields in biology, such as synthetic biology. The GENOMIKON kit is meant to change this by being cost-effective, relevant to the high school curriculum, and does not require any expensive reagents or equipment. Not to mention, our experiments fit well within the average high school class period. <br />
<br />
In order to prove the applicability of the GENOMIKON kit, we arranged for five high school students to test it out in our laboratory on Oct. 24, 2010. They built a four-piece DNA construct (AB KanR, BA ori, AB RFP, and cap) using our kit and Biobyte 2.0 assembly protocol in just under two hours. This construct was then transformed into <em> E. coli </em>:. The following day, there were red colonies present on kanamycin plates, demonstrating that their assembly was indeed successful! The students greatly enjoyed this experiment and even gave us some very valuable feedback. <br />
<br />
Here's what the students had to say when asked about what they knew about <em> E. coli </em>:</p><br />
<br />
<p><br />
* 'It's in meat' - Jillian Underwood, 15<br />
* 'It can live in our intestines' - Aymen Saidane, 17 </p><br />
<br />
<p>Not surprisingly, their comments reflect the general public opinions of <em> E. coli </em>. In order to address any misconceptions, the students were educated on the difference between pathogenic <em> E. coli </em> strains (0157:H7), and the harmless strain that we are using in our kit (DH5&alpha;). The students then stated that they were not at all apprehensive about working with the bacteria or DNA used in the experiment. </p><br />
<br />
<p> One of our team members taught the students simple theory, including general information about DNA, our assembly method and the specific BioBytes that they were using. Following this, they were led through the assembly and were also taught how to use the GENOMIKON website. The students agreed that the plasmid designer feature was "cool" and that the glossary and encyclopedia were very useful. <br />
<br />
Interestingly, Aymen Saidane (grade 12), said that he had already learned about molecular biology in his Biology 30 course in high school. However, he had not had the chance to apply his knowledge. The only experiment he had done was 'cut paper DNA sequences with scissors, to represent restriction enzymes, and then matched our pieces with classmates.' This led us to conclude that the GENOMIKON kit is ideal for complementing a grade 12 curriculum.</p><br />
<br />
<p> Here is some more feedback from the students:</p><br />
<br />
<p><br />
* 'The magnetic beads are cool' - Jill Hacking, 15<br />
* 'The plastic pipettes were easy to use and kind of fun' - Bryce Stewart, 15<br />
* They didn't mind the fact that they didn't get to do the transformation since the DNA assembly was the more interesting part.<br />
* 'I don't think I could explain this to my parents, because they wouldn't get it, but if I explained it to a friend, he would understand.' - Alan Ho, 16<br />
* 'I learned the theory already, but I got to apply it today.' - Aymen Saidane, 17 </p><br />
<br />
<br />
<p> This is just the beginning of GENOMIKON in the classroom. In future trials, students can build even more complicated constructs and even design their own experiments. GENOMIKON doubles as an educational tool and as another method to clear up any misconceptions that the public may have about synthetic biology. It will educate students, parents and teachers, first hand, on the many ways synthetic biology can be used to benefit society.<br />
</p><br />
<br />
{{Team:Alberta/endMainContent}}</div>Stjahnshttp://2010.igem.org/Team:Alberta/human_practices/HighSchoolTeam:Alberta/human practices/HighSchool2010-10-27T04:14:16Z<p>Stjahns: </p>
<hr />
<div>{{Team:Alberta/Head}}<br />
<br />
{{Team:Alberta/navbar|overview=selected}}<br />
<br />
{{Team:Alberta/beginLeftSideBar|toc=NO}}<br />
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[[Image:Alberta_highschool4.jpg|280px|thumb|right|High school students fucking around with science and shit.]]<br />
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{{Team:Alberta/endLeftSideBar}}<br />
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{{Team:Alberta/beginRightSideBar}}<br />
[[Image:Alberta highschool3.jpg|280px|thumb|left|High School Students using GENOMIKON]]<br />
{{Team:Alberta/endRightSideBar}}<br />
<br />
{{Team:Alberta/beginMainContent}}<br />
<br />
<br />
==Real World Trials==<br />
<div id="horiz-line"></div><br />
<br />
<p> Currently, the experiments that can be done at a high school level are greatly limited by a tight budget, a lack of appropriate equipment and space, as well as scheduling issues. Consequently, high school biology experiments have traditionally been centered around dissections. The current experiments neglect many exciting fields in biology, such as synthetic biology. The GENOMIKON kit is meant to change this by being cost-effective, relevant to the high school curriculum, and does not require any expensive reagents or equipment. Not to mention, our experiments fit well within the average high school class period. <br />
<br />
In order to prove the applicability of the GENOMIKON kit, we arranged for five high school students to test it out in our laboratory on Oct. 24, 2010. They built a four-piece DNA construct (AB KanR, BA ori, AB RFP, and cap) using our kit and Biobyte 2.0 assembly protocol in just under two hours. This construct was then transformed into <em> E. coli </em>:. The following day, there were red colonies present on kanamycin plates, demonstrating that their assembly was indeed successful! The students greatly enjoyed this experiment and even gave us some very valuable feedback. <br />
<br />
Here's what the students had to say when asked about what they knew about <em> E. coli </em>:</p><br />
<br />
<p><br />
* 'It's in meat' - Jillian Underwood, 15<br />
* 'It can live in our intestines' - Aymen Saidane, 17 </p><br />
<br />
<p>Not surprisingly, their comments reflect the general public opinions of <em> E. coli </em>. In order to address any misconceptions, the students were educated on the difference between pathogenic <em> E. coli </em> strains (0157:H7), and the harmless strain that we are using in our kit (DH5&alpha;). The students then stated that they were not at all apprehensive about working with the bacteria or DNA used in the experiment. </p><br />
<br />
<p> One of our team members taught the students simple theory, including general information about DNA, our assembly method and the specific BioBytes that they were using. Following this, they were led through the assembly and were also taught how to use the GENOMIKON website. The students agreed that the plasmid designer feature was "cool" and that the glossary and encyclopedia were very useful. <br />
<br />
Interestingly, Aymen Saidane (grade 12), said that he had already learned about molecular biology in his Biology 30 course in high school. However, he had not had the chance to apply his knowledge. The only experiment he had done was 'cut paper DNA sequences with scissors, to represent restriction enzymes, and then matched our pieces with classmates.' This led us to conclude that the GENOMIKON kit is ideal for complementing a grade 12 curriculum.</p><br />
<br />
<p> Here is some more feedback from the students:</p><br />
<br />
<p><br />
* 'The magnetic beads are cool' - Jill Hacking, 15<br />
* 'The plastic pipettes were easy to use and kind of fun' - Bryce Stewart, 15<br />
* They didn't mind the fact that they didn't get to do the transformation since the DNA assembly was the more interesting part.<br />
* 'I don't think I could explain this to my parents, because they wouldn't get it, but if I explained it to a friend, he would understand.' - Alan Ho, 16<br />
* 'I learned the theory already, but I got to apply it today.' - Aymen Saidane, 17 </p><br />
<br />
<br />
<p> This is just the beginning of GENOMIKON in the classroom. In future trials, students can build even more complicated constructs and even design their own experiments. GENOMIKON doubles as an educational tool and as another method to clear up any misconceptions that the public may have about synthetic biology. It will educate students, parents and teachers, first hand, on the many ways synthetic biology can be used to benefit society.<br />
</p><br />
<br />
{{Team:Alberta/endMainContent}}</div>Stjahnshttp://2010.igem.org/Team:Alberta/human_practices/HighSchoolTeam:Alberta/human practices/HighSchool2010-10-27T04:13:56Z<p>Stjahns: </p>
<hr />
<div>{{Team:Alberta/Head}}<br />
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{{Team:Alberta/navbar|overview=selected}}<br />
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{{Team:Alberta/beginLeftSideBar|toc=NO}}<br />
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[[Image:Alberta_highschool4.jpg|280px|thumb|right|High school students fucking around with science and shit.]]<br />
<br />
{{Team:Alberta/beginRightSideBar}}<br />
[[Image:Alberta highschool3.jpg|280px|thumb|left|High School Students using GENOMIKON]]<br />
{{Team:Alberta/endRightSideBar}}<br />
<br />
{{Team:Alberta/beginMainContent}}<br />
<br />
<br />
==Real World Trials==<br />
<div id="horiz-line"></div><br />
<br />
<p> Currently, the experiments that can be done at a high school level are greatly limited by a tight budget, a lack of appropriate equipment and space, as well as scheduling issues. Consequently, high school biology experiments have traditionally been centered around dissections. The current experiments neglect many exciting fields in biology, such as synthetic biology. The GENOMIKON kit is meant to change this by being cost-effective, relevant to the high school curriculum, and does not require any expensive reagents or equipment. Not to mention, our experiments fit well within the average high school class period. <br />
<br />
In order to prove the applicability of the GENOMIKON kit, we arranged for five high school students to test it out in our laboratory on Oct. 24, 2010. They built a four-piece DNA construct (AB KanR, BA ori, AB RFP, and cap) using our kit and Biobyte 2.0 assembly protocol in just under two hours. This construct was then transformed into <em> E. coli </em>:. The following day, there were red colonies present on kanamycin plates, demonstrating that their assembly was indeed successful! The students greatly enjoyed this experiment and even gave us some very valuable feedback. <br />
<br />
Here's what the students had to say when asked about what they knew about <em> E. coli </em>:</p><br />
<br />
<p><br />
* 'It's in meat' - Jillian Underwood, 15<br />
* 'It can live in our intestines' - Aymen Saidane, 17 </p><br />
<br />
<p>Not surprisingly, their comments reflect the general public opinions of <em> E. coli </em>. In order to address any misconceptions, the students were educated on the difference between pathogenic <em> E. coli </em> strains (0157:H7), and the harmless strain that we are using in our kit (DH5&alpha;). The students then stated that they were not at all apprehensive about working with the bacteria or DNA used in the experiment. </p><br />
<br />
<p> One of our team members taught the students simple theory, including general information about DNA, our assembly method and the specific BioBytes that they were using. Following this, they were led through the assembly and were also taught how to use the GENOMIKON website. The students agreed that the plasmid designer feature was "cool" and that the glossary and encyclopedia were very useful. <br />
<br />
Interestingly, Aymen Saidane (grade 12), said that he had already learned about molecular biology in his Biology 30 course in high school. However, he had not had the chance to apply his knowledge. The only experiment he had done was 'cut paper DNA sequences with scissors, to represent restriction enzymes, and then matched our pieces with classmates.' This led us to conclude that the GENOMIKON kit is ideal for complementing a grade 12 curriculum.</p><br />
<br />
<p> Here is some more feedback from the students:</p><br />
<br />
<p><br />
* 'The magnetic beads are cool' - Jill Hacking, 15<br />
* 'The plastic pipettes were easy to use and kind of fun' - Bryce Stewart, 15<br />
* They didn't mind the fact that they didn't get to do the transformation since the DNA assembly was the more interesting part.<br />
* 'I don't think I could explain this to my parents, because they wouldn't get it, but if I explained it to a friend, he would understand.' - Alan Ho, 16<br />
* 'I learned the theory already, but I got to apply it today.' - Aymen Saidane, 17 </p><br />
<br />
<br />
<p> This is just the beginning of GENOMIKON in the classroom. In future trials, students can build even more complicated constructs and even design their own experiments. GENOMIKON doubles as an educational tool and as another method to clear up any misconceptions that the public may have about synthetic biology. It will educate students, parents and teachers, first hand, on the many ways synthetic biology can be used to benefit society.<br />
</p><br />
<br />
{{Team:Alberta/endMainContent}}</div>Stjahnshttp://2010.igem.org/Team:Alberta/human_practices/HighSchoolTeam:Alberta/human practices/HighSchool2010-10-27T04:08:01Z<p>Stjahns: </p>
<hr />
<div>{{Team:Alberta/Head}}<br />
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{{Team:Alberta/navbar|overview=selected}}<br />
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{{Team:Alberta/beginMainContent}}<br />
<br />
<br />
==Real World Trials==<br />
<div id="horiz-line"></div><br />
<br />
<p> Currently, the experiments that can be done at a high school level are greatly limited by a tight budget, a lack of appropriate equipment and space, as well as scheduling issues. Consequently, high school biology experiments have traditionally been centered around dissections. The current experiments neglect many exciting fields in biology, such as synthetic biology. The GENOMIKON kit is meant to change this by being cost-effective, relevant to the high school curriculum, and does not require any expensive reagents or equipment. Not to mention, our experiments fit well within the average high school class period. <br />
<br />
In order to prove the applicability of the GENOMIKON kit, we arranged for five high school students to test it out in our laboratory on Oct. 24, 2010. They built a four-piece DNA construct (AB KanR, BA ori, AB RFP, and cap) using our kit and Biobyte 2.0 assembly protocol in just under two hours. This construct was then transformed into <em> E. coli </em>:. The following day, there were red colonies present on kanamycin plates, demonstrating that their assembly was indeed successful! The students greatly enjoyed this experiment and even gave us some very valuable feedback. <br />
<br />
Here's what the students had to say when asked about what they knew about <em> E. coli </em>:</p><br />
<br />
<p><br />
* 'It's in meat' - Jillian Underwood, 15<br />
* 'It can live in our intestines' - Aymen Saidane, 17 </p><br />
<br />
<p>Not surprisingly, their comments reflect the general public opinions of <em> E. coli </em>. In order to address any misconceptions, the students were educated on the difference between pathogenic <em> E. coli </em> strains (0157:H7), and the harmless strain that we are using in our kit (DH5&alpha;). The students then stated that they were not at all apprehensive about working with the bacteria or DNA used in the experiment. </p><br />
<br />
<p> One of our team members taught the students simple theory, including general information about DNA, our assembly method and the specific BioBytes that they were using. Following this, they were led through the assembly and were also taught how to use the GENOMIKON website. The students agreed that the plasmid designer feature was "cool" and that the glossary and encyclopedia were very useful. <br />
<br />
Interestingly, Aymen Saidane (grade 12), said that he had already learned about molecular biology in his Biology 30 course in high school. However, he had not had the chance to apply his knowledge. The only experiment he had done was 'cut paper DNA sequences with scissors, to represent restriction enzymes, and then matched our pieces with classmates.' This led us to conclude that the GENOMIKON kit is ideal for complementing a grade 12 curriculum.</p><br />
<br />
<p> Here is some more feedback from the students:</p><br />
<br />
<p><br />
* 'The magnetic beads are cool' - Jill Hacking, 15<br />
* 'The plastic pipettes were easy to use and kind of fun' - Bryce Stewart, 15<br />
* They didn't mind the fact that they didn't get to do the transformation since the DNA assembly was the more interesting part.<br />
* 'I don't think I could explain this to my parents, because they wouldn't get it, but if I explained it to a friend, he would understand.' - Alan Ho, 16<br />
* 'I learned the theory already, but I got to apply it today.' - Aymen Saidane, 17 </p><br />
<br />
<br />
<p> This is just the beginning of GENOMIKON in the classroom. In future trials, students can build even more complicated constructs and even design their own experiments. GENOMIKON doubles as an educational tool and as another method to clear up any misconceptions that the public may have about synthetic biology. It will educate students, parents and teachers, first hand, on the many ways synthetic biology can be used to benefit society.<br />
</p><br />
<br />
{{Team:Alberta/endMainContent}}</div>Stjahnshttp://2010.igem.org/Template:Team:Alberta/navbarTemplate:Team:Alberta/navbar2010-10-27T04:05:29Z<p>Stjahns: </p>
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<li><a href="https://2010.igem.org/Team:Alberta" class="</html>{{{home|}}}<html> nav-home" >HOME</a></li><br />
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<li><a href="https://2010.igem.org/Team:Alberta/project">Overview</a></li><br />
<li><a href="https://2010.igem.org/Team:Alberta/biobyte2">Biobytes 2.0</a></li><br />
<li><a href="https://2010.igem.org/Team:Alberta/Software">Software</a></li><br />
<li><a href="https://2010.igem.org/Team:Alberta/modelling">Modelling</a></li><br />
<li><a href="https://2010.igem.org/Team:Alberta/Kit">The Kit</a></li><br />
<li><a href="https://2010.igem.org/Team:Alberta/Kit_components">Kit Components</a></li><br />
</ul><br />
</li><br />
<li class="headlink" ><a href="https://2010.igem.org/Team:Alberta/Achievements/Overview" class="</html>{{{achievments|}}}<html> nav-practices" >ACHIEVEMENTS </a><br />
<ul><br />
<li><a href="https://2010.igem.org/Team:Alberta/Achievements/Overview">Overview</a></li><br />
<li><a href="https://2010.igem.org/Team:Alberta/Achievements">Medal Requirements </a></li><br />
</ul><br />
</li><br />
<li class="headlink"><a href="https://2010.igem.org/Team:Alberta/human_practices" class="</html>{{{practices|}}}<html> nav-practices" >HUMAN PRACTICES</a><br />
<ul><br />
<li><a href="https://2010.igem.org/Team:Alberta/human_practices">Overview</a></li><br />
<li><a href="https://2010.igem.org/Team:Alberta/human_practices/distribution_analysis">Distribution Analysis</a></li><br />
<li><a href="https://2010.igem.org/Team:Alberta/human_practices/HighSchool">High School</a></li><br />
<li><a href="https://2010.igem.org/Team:Alberta/human_practices/safety">Safety</a></li><br />
</ul><br />
</li><br />
<li><a href="https://2010.igem.org/Team:Alberta/parts"class="</html>{{{parts|}}}<html> nav-parts">PARTS</a></li><br />
<li class="headlink"><a href="https://2010.igem.org/Team:Alberta/Notebook" class="</html>{{{notebook|}}}<html> nav-notebook">TIMELINE & PROTOCOLS</a><br />
<ul><br />
<li><a href="https://2010.igem.org/Team:Alberta/Notebook">Overview</a></li><br />
<li><a href="https://2010.igem.org/Team:Alberta/Notebook/Software">Software</a></li><br />
<li><a href="https://2010.igem.org/Team:Alberta/Notebook/TransformingCells">Transforming Cells</a></li><br />
<li><a href="https://2010.igem.org/Team:Alberta/Notebook/CreatingParts">Creating Parts</a></li><br />
<li><a href="https://2010.igem.org/Team:Alberta/Notebook/Anchor">Anchor</a></li><br />
<li><a href="https://2010.igem.org/Team:Alberta/Notebook/Beads">Beads</a></li><br />
<li><a href="https://2010.igem.org/Team:Alberta/Notebook/Optimizations">Optimizations</a></li><br />
<li><a href="https://2010.igem.org/Team:Alberta/Notebook/protocols">General Protocols</a></li><br />
</ul><br />
</li><br />
<li><a href="https://2010.igem.org/Team:Alberta/team" class="</html>{{{team|}}}<html> nav-team" >TEAM</a></li><br />
<ul><br />
</div><br />
</html></div>Stjahnshttp://2010.igem.org/Template:Team:Alberta/navbarTemplate:Team:Alberta/navbar2010-10-27T04:04:07Z<p>Stjahns: </p>
<hr />
<div><html><br />
<div id="navbar"><br />
<ul><br />
<li><a href="https://2010.igem.org/Team:Alberta" class="</html>{{{home|}}}<html> nav-home" >HOME</a></li><br />
<li><a href="https://2010.igem.org/Team:Alberta/Tour/start" class="</html>{{{tour|}}}<html> nav-software">AT A GLANCE</a></li><br />
<li class="headlink"><a href="https://2010.igem.org/Team:Alberta/project" class="</html>{{{project|}}}<html> nav-project" >PROJECT </a><br />
<ul><br />
<li><a href="https://2010.igem.org/Team:Alberta/project">Overview</a></li><br />
<li><a href="https://2010.igem.org/Team:Alberta/biobyte2">Biobytes 2.0</a></li><br />
<li><a href="https://2010.igem.org/Team:Alberta/Software">Software</a></li><br />
<li><a href="https://2010.igem.org/Team:Alberta/modelling">Modelling</a></li><br />
<li><a href="https://2010.igem.org/Team:Alberta/Kit">The Kit</a></li><br />
<li><a href="https://2010.igem.org/Team:Alberta/Kit_components">Kit Components</a></li><br />
</ul><br />
</li><br />
<li class="headlink" ><a href="https://2010.igem.org/Team:Alberta/Achievements/Overview" class="</html>{{{achievments|}}}<html> nav-practices" >ACHIEVEMENTS </a><br />
<ul><br />
<li><a href="https://2010.igem.org/Team:Alberta/Achievements/Overview">Overview</a></li><br />
<li><a href="https://2010.igem.org/Team:Alberta/Achievements">Medal Requirements </a></li><br />
</ul><br />
</li><br />
<li class="headlink"><a href="https://2010.igem.org/Team:Alberta/human_practices" class="</html>{{{practices|}}}<html> nav-practices" >HUMAN PRACTICES</a><br />
<ul><br />
<li><a href="https://2010.igem.org/Team:Alberta/human_practices">Overview</a></li><br />
<li><a href="https://2010.igem.org/Team:Alberta/human_practices/distribution_analysis">Distribution Analysis</a></li><br />
<li><a href="https://2010.igem.org/Team:Alberta/human_practices/HighSchool">High School Trials</a></li><br />
<li><a href="https://2010.igem.org/Team:Alberta/human_practices/safety">Safety</a></li><br />
</ul><br />
</li><br />
<li><a href="https://2010.igem.org/Team:Alberta/parts"class="</html>{{{parts|}}}<html> nav-parts">PARTS</a></li><br />
<li class="headlink"><a href="https://2010.igem.org/Team:Alberta/Notebook" class="</html>{{{notebook|}}}<html> nav-notebook">TIMELINE & PROTOCOLS</a><br />
<ul><br />
<li><a href="https://2010.igem.org/Team:Alberta/Notebook">Overview</a></li><br />
<li><a href="https://2010.igem.org/Team:Alberta/Notebook/Software">Software</a></li><br />
<li><a href="https://2010.igem.org/Team:Alberta/Notebook/TransformingCells">Transforming Cells</a></li><br />
<li><a href="https://2010.igem.org/Team:Alberta/Notebook/CreatingParts">Creating Parts</a></li><br />
<li><a href="https://2010.igem.org/Team:Alberta/Notebook/Anchor">Anchor</a></li><br />
<li><a href="https://2010.igem.org/Team:Alberta/Notebook/Beads">Beads</a></li><br />
<li><a href="https://2010.igem.org/Team:Alberta/Notebook/Optimizations">Optimizations</a></li><br />
<li><a href="https://2010.igem.org/Team:Alberta/Notebook/protocols">General Protocols</a></li><br />
</ul><br />
</li><br />
<li><a href="https://2010.igem.org/Team:Alberta/team" class="</html>{{{team|}}}<html> nav-team" >TEAM</a></li><br />
<ul><br />
</div><br />
</html></div>Stjahnshttp://2010.igem.org/Team:Alberta/Tour/conclusionTeam:Alberta/Tour/conclusion2010-10-27T03:58:37Z<p>Stjahns: </p>
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[[Image:Alberta_Rfpkan.jpg|right|280px|thumb|Cells transformed with a plasmid created using BioBytes 2.0 and a negative control]]<br />
<br />
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[[Image:Team-alberta-closed-kit-image-w264.png|left|280px|thumb|GENOMIKON: The Kit]]<br />
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==Conclusion==<br />
<div id="horiz-line"></div><br />
<br />
GENOMIKON makes synthetic biology easier and faster than ever before bringing the field closer to a young vibrant high school audience. As you have seen our BioBytes Assembly System 2.0 and our GENOMIKON.ca software tools have been integrated together allowing for students to have most enriched learning experience. It brings synthetic biology to people and places it has never been while pushing the development of synthetic biology in new and exciting directions. <br />
<br />
<b>Still have questions? Please see these links for more detailed information:</b><br />
<br />
[[Team:Alberta/biobyte2| BioBytes 2.0]] details the GENOMIKON assembly method.<br />
<br />
[[Team:Alberta/human_practices/safety|Safety]]: read about lab and GENOMIKON kit safety.<br />
<br />
[[Team:Alberta/Notebook/protocols|Protocols]]: all our lab procedures<br />
<br />
[[Team:Alberta/modelling|Modeling]]: learn about the model that demonstrates the efficiency of our assembly method from our experimental results<br />
<br />
[[Team:Alberta/Achievements|Achievements]]: details our many amazing accomplishments<br />
<br />
[[Team:Alberta/human_practices/distribution_analysis|Human practices]]: Details our research into distributing GENOMIKON and the high school curriculum <br />
<br />
[[Team:Alberta/team |Team]]: Meet the team<br />
<br />
[[Team:Alberta/Software|Software]]: outlines the GENOMIKON ONLINE tool, and the technology used to do it<br />
<br />
[[Team:Alberta/Notebook |Notebook]]: is a time line of our summer<br />
<br />
[[Team:Alberta/parts |Parts]]: details the parts we submitted<br />
{{Team:Alberta/endMainContent}}</div>Stjahnshttp://2010.igem.org/Team:Alberta/Tour/achievementsTeam:Alberta/Tour/achievements2010-10-27T03:58:16Z<p>Stjahns: </p>
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<div>{{Team:Alberta/Head}}<br />
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<br />
{{Team:Alberta/beginLeftSideBar|class=not-top|toc=NO}}<br />
[[Image:Alberta Coolachievements.jpg|right|x350px|thumb|The University of Alberta lab]]<br />
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<br />
[[Image:Alberta Working.jpg|left|x350px|thumb|High school students using GENOMIKON]]<br />
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<br />
==Our Achievements==<br />
<div id="horiz-line"></div><br />
<br />
Here are our key achievements from the summer. For more, see the [[Team:Alberta/Achievements|achievements page.]] <br />
*We completed the gold medal requirements for iGEM. <br />
*We continued to develop the BioBytes assembly method developed by last year’s team. <br />
*We successfully assemble an 8-Bytes long construct using our BioBytes 2.0 system.<br />
*We created a model to further understand the efficiency of BioBytes 2.0.<br />
*We sourced the tools, reagents and materials that would be required to make our kit almost entirely self contained and created a prototype of the GENOMIKON educational kit.<br />
*We created a set of experiments designed to teach the student how to use the kit, as well as various topics from the high school biology curriculum.<br />
*We developed a software tool to accompany the lab kit. <br />
*We researched and developed a business plan investigating the potential of bringing the GENOMIKON kit into high school classrooms.<br />
*We tested the ability to multiplex BioByte constructs into larger constructs.<br />
*We had high school students successfully create and transform a plasmid created using GENOMIKON.<br />
<br />
{{Team:Alberta/endMainContent}}</div>Stjahnshttp://2010.igem.org/Team:Alberta/Tour/achievementsTeam:Alberta/Tour/achievements2010-10-27T03:57:53Z<p>Stjahns: </p>
<hr />
<div>{{Team:Alberta/Head}}<br />
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__NOTOC__<br />
{{Team:Alberta/tourbar|achievements=selected|left=software|right=conclusion}}<br />
<br />
{{Team:Alberta/beginLeftSideBar|class=not-top}}<br />
[[Image:Alberta Coolachievements.jpg|right|x350px|thumb|The University of Alberta lab]]<br />
{{Team:Alberta/endLeftSideBar}}<br />
{{Team:Alberta/beginRightSideBar|class=not-top}}<br />
<br />
[[Image:Alberta Working.jpg|left|x350px|thumb|High school students using GENOMIKON]]<br />
<br />
{{Team:Alberta/endRightSideBar}}<br />
<br />
{{Team:Alberta/beginMainContent|class=not-top}}<br />
<br />
==Our Achievements==<br />
<div id="horiz-line"></div><br />
<br />
Here are our key achievements from the summer. For more, see the [[Team:Alberta/Achievements|achievements page.]] <br />
*We completed the gold medal requirements for iGEM. <br />
*We continued to develop the BioBytes assembly method developed by last year’s team. <br />
*We successfully assemble an 8-Bytes long construct using our BioBytes 2.0 system.<br />
*We created a model to further understand the efficiency of BioBytes 2.0.<br />
*We sourced the tools, reagents and materials that would be required to make our kit almost entirely self contained and created a prototype of the GENOMIKON educational kit.<br />
*We created a set of experiments designed to teach the student how to use the kit, as well as various topics from the high school biology curriculum.<br />
*We developed a software tool to accompany the lab kit. <br />
*We researched and developed a business plan investigating the potential of bringing the GENOMIKON kit into high school classrooms.<br />
*We tested the ability to multiplex BioByte constructs into larger constructs.<br />
*We had high school students successfully create and transform a plasmid created using GENOMIKON.<br />
<br />
{{Team:Alberta/endMainContent}}</div>Stjahnshttp://2010.igem.org/Team:Alberta/Tour/softwareTeam:Alberta/Tour/software2010-10-27T03:57:28Z<p>Stjahns: </p>
<hr />
<div>{{Team:Alberta/Head}}<br />
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__NOTOC__<br />
{{Team:Alberta/tourbar|software=selected|left=the_kit|right=achievements}}<br />
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{{Team:Alberta/beginLeftSideBar|toc=NO|class=not-top}}<br />
[[Image:Alberta-Screen1.png|right|thumb|280px|The part designer software interface.]]<br />
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[[Image:Alberta-Screen2.png|left|thumb|280px|A page out of the lab manual.]]<br />
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{{Team:Alberta/beginMainContent|class=not-top}}<br />
==Online Companion Software==<br />
<div id="horiz-line"></div><br />
<br />
Complimentary to GENOMIKON is a online lab manual and plasmid design tool, found at [http://www.genomikon.ca GENOMIKON.ca.] <br />
The online tool contains pre-made experiments, articles explaining various topics in biology, and an integrated glossary.<br />
<br />
Students can use the online plasmid design tool to create their own experiments. Building the plasmid automatically generates the complimentary protocol to follow in the lab. Experiments can be published so others can try them also. <br />
<br />
GENOMIKON ONLINE is an excellent companion to the kit empowering students to go beyond the initial experiments we designed and create their own plasmid designs!<br />
<br />
{{Team:Alberta/endMainContent}}</div>Stjahnshttp://2010.igem.org/Team:Alberta/Tour/the_kitTeam:Alberta/Tour/the kit2010-10-27T03:52:50Z<p>Stjahns: </p>
<hr />
<div>{{Team:Alberta/Head}}<br />
{{Team:Alberta/navbar|tour=selected}}<br />
__NOTOC__<br />
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[[Image:Alberta Spread.jpg|330px|thumb|280px|right|GENOMIKON: All the parts spread out.]]<br />
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[[Image:Alberta Tubesandrack.jpg|thumb|280px|left|GENOMIKON's magnetic racks]]<br />
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<br />
==Bring SynBio to the High School Classroom==<br />
<div id="horiz-line"></div><br />
<br />
[[Team:Alberta/BioByte 2|BioBytes 2.0]] is the basis of GENOMIKION the educational toolkit for the high school classroom. The kit contains all the tools, media, reagents and biobytes needed for a classroom's worth of experiments.<br />
<br />
The GENOMIKON kit overcomes a number of design challenges. Specifically, the high school lacks sterilization equipment and laboratory machinery. These issues are solved by sending all parts that must be sterile pre-sterilized. The [[Team:Alberta/BioByte 2|BioBytes 2.0]] assembly method fortunately does not require laboratory machinery. <br />
<br />
A hotplate is all that is needed to complete all the experiments you find at [http://www.genomikon.ca GENOMIKON.ca].<br />
<br />
Presenting GENOMIKON.<br />
{{Team:Alberta/endMainContent}}</div>Stjahnshttp://2010.igem.org/Team:Alberta/Tour/biobytesTeam:Alberta/Tour/biobytes2010-10-27T03:51:43Z<p>Stjahns: </p>
<hr />
<div>{{Team:Alberta/Head}}<br />
{{Team:Alberta/navbar|tour=selected}}<br />
<br />
{{Team:Alberta/tourbar|biobytes=selected|left=start|right=the_kit}}<br />
<br />
{{Team:Alberta/beginLeftSideBar|toc=NO|class=not-top}}<br />
[[Image:Team-alberta-biobyteprocess-tour.jpg|right|280px|thumb|This is the BioByte 2.0 system]]<br />
{{Team:Alberta/endLeftSideBar}}<br />
<br />
{{Team:Alberta/beginRightSideBar|class=not-top}}<br />
[[Image:Box.jpg|left|280px|thumb|GENOMIKON's box of parts]]<br />
<p></p><br />
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<br />
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<br />
==Accelerated Construction==<br />
<div id="horiz-line"></div><br />
<br />
<p><br />
This year's project required a new approach to assembling DNA constructs. This need for a fast and efficient assembly standard was filled by BioByte 2.0. As such Biobyte 2.0 represents an innovative step forward from last year's BioByte 1.0.<br />
</p><p><br />
It utilized iron micro beads to anchor the DNA which allows for the DNA pieces to be added in a controlled sequential manner ensuring the proper orientation and order of parts. This is made possible because of the design of our unique anchor part. When paired with our unique terminal cap part will allow the assembly to be circularized and transformed into ''E. coli''<br />
</p><br />
<br />
{{Team:Alberta/endMainContent}}</div>Stjahnshttp://2010.igem.org/Team:Alberta/Tour/startTeam:Alberta/Tour/start2010-10-27T03:50:56Z<p>Stjahns: </p>
<hr />
<div>{{Team:Alberta/Head}}<br />
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__NOTOC__<br />
{{Team:Alberta/tourbar|start=selected|left=conclusion|right=biobytes}}<br />
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[[Image:Alberta-genomikon-tour.png|right|280px|thumb|GENOMIKON: An educational toolkit for rapid genomic construction]]<br />
{{Team:Alberta/endLeftSideBar}}<br />
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[[Image:Alberta-kitclose.jpg|left|280px|thumb|The heart of GENOMIKON, the DNA parts.]]<br />
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<br />
{{Team:Alberta/beginMainContent|class=not-top}}<br />
<br />
==Genomikon==<br />
<div id="horiz-line"></div><br />
<br />
We set out to create a kit that would revolutionize the biology classroom. The GENOMIKON kit is an educational experience that allows students to design and actually assemble their own plasmid in an afternoon and transform bacteria in a day. Students will learn fundamentals of biotechnology, molecular and synthetic biology by actually doing it.<br />
<br />
This tour briefly describes some of what we accomplished. We introduce the technology that allows our kit to function, the kit itself, and the kits supporting software. GENOMIKON facilitates learning synthetic biology by those who wish to know and practicing synthetic biology by those who do. <br />
<br />
<br />
{{Team:Alberta/endMainContent}}</div>Stjahnshttp://2010.igem.org/Team:Alberta/Tour/startTeam:Alberta/Tour/start2010-10-27T03:49:49Z<p>Stjahns: </p>
<hr />
<div>{{Team:Alberta/Head}}<br />
{{Team:Alberta/navbar|tour=selected}}<br />
__NOTOC__<br />
{{Team:Alberta/tourbar|start=selected|left=conclusion|right=biobytes}}<br />
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[[Image:Alberta-genomikon-tour.png|right|280px|thumb|GENOMIKON: An educational toolkit for rapid genomic construction]]<br />
{{Team:Alberta/endLeftSideBar}}<br />
{{Team:Alberta/beginRightSideBar|class=not-top}}<br />
[[Image:Alberta-kitclose.jpg|left|280px|thumb|The heart of GENOMIKON, the DNA parts.]]<br />
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<br />
{{Team:Alberta/beginMainContent|class=not-top}}<br />
<br />
==Genomikon==<br />
<div id="horiz-line"></div><br />
<br />
We set out to create a kit that would revolutionize the biology classroom. The GENOMIKON kit is an educational experience that allows students to design and actually assemble their own plasmid in an afternoon and transform bacteria in a day. Students will learn fundamentals of biotechnology, molecular and synthetic biology by actually doing it.<br />
<br />
This tour briefly describes some of what we accomplished. We introduce the technology that allows our kit to function, the kit itself, and the kits supporting software. GENOMIKON facilitates learning synthetic biology by those who wish to know and practicing synthetic biology by those who do. <br />
<br />
<br />
{{Team:Alberta/endMainContent}}</div>Stjahnshttp://2010.igem.org/Team:AlbertaTeam:Alberta2010-10-27T03:48:56Z<p>Stjahns: </p>
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==GENOMIKON: An Educational Toolkit for Rapid Genetic Construction.==<br />
<div id="horiz-line"></div><br />
<div style="margin: 0pt; height: 70px;"><br />
GENOMIKON is a kit designed to bring synthetic biology into the high-school classroom. By integrating the BioByte 2.0 assembly method and our innovative website GENOMIKON.ca, we are making synthetic biology accessible, reliable and easy to use. To learn more, see "GENOMIKON AT A GLANCE", and feel free to explore the rest of the site.<br />
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<div id="tour-link" class="tour-link"><p>GENOMIKON AT A GLANCE</p></div><br />
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</a><br />
</div><br />
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==Our Achievements==<br />
# BioBytes 2.0 plasmid assembly technology.<br />
# Plasmid assembly kit for the high school classroom.<br />
# Online educational lab manual software.<br />
# Demonstrated that high school students can successfully assemble plasmids.<br />
<br />
</div><br />
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==THE SOFTWARE==<br />
Learn how to use the kit then, create and share your own designs!<br />
<html><br />
<!---[[Image:team-alberta-main-page-plasmid-builder.png]]--><br />
<img width="242" height="96" border="0" src="/wiki/images/a/a9/Team-alberta-main-page-plasmid-builder.png" alt="Image:team-alberta-main-page-plasmid-builder.png" style="position: relative; top: 60px; left: -9px;"><br />
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<br />
==BioBytes 2.0==<br />
Continually developing the BioByte assembly technology created by the Alberta 2009 team, we were able to make this rapid plasmid assembly method amenable to a high school teaching kit. <br />
</div><br />
<div id="info-box4" class="center-info-box kit-link"><br />
==The kit==<br />
Everything you need to put together a plasmid in an afternoon.<br />
<!--[[Image:team-alberta-closed-kit-image-w264.png||x171px]]--><br />
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==[[Team:Alberta/Sponsors|THANK YOU TO OUR GENEROUS CONTRIBUTORS]]==<br />
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{{Team:Alberta/endMainContent}}</div>Stjahnshttp://2010.igem.org/Team:AlbertaTeam:Alberta2010-10-27T03:47:40Z<p>Stjahns: /* GENOMIKON: An Educational Toolkit for Rapid Genetic Construction. */</p>
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==GENOMIKON: An Educational Toolkit for Rapid Genetic Construction.==<br />
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GENOMIKON is a kit designed to bring synthetic biology into the high-school classroom. By integrating the BioByte 2.0 assembly method and our innovative website GENOMIKON.ca, we are making synthetic biology accessible, reliable and easy to use. To learn more, see "GENOMIKON AT A GLANCE", and feel free to explore the rest of the site.<br />
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<div id="tour-link" class="tour-link"><p>GENOMIKON AT A GLANCE</p></div><br />
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<br />
==Our Achievements==<br />
# BioBytes 2.0 plasmid assembly technology.<br />
# Plasmid assembly kit for the high school classroom.<br />
# Online educational lab manual software.<br />
# Demonstrated that high school students can successfully assemble plasmids.<br />
<br />
</div><br />
<div id="info-box2" class="right-info-box software-link"><br />
<br />
==THE SOFTWARE==<br />
Learn how to use the kit then, create and share your own designs!<br />
<html><br />
<!---[[Image:team-alberta-main-page-plasmid-builder.png]]--><br />
<img width="242" height="96" border="0" src="/wiki/images/a/a9/Team-alberta-main-page-plasmid-builder.png" alt="Image:team-alberta-main-page-plasmid-builder.png" style="position: relative; top: 60px; left: -9px;"><br />
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<br />
==BioBytes 2.0==<br />
Continually developing the BioByte assembly technology created by the Alberta 2009 team, we were able to make this rapid plasmid assembly method amenable to a high school teaching kit. <br />
</div><br />
<div id="info-box4" class="center-info-box kit-link"><br />
==The kit==<br />
Everything you need to put together a plasmid in an afternoon.<br />
<!--[[Image:team-alberta-closed-kit-image-w264.png||x171px]]--><br />
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==[[Team:Alberta/Sponsors|THANK YOU TO OUR GENEROUS CONTRIBUTORS]]==<br />
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{{Team:Alberta/endMainContent}}</div>Stjahnshttp://2010.igem.org/Team:Alberta/modellingTeam:Alberta/modelling2010-10-27T03:40:42Z<p>Stjahns: </p>
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{{Team:Alberta/navbar|project=selected}}<br />
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==Goal of the Model==<br />
<div id="horiz-line"></div><br />
<br />
[[Image:Cropped_labeled_gel_Alberta.png|200px|thumb|left|Relative band intensities can be used to determine assembly efficiencies.]]<br />
<br />
<p><br />
Efficiency is the key to the BioByte assembly method. For this reason, it is important to determine the efficiency by which each Byte can be added to a growing construct. Our modeling efforts have made it possible for us to determine assembly efficiency and predict future efficiencies of constructs, which have not yet been attempted.<br />
<br />
After assembling a series of Bytes, the construct can be run on a gel. Multiple bands appear. The top band contains the full construct while all of the bands below contain failed intermediate constructs of lower length. <br />
</p><br />
<br />
<p><br><b>Why do the band’s intensities alternate in intensity like that? How can the Byte addition efficiency be calculated from the gel?</b><br />
<br />
To answer these questions, we must consider the assembly process of a construct. If we follow through the assembly process while considering the efficiency k of Byte addition at each step, the expected relative intensities of the bands in the gel can be calculated.<br />
</p><br />
<br />
==Characterizing the Assembly Process==<br />
<div id="horiz-line"></div><br />
<br />
For this model, there are a few points to consider that characterize the assembly process:<br />
<br />
*First, Byte addition occurs with a constant efficiency k, which is the same for AB Byte additions and BA Byte additions. This means that for a given Byte addition, a fraction k of the existing construct is successful in growing in construct size, while (1-k) remains at the same construct size because of no ligation. <br />
<br />
*Secondly, AB Bytes can ligate only to BA Bytes, while BA Bytes can ligate only to AB Bytes.<br> <br />
<br />
Considering these points, we see that during the creation of a 8-Bytes long construct, there will be some intermediate sized constructs that will be visible on a gel. With some thought on the second point, we see that intermediate constructs can be made up of multiple arrangements of Bytes. <br />
<br />
For instance, during the creation of a 8-Bytes long construct, a medium sized 4-Byte long construct will be made up of the following combinations of Bytes:<br />
<div style="float:left; margin-right:30px;"><br />
*1,2,3,4<br />
*1,2,3,6<br />
*1,2,3,8<br />
*1,2,5,6<br />
</div><br />
<div style="float:left; margin-right:30px;"><br />
*1,2,5,8<br />
*1,2,7,8<br />
*1,4,5,6<br />
*1,4,5,8<br />
</div><br />
<div style="float:left; margin-right:30px;"><br />
*1,4,7,8<br />
*1,6,7,8<br />
*3,4,5,6<br />
*3,4,5,8<br />
</div><br />
<div style="float:left; margin-right:30px;"><br />
*3,4,7,8<br />
*3,6,7,8<br />
*5,6,7,8<br />
</div><br />
<div style="clear:both;"></div><br />
<br />
''Note that if all even numbered Bytes are of equal length and if all odd numbered Bytes are of equal length, then all of the aforementioned 4-Bytes long constructs are all of the same length. This means that their corresponding bands on a gel would all be superimposed into one band on the gel.'' <br />
<br />
This occurs for all the intermediate sized (failed) constructs. This concept is important for the derivation of a general set of equations describing the expected relative band intensities for each band in a post-assembly gel.<br />
<br />
==Creating the Model==<br />
<div id="horiz-line"></div><br />
Now imagine the construction process of a 8-Byte long construct. We’ll call it the octamer. It will be made up of alternating 1kbp AB Bytes and 2kbp BA Bytes. We’ll follow the construction of it while keeping track of what fraction of all of the intermediate constructs ends up at particular sizes (as a function of the ligation efficiency k). <br />
<br />
First, the anchor is added to the bead. We’ll say that 100% (k=1) of the construct is at anchor length at this point. Then, Byte 1 is added to the anchor with efficiency k. Now, k of the constructs are made up of anchor and Byte 1, while (1-k) is left as anchor. Adding Byte 2, we see that k squared of the constructs are made up of anchor, Byte 1 and Byte 2, whereas (1-k)k are left as anchor plus Byte 1, and (1-k) is still left as just anchor. It is still (1-k) because Byte 2 could not ligate to the anchor at all (because the ends are not compatible). It becomes more complicated for higher Byte additions. This process can be mapped and placed in the following table.<br><br />
<br />
[[Image:team-alberta-modelling-table-bytes.jpg|frame|Fractions of constructs produced.]]<br />
<br />
<br>Each column represents the addition of a Byte. The “Fraction” column describes the fraction of the corresponding construct in the “Construct” column. “A” refers to anchor, and the numbers beside it refer to the Bytes attached to the anchor. For instance, A34 refers to the construct made up of the anchor, Byte 3 and Byte 4.<br />
<br />
The table can be continued indefinitely (up to Byte 8 in this example).<br />
<br />
The key thing to keep in mind when creating this table is that whenever there is a Byte addition, k constructs are successful, and (1-k) are not, and this can only happen for Bytes with the appropriate sticky ends.<br />
<br />
Now assuming that all even numbered Bytes are of equal length and that all odd numbered Bytes are of equal length, these fractions can be combined. For instance, in the “Byte 4” column, since A12, A14, and A34 are of the same length and would therefore superimpose on a gel, these fractions can be summed together resulting in the total fraction of constructs at the 2-Bytes long construct length. This can be done for each construct size in the “Byte 4” column and repeated for every other “Byte #” column. The results of doing this are shown below in the following table for up to step 8 – where the 8th Byte is added.<br><br />
<br />
[[Image:team-alberta-modelling-table.jpg|frame|Combined fractions.]]<br />
<br />
<br>From the table, we can see that the k exponents and the (1-k) exponents are easily predictable as the steps continue. The coefficients are not, but it can be shown that the coefficients for the equations in Step n correspond to row n of a special kind of Pascal’s triangle. They follow the integer sequence of [http://www.research.att.com/~njas/sequences/A065941 A065941 from the Encyclopedia of Integer Sequences], which can be created with the following Matlab code:<br />
<br />
<pre lang="matlab"><br />
<br />
g=1; nBytes=8;<br />
for n=1:nBytes<br />
for k=1:g<br />
Triangle(n,k)=nchoosek(n-1-floor((k)/2),floor((k-1)/2));<br />
end<br />
g=g+1;<br />
end<br />
<br />
</pre><br />
<br />
where nBytes is the number of bytes the construct is made up of (including the anchor for this code). For a construct of length n, only the nth column is needed.<br />
<br />
Back to our octomer. Now that construction is complete and now that we have our handy table, we know the theoretical proportions of construct at each length. For our octomer assembly process, the brightness of each band can be predicted with the set of equations in the “Step 8” column and multiplying with the corresponding length. This was done for k values ranging from 0 all the way up to 1 in steps of 0.05. When exposing a gel, usually the brightness is adjusted so that the bands are within a visible range. In the model, the results of each equation evaluated at a given k were normalized to the largest value. This is analogous to adjusting the exposure time of your gel such that the brightest band just about saturates the pixels in the output image. The results were output to an image. Each column is the set of equations (in the “Step 8” column) evaluated at a specific k value, multiplied by the corresponding length, and normalized to the brightest band.<br />
<br />
[[Image:team-alberta-computed-lanes.png|thumb|500px|center|Band intensities predicted by model.]]<br />
<br />
Each lane represents the construction of an octomer at a different ligation efficiency. Each row represents the construct length. The top row represents the 8-Bytes long construct, the next row is the 7-Byte long construct and so on. At 0% efficiency, the only DNA left after construction is anchor so it is the only band seen on a gel after the assembly process. At 100% efficiency, all of the DNA has ligated perfectly and every construct is exactly 8-Bytes long. This results in only one band at the corresponding octamer length. For the intermediate efficiencies, we see a variety of band patterns. For the higher efficiencies, we see the same alternating brightness in the band pattern that was seen in our actual construction of the octamer in the lab.<br />
<br />
==Octamer Efficiency==<br />
<div id="horiz-line"></div><br />
<br />
So how efficient was our construction of the octamer in the laboratory? From the model, and the figure above, we can tell easily that the efficiency k is above 85% since our 8-Byte long construct band was the brightest band. <br />
<br />
Looking closely at our octamer gel, we can say that the band for the 8-Byte long construct is at least three times brighter than the band for the 6-Byte long construct. Since the octamer gel appears to have been over exposed (and saturated the pixels), it is hard to tell, but 3 times seems to be a good estimate. Keeping this in mind and looking at the Matlab output for finer efficiency simulations, we can see that this corresponds to a '''Byte addition efficiency of at least 94.5%'''.<br />
<br />
==The Matlab Code==<br />
<div id="horiz-line"></div><br />
<br />
<div><br />
<pre><br />
% This program will take in the lengths of each of your Bytes and output<br />
% the relative intensities of the bands expected.<br />
<br />
function [Intensities] = findIntensities(nBytes,AnchorLength,OddByteLengths,<br />
EvenByteLengths)<br />
<br />
% The anchor counts as a Byte in this code. So for octamer, nBytes == 9.<br />
<br />
x = 1 ;<br />
<br />
% Create the proportion coefficients<br />
<br />
for g=1:nBytes<br />
<br />
cT(g,1) = nchoosek(nBytes-1-floor((g)/2),floor((g-1)/2)) ;<br />
<br />
end<br />
<br />
% Create the (1-K) exponents<br />
<br />
b = 0.5:0.5:nBytes/2 ;<br />
<br />
exps1_k = floor(b)'; % The (1-k) exponents<br />
<br />
% Create the K exponents<br />
<br />
kExps = (nBytes-1:-1:0)' ; % The k exponents<br />
<br />
% Create the length coefficients<br />
<br />
cL(1:nBytes,1) = EvenByteLengths ;<br />
<br />
cL(1,1) = AnchorLength ;<br />
<br />
cL(2:2:nBytes,1) = OddByteLengths ;<br />
<br />
for h=2:length(cL)<br />
<br />
cL(h) = cL(h) + cL(h-1) ;<br />
<br />
end<br />
<br />
cL = flipud(cL)<br />
<br />
cT<br />
<br />
% Compute the intensities for each length (leaving k as a variable)<br />
<br />
syms k ;<br />
<br />
for R=1:nBytes<br />
<br />
IntenSym(R,1) = cT(R)*((1-k)^exps1_k(R))*(k^kExps(R))*cL(R) ;<br />
<br />
end<br />
<br />
IntenSym<br />
<br />
% Compute the intensities at various values of k. Also normalize<br />
% intensities to the brightest band (per lane)<br />
<br />
for k = 0 : 0.05 : 1 % Being evaluated at every 5% efficiency<br />
<br />
IntensEval(:,x)=eval(IntenSym) ; % Evaluate<br />
<br />
Intensities(:,x)=IntensEval(:,x)/max(IntensEval(:,x)) ; % Normalize<br />
<br />
x = x + 1 ;<br />
<br />
end<br />
<br />
% Now create a picture<br />
<br />
w = 0 ; p = 0 ; t = 3 ;<br />
<br />
for a=1:length(Intensities(1,:))<br />
<br />
<br />
for b = 1 : length(Intensities(:,a)) % cycles through rows in the a'th column<br />
<br />
Pic(b+w,a+p:a+p+t) = Intensities(b,a);<br />
<br />
w = w + 2 ;<br />
<br />
end<br />
<br />
w = 0 ; p = p + 1 + t ;<br />
<br />
end<br />
<br />
set(gcf, 'Position', [0 0 1300 400]) % Stretch image so bands look rectangular <br />
like a real gel<br />
<br />
colormap(gray); imagesc(Pic)<br />
<br />
title('Expected Relative Band Intensities for Variable Efficiency')<br />
<br />
xlabel('Efficiency (%)')<br />
</pre><br />
</div><br />
<br />
For the octamer built in the lab, the anchor was 56 base pairs long, the odd numbered bytes were 976 base pairs long, and the even numbered Bytes were 2083 Bytes long. To run the code for the expected bands for this octomer, the following code must be typed into the command window:<br />
<br />
<code>findIntensities(9,56,976,2083)</code><br />
<br />
{{Team:Alberta/endMainContent}}</div>Stjahnshttp://2010.igem.org/Team:Alberta/modellingTeam:Alberta/modelling2010-10-27T03:39:31Z<p>Stjahns: /* Creating the Model */</p>
<hr />
<div>{{Team:Alberta/Head}}<br />
<br />
{{Team:Alberta/navbar|project=selected}}<br />
<br />
{{Team:Alberta/beginLeftSideBar}}<br />
{{Team:Alberta/endLeftSideBar}}<br />
{{Team:Alberta/beginMainContent}}<br />
==Goal of the Model==<br />
<div id="horiz-line"></div><br />
<br />
[[Image:Cropped_labeled_gel_Alberta.png|200px|thumb|left|Relative band intensities can be used to determine assembly efficiencies.]]<br />
<br />
<p><br />
Efficiency is the key to the BioByte assembly method. For this reason, it is important to determine the efficiency by which each Byte can be added to a growing construct. Our modeling efforts have made it possible for us to determine assembly efficiency and predict future efficiencies of constructs, which have not yet been attempted.<br />
<br />
After assembling a series of Bytes, the construct can be run on a gel. Multiple bands appear. The top band contains the full construct while all of the bands below contain failed intermediate constructs of lower length. <br />
</p><br />
<br />
<p><br><b>Why do the band’s intensities alternate in intensity like that? How can the Byte addition efficiency be calculated from the gel?</b><br />
<br />
To answer these questions, we must consider the assembly process of a construct. If we follow through the assembly process while considering the efficiency k of Byte addition at each step, the expected relative intensities of the bands in the gel can be calculated.<br />
</p><br />
<br />
==Characterizing the Assembly Process==<br />
<div id="horiz-line"></div><br />
<br />
For this model, there are a few points to consider that characterize the assembly process:<br />
<br />
*First, Byte addition occurs with a constant efficiency k, which is the same for AB Byte additions and BA Byte additions. This means that for a given Byte addition, a fraction k of the existing construct is successful in growing in construct size, while (1-k) remains at the same construct size because of no ligation. <br />
<br />
*Secondly, AB Bytes can ligate only to BA Bytes, while BA Bytes can ligate only to AB Bytes.<br> <br />
<br />
Considering these points, we see that during the creation of a 8-Bytes long construct, there will be some intermediate sized constructs that will be visible on a gel. With some thought on the second point, we see that intermediate constructs can be made up of multiple arrangements of Bytes. <br />
<br />
For instance, during the creation of a 8-Bytes long construct, a medium sized 4-Byte long construct will be made up of the following combinations of Bytes:<br />
<div style="float:left; margin-right:30px;"><br />
*1,2,3,4<br />
*1,2,3,6<br />
*1,2,3,8<br />
*1,2,5,6<br />
</div><br />
<div style="float:left; margin-right:30px;"><br />
*1,2,5,8<br />
*1,2,7,8<br />
*1,4,5,6<br />
*1,4,5,8<br />
</div><br />
<div style="float:left; margin-right:30px;"><br />
*1,4,7,8<br />
*1,6,7,8<br />
*3,4,5,6<br />
*3,4,5,8<br />
</div><br />
<div style="float:left; margin-right:30px;"><br />
*3,4,7,8<br />
*3,6,7,8<br />
*5,6,7,8<br />
</div><br />
<div style="clear:both;"></div><br />
<br />
''Note that if all even numbered Bytes are of equal length and if all odd numbered Bytes are of equal length, then all of the aforementioned 4-Bytes long constructs are all of the same length. This means that their corresponding bands on a gel would all be superimposed into one band on the gel.'' <br />
<br />
This occurs for all the intermediate sized (failed) constructs. This concept is important for the derivation of a general set of equations describing the expected relative band intensities for each band in a post-assembly gel.<br />
<br />
==Creating the Model==<br />
<div id="horiz-line"></div><br />
Now imagine the construction process of a 8-Byte long construct. We’ll call it the octamer. It will be made up of alternating 1kbp AB Bytes and 2kbp BA Bytes. We’ll follow the construction of it while keeping track of what fraction of all of the intermediate constructs ends up at particular sizes (as a function of the ligation efficiency k). <br />
<br />
First, the anchor is added to the bead. We’ll say that 100% (k=1) of the construct is at anchor length at this point. Then, Byte 1 is added to the anchor with efficiency k. Now, k of the constructs are made up of anchor and Byte 1, while (1-k) is left as anchor. Adding Byte 2, we see that k squared of the constructs are made up of anchor, Byte 1 and Byte 2, whereas (1-k)k are left as anchor plus Byte 1, and (1-k) is still left as just anchor. It is still (1-k) because Byte 2 could not ligate to the anchor at all (because the ends are not compatible). It becomes more complicated for higher Byte additions. This process can be mapped and placed in the following table.<br><br />
<br />
[[Image:team-alberta-modelling-table-bytes.jpg|frame|Fractions of constructs produced.]]<br />
<br />
<br>Each column represents the addition of a Byte. The “Fraction” column describes the fraction of the corresponding construct in the “Construct” column. “A” refers to anchor, and the numbers beside it refer to the Bytes attached to the anchor. For instance, A34 refers to the construct made up of the anchor, Byte 3 and Byte 4.<br />
<br />
The table can be continued indefinitely (up to Byte 8 in this example).<br />
<br />
The key thing to keep in mind when creating this table is that whenever there is a Byte addition, k constructs are successful, and (1-k) are not, and this can only happen for Bytes with the appropriate sticky ends.<br />
<br />
Now assuming that all even numbered Bytes are of equal length and that all odd numbered Bytes are of equal length, these fractions can be combined. For instance, in the “Byte 4” column, since A12, A14, and A34 are of the same length and would therefore superimpose on a gel, these fractions can be summed together resulting in the total fraction of constructs at the 2-Bytes long construct length. This can be done for each construct size in the “Byte 4” column and repeated for every other “Byte #” column. The results of doing this are shown below in the following table for up to step 8 – where the 8th Byte is added.<br><br />
<br />
[[Image:team-alberta-modelling-table.jpg|frame|Combined fractions.]]<br />
<br />
<br>From the table, we can see that the k exponents and the (1-k) exponents are easily predictable as the steps continue. The coefficients are not, but it can be shown that the coefficients for the equations in Step n correspond to row n of a special kind of Pascal’s triangle. They follow the integer sequence of [http://www.research.att.com/~njas/sequences/A065941 A065941 from the Encyclopedia of Integer Sequences], which can be created with the following Matlab code:<br />
<br />
<pre lang="matlab"><br />
<br />
g=1; nBytes=8;<br />
for n=1:nBytes<br />
for k=1:g<br />
Triangle(n,k)=nchoosek(n-1-floor((k)/2),floor((k-1)/2));<br />
end<br />
g=g+1;<br />
end<br />
<br />
</pre><br />
<br />
where nBytes is the number of bytes the construct is made up of (including the anchor for this code). For a construct of length n, only the nth column is needed.<br />
<br />
Back to our octomer. Now that construction is complete and now that we have our handy table, we know the theoretical proportions of construct at each length. For our octomer assembly process, the brightness of each band can be predicted with the set of equations in the “Step 8” column and multiplying with the corresponding length. This was done for k values ranging from 0 all the way up to 1 in steps of 0.05. When exposing a gel, usually the brightness is adjusted so that the bands are within a visible range. In the model, the results of each equation evaluated at a given k were normalized to the largest value. This is analogous to adjusting the exposure time of your gel such that the brightest band just about saturates the pixels in the output image. The results were output to an image. Each column is the set of equations (in the “Step 8” column) evaluated at a specific k value, multiplied by the corresponding length, and normalized to the brightest band.<br />
<br />
<div style="position: relative; left: -100px;"><br />
[[Image:team-alberta-computed-lanes.png|thumb|500px|center|Band intensities predicted by model.]]<br />
</div><br />
<br />
Each lane represents the construction of an octomer at a different ligation efficiency. Each row represents the construct length. The top row represents the 8-Bytes long construct, the next row is the 7-Byte long construct and so on. At 0% efficiency, the only DNA left after construction is anchor so it is the only band seen on a gel after the assembly process. At 100% efficiency, all of the DNA has ligated perfectly and every construct is exactly 8-Bytes long. This results in only one band at the corresponding octamer length. For the intermediate efficiencies, we see a variety of band patterns. For the higher efficiencies, we see the same alternating brightness in the band pattern that was seen in our actual construction of the octamer in the lab.<br />
<br />
==Octamer Efficiency==<br />
<div id="horiz-line"></div><br />
<br />
So how efficient was our construction of the octamer in the laboratory? From the model, and the figure above, we can tell easily that the efficiency k is above 85% since our 8-Byte long construct band was the brightest band. <br />
<br />
Looking closely at our octamer gel, we can say that the band for the 8-Byte long construct is at least three times brighter than the band for the 6-Byte long construct. Since the octamer gel appears to have been over exposed (and saturated the pixels), it is hard to tell, but 3 times seems to be a good estimate. Keeping this in mind and looking at the Matlab output for finer efficiency simulations, we can see that this corresponds to a '''Byte addition efficiency of at least 94.5%'''.<br />
<br />
==The Matlab Code==<br />
<div id="horiz-line"></div><br />
<br />
<div><br />
<pre><br />
% This program will take in the lengths of each of your Bytes and output<br />
% the relative intensities of the bands expected.<br />
<br />
function [Intensities] = findIntensities(nBytes,AnchorLength,OddByteLengths,<br />
EvenByteLengths)<br />
<br />
% The anchor counts as a Byte in this code. So for octamer, nBytes == 9.<br />
<br />
x = 1 ;<br />
<br />
% Create the proportion coefficients<br />
<br />
for g=1:nBytes<br />
<br />
cT(g,1) = nchoosek(nBytes-1-floor((g)/2),floor((g-1)/2)) ;<br />
<br />
end<br />
<br />
% Create the (1-K) exponents<br />
<br />
b = 0.5:0.5:nBytes/2 ;<br />
<br />
exps1_k = floor(b)'; % The (1-k) exponents<br />
<br />
% Create the K exponents<br />
<br />
kExps = (nBytes-1:-1:0)' ; % The k exponents<br />
<br />
% Create the length coefficients<br />
<br />
cL(1:nBytes,1) = EvenByteLengths ;<br />
<br />
cL(1,1) = AnchorLength ;<br />
<br />
cL(2:2:nBytes,1) = OddByteLengths ;<br />
<br />
for h=2:length(cL)<br />
<br />
cL(h) = cL(h) + cL(h-1) ;<br />
<br />
end<br />
<br />
cL = flipud(cL)<br />
<br />
cT<br />
<br />
% Compute the intensities for each length (leaving k as a variable)<br />
<br />
syms k ;<br />
<br />
for R=1:nBytes<br />
<br />
IntenSym(R,1) = cT(R)*((1-k)^exps1_k(R))*(k^kExps(R))*cL(R) ;<br />
<br />
end<br />
<br />
IntenSym<br />
<br />
% Compute the intensities at various values of k. Also normalize<br />
% intensities to the brightest band (per lane)<br />
<br />
for k = 0 : 0.05 : 1 % Being evaluated at every 5% efficiency<br />
<br />
IntensEval(:,x)=eval(IntenSym) ; % Evaluate<br />
<br />
Intensities(:,x)=IntensEval(:,x)/max(IntensEval(:,x)) ; % Normalize<br />
<br />
x = x + 1 ;<br />
<br />
end<br />
<br />
% Now create a picture<br />
<br />
w = 0 ; p = 0 ; t = 3 ;<br />
<br />
for a=1:length(Intensities(1,:))<br />
<br />
<br />
for b = 1 : length(Intensities(:,a)) % cycles through rows in the a'th column<br />
<br />
Pic(b+w,a+p:a+p+t) = Intensities(b,a);<br />
<br />
w = w + 2 ;<br />
<br />
end<br />
<br />
w = 0 ; p = p + 1 + t ;<br />
<br />
end<br />
<br />
set(gcf, 'Position', [0 0 1300 400]) % Stretch image so bands look rectangular <br />
like a real gel<br />
<br />
colormap(gray); imagesc(Pic)<br />
<br />
title('Expected Relative Band Intensities for Variable Efficiency')<br />
<br />
xlabel('Efficiency (%)')<br />
</pre><br />
</div><br />
<br />
For the octamer built in the lab, the anchor was 56 base pairs long, the odd numbered bytes were 976 base pairs long, and the even numbered Bytes were 2083 Bytes long. To run the code for the expected bands for this octomer, the following code must be typed into the command window:<br />
<br />
<code>findIntensities(9,56,976,2083)</code><br />
<br />
{{Team:Alberta/endMainContent}}</div>Stjahnshttp://2010.igem.org/Team:Alberta/modellingTeam:Alberta/modelling2010-10-27T03:38:24Z<p>Stjahns: /* Creating the Model */</p>
<hr />
<div>{{Team:Alberta/Head}}<br />
<br />
{{Team:Alberta/navbar|project=selected}}<br />
<br />
{{Team:Alberta/beginLeftSideBar}}<br />
{{Team:Alberta/endLeftSideBar}}<br />
{{Team:Alberta/beginMainContent}}<br />
==Goal of the Model==<br />
<div id="horiz-line"></div><br />
<br />
[[Image:Cropped_labeled_gel_Alberta.png|200px|thumb|left|Relative band intensities can be used to determine assembly efficiencies.]]<br />
<br />
<p><br />
Efficiency is the key to the BioByte assembly method. For this reason, it is important to determine the efficiency by which each Byte can be added to a growing construct. Our modeling efforts have made it possible for us to determine assembly efficiency and predict future efficiencies of constructs, which have not yet been attempted.<br />
<br />
After assembling a series of Bytes, the construct can be run on a gel. Multiple bands appear. The top band contains the full construct while all of the bands below contain failed intermediate constructs of lower length. <br />
</p><br />
<br />
<p><br><b>Why do the band’s intensities alternate in intensity like that? How can the Byte addition efficiency be calculated from the gel?</b><br />
<br />
To answer these questions, we must consider the assembly process of a construct. If we follow through the assembly process while considering the efficiency k of Byte addition at each step, the expected relative intensities of the bands in the gel can be calculated.<br />
</p><br />
<br />
==Characterizing the Assembly Process==<br />
<div id="horiz-line"></div><br />
<br />
For this model, there are a few points to consider that characterize the assembly process:<br />
<br />
*First, Byte addition occurs with a constant efficiency k, which is the same for AB Byte additions and BA Byte additions. This means that for a given Byte addition, a fraction k of the existing construct is successful in growing in construct size, while (1-k) remains at the same construct size because of no ligation. <br />
<br />
*Secondly, AB Bytes can ligate only to BA Bytes, while BA Bytes can ligate only to AB Bytes.<br> <br />
<br />
Considering these points, we see that during the creation of a 8-Bytes long construct, there will be some intermediate sized constructs that will be visible on a gel. With some thought on the second point, we see that intermediate constructs can be made up of multiple arrangements of Bytes. <br />
<br />
For instance, during the creation of a 8-Bytes long construct, a medium sized 4-Byte long construct will be made up of the following combinations of Bytes:<br />
<div style="float:left; margin-right:30px;"><br />
*1,2,3,4<br />
*1,2,3,6<br />
*1,2,3,8<br />
*1,2,5,6<br />
</div><br />
<div style="float:left; margin-right:30px;"><br />
*1,2,5,8<br />
*1,2,7,8<br />
*1,4,5,6<br />
*1,4,5,8<br />
</div><br />
<div style="float:left; margin-right:30px;"><br />
*1,4,7,8<br />
*1,6,7,8<br />
*3,4,5,6<br />
*3,4,5,8<br />
</div><br />
<div style="float:left; margin-right:30px;"><br />
*3,4,7,8<br />
*3,6,7,8<br />
*5,6,7,8<br />
</div><br />
<div style="clear:both;"></div><br />
<br />
''Note that if all even numbered Bytes are of equal length and if all odd numbered Bytes are of equal length, then all of the aforementioned 4-Bytes long constructs are all of the same length. This means that their corresponding bands on a gel would all be superimposed into one band on the gel.'' <br />
<br />
This occurs for all the intermediate sized (failed) constructs. This concept is important for the derivation of a general set of equations describing the expected relative band intensities for each band in a post-assembly gel.<br />
<br />
==Creating the Model==<br />
<div id="horiz-line"></div><br />
Now imagine the construction process of a 8-Byte long construct. We’ll call it the octamer. It will be made up of alternating 1kbp AB Bytes and 2kbp BA Bytes. We’ll follow the construction of it while keeping track of what fraction of all of the intermediate constructs ends up at particular sizes (as a function of the ligation efficiency k). <br />
<br />
First, the anchor is added to the bead. We’ll say that 100% (k=1) of the construct is at anchor length at this point. Then, Byte 1 is added to the anchor with efficiency k. Now, k of the constructs are made up of anchor and Byte 1, while (1-k) is left as anchor. Adding Byte 2, we see that k squared of the constructs are made up of anchor, Byte 1 and Byte 2, whereas (1-k)k are left as anchor plus Byte 1, and (1-k) is still left as just anchor. It is still (1-k) because Byte 2 could not ligate to the anchor at all (because the ends are not compatible). It becomes more complicated for higher Byte additions. This process can be mapped and placed in the following table.<br><br />
<br />
[[Image:team-alberta-modelling-table-bytes.jpg|frame|Fractions of constructs produced.]]<br />
<br />
<br>Each column represents the addition of a Byte. The “Fraction” column describes the fraction of the corresponding construct in the “Construct” column. “A” refers to anchor, and the numbers beside it refer to the Bytes attached to the anchor. For instance, A34 refers to the construct made up of the anchor, Byte 3 and Byte 4.<br />
<br />
The table can be continued indefinitely (up to Byte 8 in this example).<br />
<br />
The key thing to keep in mind when creating this table is that whenever there is a Byte addition, k constructs are successful, and (1-k) are not, and this can only happen for Bytes with the appropriate sticky ends.<br />
<br />
Now assuming that all even numbered Bytes are of equal length and that all odd numbered Bytes are of equal length, these fractions can be combined. For instance, in the “Byte 4” column, since A12, A14, and A34 are of the same length and would therefore superimpose on a gel, these fractions can be summed together resulting in the total fraction of constructs at the 2-Bytes long construct length. This can be done for each construct size in the “Byte 4” column and repeated for every other “Byte #” column. The results of doing this are shown below in the following table for up to step 8 – where the 8th Byte is added.<br><br />
<br />
[[Image:team-alberta-modelling-table.jpg|frame|Combined fractions.]]<br />
<br />
<br>From the table, we can see that the k exponents and the (1-k) exponents are easily predictable as the steps continue. The coefficients are not, but it can be shown that the coefficients for the equations in Step n correspond to row n of a special kind of Pascal’s triangle. They follow the integer sequence of [http://www.research.att.com/~njas/sequences/A065941 A065941 from the Encyclopedia of Integer Sequences], which can be created with the following Matlab code:<br />
<br />
<pre lang="matlab"><br />
<br />
g=1; nBytes=8;<br />
for n=1:nBytes<br />
for k=1:g<br />
Triangle(n,k)=nchoosek(n-1-floor((k)/2),floor((k-1)/2));<br />
end<br />
g=g+1;<br />
end<br />
<br />
</pre><br />
<br />
where nBytes is the number of bytes the construct is made up of (including the anchor for this code). For a construct of length n, only the nth column is needed.<br />
<br />
Back to our octomer. Now that construction is complete and now that we have our handy table, we know the theoretical proportions of construct at each length. For our octomer assembly process, the brightness of each band can be predicted with the set of equations in the “Step 8” column and multiplying with the corresponding length. This was done for k values ranging from 0 all the way up to 1 in steps of 0.05. When exposing a gel, usually the brightness is adjusted so that the bands are within a visible range. In the model, the results of each equation evaluated at a given k were normalized to the largest value. This is analogous to adjusting the exposure time of your gel such that the brightest band just about saturates the pixels in the output image. The results were output to an image. Each column is the set of equations (in the “Step 8” column) evaluated at a specific k value, multiplied by the corresponding length, and normalized to the brightest band.<br />
<br />
<div style="position: relative; left: -100px;"><br />
[[Image:team-alberta-computed-lanes.png|750px|center|Band intensities predicted by model.]]<br />
</div><br />
<br />
Each lane represents the construction of an octomer at a different ligation efficiency. Each row represents the construct length. The top row represents the 8-Bytes long construct, the next row is the 7-Byte long construct and so on. At 0% efficiency, the only DNA left after construction is anchor so it is the only band seen on a gel after the assembly process. At 100% efficiency, all of the DNA has ligated perfectly and every construct is exactly 8-Bytes long. This results in only one band at the corresponding octamer length. For the intermediate efficiencies, we see a variety of band patterns. For the higher efficiencies, we see the same alternating brightness in the band pattern that was seen in our actual construction of the octamer in the lab.<br />
<br />
==Octamer Efficiency==<br />
<div id="horiz-line"></div><br />
<br />
So how efficient was our construction of the octamer in the laboratory? From the model, and the figure above, we can tell easily that the efficiency k is above 85% since our 8-Byte long construct band was the brightest band. <br />
<br />
Looking closely at our octamer gel, we can say that the band for the 8-Byte long construct is at least three times brighter than the band for the 6-Byte long construct. Since the octamer gel appears to have been over exposed (and saturated the pixels), it is hard to tell, but 3 times seems to be a good estimate. Keeping this in mind and looking at the Matlab output for finer efficiency simulations, we can see that this corresponds to a '''Byte addition efficiency of at least 94.5%'''.<br />
<br />
==The Matlab Code==<br />
<div id="horiz-line"></div><br />
<br />
<div><br />
<pre><br />
% This program will take in the lengths of each of your Bytes and output<br />
% the relative intensities of the bands expected.<br />
<br />
function [Intensities] = findIntensities(nBytes,AnchorLength,OddByteLengths,<br />
EvenByteLengths)<br />
<br />
% The anchor counts as a Byte in this code. So for octamer, nBytes == 9.<br />
<br />
x = 1 ;<br />
<br />
% Create the proportion coefficients<br />
<br />
for g=1:nBytes<br />
<br />
cT(g,1) = nchoosek(nBytes-1-floor((g)/2),floor((g-1)/2)) ;<br />
<br />
end<br />
<br />
% Create the (1-K) exponents<br />
<br />
b = 0.5:0.5:nBytes/2 ;<br />
<br />
exps1_k = floor(b)'; % The (1-k) exponents<br />
<br />
% Create the K exponents<br />
<br />
kExps = (nBytes-1:-1:0)' ; % The k exponents<br />
<br />
% Create the length coefficients<br />
<br />
cL(1:nBytes,1) = EvenByteLengths ;<br />
<br />
cL(1,1) = AnchorLength ;<br />
<br />
cL(2:2:nBytes,1) = OddByteLengths ;<br />
<br />
for h=2:length(cL)<br />
<br />
cL(h) = cL(h) + cL(h-1) ;<br />
<br />
end<br />
<br />
cL = flipud(cL)<br />
<br />
cT<br />
<br />
% Compute the intensities for each length (leaving k as a variable)<br />
<br />
syms k ;<br />
<br />
for R=1:nBytes<br />
<br />
IntenSym(R,1) = cT(R)*((1-k)^exps1_k(R))*(k^kExps(R))*cL(R) ;<br />
<br />
end<br />
<br />
IntenSym<br />
<br />
% Compute the intensities at various values of k. Also normalize<br />
% intensities to the brightest band (per lane)<br />
<br />
for k = 0 : 0.05 : 1 % Being evaluated at every 5% efficiency<br />
<br />
IntensEval(:,x)=eval(IntenSym) ; % Evaluate<br />
<br />
Intensities(:,x)=IntensEval(:,x)/max(IntensEval(:,x)) ; % Normalize<br />
<br />
x = x + 1 ;<br />
<br />
end<br />
<br />
% Now create a picture<br />
<br />
w = 0 ; p = 0 ; t = 3 ;<br />
<br />
for a=1:length(Intensities(1,:))<br />
<br />
<br />
for b = 1 : length(Intensities(:,a)) % cycles through rows in the a'th column<br />
<br />
Pic(b+w,a+p:a+p+t) = Intensities(b,a);<br />
<br />
w = w + 2 ;<br />
<br />
end<br />
<br />
w = 0 ; p = p + 1 + t ;<br />
<br />
end<br />
<br />
set(gcf, 'Position', [0 0 1300 400]) % Stretch image so bands look rectangular <br />
like a real gel<br />
<br />
colormap(gray); imagesc(Pic)<br />
<br />
title('Expected Relative Band Intensities for Variable Efficiency')<br />
<br />
xlabel('Efficiency (%)')<br />
</pre><br />
</div><br />
<br />
For the octamer built in the lab, the anchor was 56 base pairs long, the odd numbered bytes were 976 base pairs long, and the even numbered Bytes were 2083 Bytes long. To run the code for the expected bands for this octomer, the following code must be typed into the command window:<br />
<br />
<code>findIntensities(9,56,976,2083)</code><br />
<br />
{{Team:Alberta/endMainContent}}</div>Stjahnshttp://2010.igem.org/Team:Alberta/modellingTeam:Alberta/modelling2010-10-27T03:33:13Z<p>Stjahns: /* Goal of the Model */</p>
<hr />
<div>{{Team:Alberta/Head}}<br />
<br />
{{Team:Alberta/navbar|project=selected}}<br />
<br />
{{Team:Alberta/beginLeftSideBar}}<br />
{{Team:Alberta/endLeftSideBar}}<br />
{{Team:Alberta/beginMainContent}}<br />
==Goal of the Model==<br />
<div id="horiz-line"></div><br />
<br />
[[Image:Cropped_labeled_gel_Alberta.png|200px|thumb|left|Relative band intensities can be used to determine assembly efficiencies.]]<br />
<br />
<p><br />
Efficiency is the key to the BioByte assembly method. For this reason, it is important to determine the efficiency by which each Byte can be added to a growing construct. Our modeling efforts have made it possible for us to determine assembly efficiency and predict future efficiencies of constructs, which have not yet been attempted.<br />
<br />
After assembling a series of Bytes, the construct can be run on a gel. Multiple bands appear. The top band contains the full construct while all of the bands below contain failed intermediate constructs of lower length. <br />
</p><br />
<br />
<p><br><b>Why do the band’s intensities alternate in intensity like that? How can the Byte addition efficiency be calculated from the gel?</b><br />
<br />
To answer these questions, we must consider the assembly process of a construct. If we follow through the assembly process while considering the efficiency k of Byte addition at each step, the expected relative intensities of the bands in the gel can be calculated.<br />
</p><br />
<br />
==Characterizing the Assembly Process==<br />
<div id="horiz-line"></div><br />
<br />
For this model, there are a few points to consider that characterize the assembly process:<br />
<br />
*First, Byte addition occurs with a constant efficiency k, which is the same for AB Byte additions and BA Byte additions. This means that for a given Byte addition, a fraction k of the existing construct is successful in growing in construct size, while (1-k) remains at the same construct size because of no ligation. <br />
<br />
*Secondly, AB Bytes can ligate only to BA Bytes, while BA Bytes can ligate only to AB Bytes.<br> <br />
<br />
Considering these points, we see that during the creation of a 8-Bytes long construct, there will be some intermediate sized constructs that will be visible on a gel. With some thought on the second point, we see that intermediate constructs can be made up of multiple arrangements of Bytes. <br />
<br />
For instance, during the creation of a 8-Bytes long construct, a medium sized 4-Byte long construct will be made up of the following combinations of Bytes:<br />
<div style="float:left; margin-right:30px;"><br />
*1,2,3,4<br />
*1,2,3,6<br />
*1,2,3,8<br />
*1,2,5,6<br />
</div><br />
<div style="float:left; margin-right:30px;"><br />
*1,2,5,8<br />
*1,2,7,8<br />
*1,4,5,6<br />
*1,4,5,8<br />
</div><br />
<div style="float:left; margin-right:30px;"><br />
*1,4,7,8<br />
*1,6,7,8<br />
*3,4,5,6<br />
*3,4,5,8<br />
</div><br />
<div style="float:left; margin-right:30px;"><br />
*3,4,7,8<br />
*3,6,7,8<br />
*5,6,7,8<br />
</div><br />
<div style="clear:both;"></div><br />
<br />
''Note that if all even numbered Bytes are of equal length and if all odd numbered Bytes are of equal length, then all of the aforementioned 4-Bytes long constructs are all of the same length. This means that their corresponding bands on a gel would all be superimposed into one band on the gel.'' <br />
<br />
This occurs for all the intermediate sized (failed) constructs. This concept is important for the derivation of a general set of equations describing the expected relative band intensities for each band in a post-assembly gel.<br />
<br />
==Creating the Model==<br />
<div id="horiz-line"></div><br />
Now imagine the construction process of a 8-Byte long construct. We’ll call it the octamer. It will be made up of alternating 1kbp AB Bytes and 2kbp BA Bytes. We’ll follow the construction of it while keeping track of what fraction of all of the intermediate constructs ends up at particular sizes (as a function of the ligation efficiency k). <br />
<br />
First, the anchor is added to the bead. We’ll say that 100% (k=1) of the construct is at anchor length at this point. Then, Byte 1 is added to the anchor with efficiency k. Now, k of the constructs are made up of anchor and Byte 1, while (1-k) is left as anchor. Adding Byte 2, we see that k squared of the constructs are made up of anchor, Byte 1 and Byte 2, whereas (1-k)k are left as anchor plus Byte 1, and (1-k) is still left as just anchor. It is still (1-k) because Byte 2 could not ligate to the anchor at all (because the ends are not compatible). It becomes more complicated for higher Byte additions. This process can be mapped and placed in the following table.<br><br />
<br />
[[Image:team-alberta-modelling-table-bytes.jpg]]<br />
<br />
<br>Each column represents the addition of a Byte. The “Fraction” column describes the fraction of the corresponding construct in the “Construct” column. “A” refers to anchor, and the numbers beside it refer to the Bytes attached to the anchor. For instance, A34 refers to the construct made up of the anchor, Byte 3 and Byte 4.<br />
<br />
The table can be continued indefinitely (up to Byte 8 in this example).<br />
<br />
The key thing to keep in mind when creating this table is that whenever there is a Byte addition, k constructs are successful, and (1-k) are not, and this can only happen for Bytes with the appropriate sticky ends.<br />
<br />
Now assuming that all even numbered Bytes are of equal length and that all odd numbered Bytes are of equal length, these fractions can be combined. For instance, in the “Byte 4” column, since A12, A14, and A34 are of the same length and would therefore superimpose on a gel, these fractions can be summed together resulting in the total fraction of constructs at the 2-Bytes long construct length. This can be done for each construct size in the “Byte 4” column and repeated for every other “Byte #” column. The results of doing this are shown below in the following table for up to step 8 – where the 8th Byte is added.<br><br />
<br />
[[Image:team-alberta-modelling-table.jpg]]<br />
<br />
<br>From the table, we can see that the k exponents and the (1-k) exponents are easily predictable as the steps continue. The coefficients are not, but it can be shown that the coefficients for the equations in Step n correspond to row n of a special kind of Pascal’s triangle. They follow the integer sequence of [http://www.research.att.com/~njas/sequences/A065941 A065941 from the Encyclopedia of Integer Sequences], which can be created with the following Matlab code:<br />
<br />
<pre lang="matlab"><br />
<br />
g=1; nBytes=8;<br />
for n=1:nBytes<br />
for k=1:g<br />
Triangle(n,k)=nchoosek(n-1-floor((k)/2),floor((k-1)/2));<br />
end<br />
g=g+1;<br />
end<br />
<br />
</pre><br />
<br />
where nBytes is the number of bytes the construct is made up of (including the anchor for this code). For a construct of length n, only the nth column is needed.<br />
<br />
Back to our octomer. Now that construction is complete and now that we have our handy table, we know the theoretical proportions of construct at each length. For our octomer assembly process, the brightness of each band can be predicted with the set of equations in the “Step 8” column and multiplying with the corresponding length. This was done for k values ranging from 0 all the way up to 1 in steps of 0.05. When exposing a gel, usually the brightness is adjusted so that the bands are within a visible range. In the model, the results of each equation evaluated at a given k were normalized to the largest value. This is analogous to adjusting the exposure time of your gel such that the brightest band just about saturates the pixels in the output image. The results were output to an image. Each column is the set of equations (in the “Step 8” column) evaluated at a specific k value, multiplied by the corresponding length, and normalized to the brightest band.<br />
<br />
<div style="position: relative; left: -100px;"><br />
[[Image:team-alberta-computed-lanes.png|750px|center]]<br />
</div><br />
<br />
Each lane represents the construction of an octomer at a different ligation efficiency. Each row represents the construct length. The top row represents the 8-Bytes long construct, the next row is the 7-Byte long construct and so on. At 0% efficiency, the only DNA left after construction is anchor so it is the only band seen on a gel after the assembly process. At 100% efficiency, all of the DNA has ligated perfectly and every construct is exactly 8-Bytes long. This results in only one band at the corresponding octamer length. For the intermediate efficiencies, we see a variety of band patterns. For the higher efficiencies, we see the same alternating brightness in the band pattern that was seen in our actual construction of the octamer in the lab.<br />
<br />
==Octamer Efficiency==<br />
<div id="horiz-line"></div><br />
<br />
So how efficient was our construction of the octamer in the laboratory? From the model, and the figure above, we can tell easily that the efficiency k is above 85% since our 8-Byte long construct band was the brightest band. <br />
<br />
Looking closely at our octamer gel, we can say that the band for the 8-Byte long construct is at least three times brighter than the band for the 6-Byte long construct. Since the octamer gel appears to have been over exposed (and saturated the pixels), it is hard to tell, but 3 times seems to be a good estimate. Keeping this in mind and looking at the Matlab output for finer efficiency simulations, we can see that this corresponds to a '''Byte addition efficiency of at least 94.5%'''.<br />
<br />
==The Matlab Code==<br />
<div id="horiz-line"></div><br />
<br />
<div><br />
<pre><br />
% This program will take in the lengths of each of your Bytes and output<br />
% the relative intensities of the bands expected.<br />
<br />
function [Intensities] = findIntensities(nBytes,AnchorLength,OddByteLengths,<br />
EvenByteLengths)<br />
<br />
% The anchor counts as a Byte in this code. So for octamer, nBytes == 9.<br />
<br />
x = 1 ;<br />
<br />
% Create the proportion coefficients<br />
<br />
for g=1:nBytes<br />
<br />
cT(g,1) = nchoosek(nBytes-1-floor((g)/2),floor((g-1)/2)) ;<br />
<br />
end<br />
<br />
% Create the (1-K) exponents<br />
<br />
b = 0.5:0.5:nBytes/2 ;<br />
<br />
exps1_k = floor(b)'; % The (1-k) exponents<br />
<br />
% Create the K exponents<br />
<br />
kExps = (nBytes-1:-1:0)' ; % The k exponents<br />
<br />
% Create the length coefficients<br />
<br />
cL(1:nBytes,1) = EvenByteLengths ;<br />
<br />
cL(1,1) = AnchorLength ;<br />
<br />
cL(2:2:nBytes,1) = OddByteLengths ;<br />
<br />
for h=2:length(cL)<br />
<br />
cL(h) = cL(h) + cL(h-1) ;<br />
<br />
end<br />
<br />
cL = flipud(cL)<br />
<br />
cT<br />
<br />
% Compute the intensities for each length (leaving k as a variable)<br />
<br />
syms k ;<br />
<br />
for R=1:nBytes<br />
<br />
IntenSym(R,1) = cT(R)*((1-k)^exps1_k(R))*(k^kExps(R))*cL(R) ;<br />
<br />
end<br />
<br />
IntenSym<br />
<br />
% Compute the intensities at various values of k. Also normalize<br />
% intensities to the brightest band (per lane)<br />
<br />
for k = 0 : 0.05 : 1 % Being evaluated at every 5% efficiency<br />
<br />
IntensEval(:,x)=eval(IntenSym) ; % Evaluate<br />
<br />
Intensities(:,x)=IntensEval(:,x)/max(IntensEval(:,x)) ; % Normalize<br />
<br />
x = x + 1 ;<br />
<br />
end<br />
<br />
% Now create a picture<br />
<br />
w = 0 ; p = 0 ; t = 3 ;<br />
<br />
for a=1:length(Intensities(1,:))<br />
<br />
<br />
for b = 1 : length(Intensities(:,a)) % cycles through rows in the a'th column<br />
<br />
Pic(b+w,a+p:a+p+t) = Intensities(b,a);<br />
<br />
w = w + 2 ;<br />
<br />
end<br />
<br />
w = 0 ; p = p + 1 + t ;<br />
<br />
end<br />
<br />
set(gcf, 'Position', [0 0 1300 400]) % Stretch image so bands look rectangular <br />
like a real gel<br />
<br />
colormap(gray); imagesc(Pic)<br />
<br />
title('Expected Relative Band Intensities for Variable Efficiency')<br />
<br />
xlabel('Efficiency (%)')<br />
</pre><br />
</div><br />
<br />
For the octamer built in the lab, the anchor was 56 base pairs long, the odd numbered bytes were 976 base pairs long, and the even numbered Bytes were 2083 Bytes long. To run the code for the expected bands for this octomer, the following code must be typed into the command window:<br />
<br />
<code>findIntensities(9,56,976,2083)</code><br />
<br />
{{Team:Alberta/endMainContent}}</div>Stjahnshttp://2010.igem.org/Team:Alberta/modellingTeam:Alberta/modelling2010-10-27T03:32:46Z<p>Stjahns: /* Goal of the Model */</p>
<hr />
<div>{{Team:Alberta/Head}}<br />
<br />
{{Team:Alberta/navbar|project=selected}}<br />
<br />
{{Team:Alberta/beginLeftSideBar}}<br />
{{Team:Alberta/endLeftSideBar}}<br />
{{Team:Alberta/beginMainContent}}<br />
==Goal of the Model==<br />
<div id="horiz-line"></div><br />
<p><br />
Efficiency is the key to the BioByte assembly method. For this reason, it is important to determine the efficiency by which each Byte can be added to a growing construct. Our modeling efforts have made it possible for us to determine assembly efficiency and predict future efficiencies of constructs, which have not yet been attempted.<br />
<br />
After assembling a series of Bytes, the construct can be run on a gel. Multiple bands appear. The top band contains the full construct while all of the bands below contain failed intermediate constructs of lower length. <br />
</p><br />
<br />
[[Image:Cropped_labeled_gel_Alberta.png|200px|thumb|left|Relative band intensities can be used to determine assembly efficiencies.]]<br />
<br />
<p><br><b>Why do the band’s intensities alternate in intensity like that? How can the Byte addition efficiency be calculated from the gel?</b><br />
<br />
To answer these questions, we must consider the assembly process of a construct. If we follow through the assembly process while considering the efficiency k of Byte addition at each step, the expected relative intensities of the bands in the gel can be calculated.<br />
</p><br />
<br />
==Characterizing the Assembly Process==<br />
<div id="horiz-line"></div><br />
<br />
For this model, there are a few points to consider that characterize the assembly process:<br />
<br />
*First, Byte addition occurs with a constant efficiency k, which is the same for AB Byte additions and BA Byte additions. This means that for a given Byte addition, a fraction k of the existing construct is successful in growing in construct size, while (1-k) remains at the same construct size because of no ligation. <br />
<br />
*Secondly, AB Bytes can ligate only to BA Bytes, while BA Bytes can ligate only to AB Bytes.<br> <br />
<br />
Considering these points, we see that during the creation of a 8-Bytes long construct, there will be some intermediate sized constructs that will be visible on a gel. With some thought on the second point, we see that intermediate constructs can be made up of multiple arrangements of Bytes. <br />
<br />
For instance, during the creation of a 8-Bytes long construct, a medium sized 4-Byte long construct will be made up of the following combinations of Bytes:<br />
<div style="float:left; margin-right:30px;"><br />
*1,2,3,4<br />
*1,2,3,6<br />
*1,2,3,8<br />
*1,2,5,6<br />
</div><br />
<div style="float:left; margin-right:30px;"><br />
*1,2,5,8<br />
*1,2,7,8<br />
*1,4,5,6<br />
*1,4,5,8<br />
</div><br />
<div style="float:left; margin-right:30px;"><br />
*1,4,7,8<br />
*1,6,7,8<br />
*3,4,5,6<br />
*3,4,5,8<br />
</div><br />
<div style="float:left; margin-right:30px;"><br />
*3,4,7,8<br />
*3,6,7,8<br />
*5,6,7,8<br />
</div><br />
<div style="clear:both;"></div><br />
<br />
''Note that if all even numbered Bytes are of equal length and if all odd numbered Bytes are of equal length, then all of the aforementioned 4-Bytes long constructs are all of the same length. This means that their corresponding bands on a gel would all be superimposed into one band on the gel.'' <br />
<br />
This occurs for all the intermediate sized (failed) constructs. This concept is important for the derivation of a general set of equations describing the expected relative band intensities for each band in a post-assembly gel.<br />
<br />
==Creating the Model==<br />
<div id="horiz-line"></div><br />
Now imagine the construction process of a 8-Byte long construct. We’ll call it the octamer. It will be made up of alternating 1kbp AB Bytes and 2kbp BA Bytes. We’ll follow the construction of it while keeping track of what fraction of all of the intermediate constructs ends up at particular sizes (as a function of the ligation efficiency k). <br />
<br />
First, the anchor is added to the bead. We’ll say that 100% (k=1) of the construct is at anchor length at this point. Then, Byte 1 is added to the anchor with efficiency k. Now, k of the constructs are made up of anchor and Byte 1, while (1-k) is left as anchor. Adding Byte 2, we see that k squared of the constructs are made up of anchor, Byte 1 and Byte 2, whereas (1-k)k are left as anchor plus Byte 1, and (1-k) is still left as just anchor. It is still (1-k) because Byte 2 could not ligate to the anchor at all (because the ends are not compatible). It becomes more complicated for higher Byte additions. This process can be mapped and placed in the following table.<br><br />
<br />
[[Image:team-alberta-modelling-table-bytes.jpg]]<br />
<br />
<br>Each column represents the addition of a Byte. The “Fraction” column describes the fraction of the corresponding construct in the “Construct” column. “A” refers to anchor, and the numbers beside it refer to the Bytes attached to the anchor. For instance, A34 refers to the construct made up of the anchor, Byte 3 and Byte 4.<br />
<br />
The table can be continued indefinitely (up to Byte 8 in this example).<br />
<br />
The key thing to keep in mind when creating this table is that whenever there is a Byte addition, k constructs are successful, and (1-k) are not, and this can only happen for Bytes with the appropriate sticky ends.<br />
<br />
Now assuming that all even numbered Bytes are of equal length and that all odd numbered Bytes are of equal length, these fractions can be combined. For instance, in the “Byte 4” column, since A12, A14, and A34 are of the same length and would therefore superimpose on a gel, these fractions can be summed together resulting in the total fraction of constructs at the 2-Bytes long construct length. This can be done for each construct size in the “Byte 4” column and repeated for every other “Byte #” column. The results of doing this are shown below in the following table for up to step 8 – where the 8th Byte is added.<br><br />
<br />
[[Image:team-alberta-modelling-table.jpg]]<br />
<br />
<br>From the table, we can see that the k exponents and the (1-k) exponents are easily predictable as the steps continue. The coefficients are not, but it can be shown that the coefficients for the equations in Step n correspond to row n of a special kind of Pascal’s triangle. They follow the integer sequence of [http://www.research.att.com/~njas/sequences/A065941 A065941 from the Encyclopedia of Integer Sequences], which can be created with the following Matlab code:<br />
<br />
<pre lang="matlab"><br />
<br />
g=1; nBytes=8;<br />
for n=1:nBytes<br />
for k=1:g<br />
Triangle(n,k)=nchoosek(n-1-floor((k)/2),floor((k-1)/2));<br />
end<br />
g=g+1;<br />
end<br />
<br />
</pre><br />
<br />
where nBytes is the number of bytes the construct is made up of (including the anchor for this code). For a construct of length n, only the nth column is needed.<br />
<br />
Back to our octomer. Now that construction is complete and now that we have our handy table, we know the theoretical proportions of construct at each length. For our octomer assembly process, the brightness of each band can be predicted with the set of equations in the “Step 8” column and multiplying with the corresponding length. This was done for k values ranging from 0 all the way up to 1 in steps of 0.05. When exposing a gel, usually the brightness is adjusted so that the bands are within a visible range. In the model, the results of each equation evaluated at a given k were normalized to the largest value. This is analogous to adjusting the exposure time of your gel such that the brightest band just about saturates the pixels in the output image. The results were output to an image. Each column is the set of equations (in the “Step 8” column) evaluated at a specific k value, multiplied by the corresponding length, and normalized to the brightest band.<br />
<br />
<div style="position: relative; left: -100px;"><br />
[[Image:team-alberta-computed-lanes.png|750px|center]]<br />
</div><br />
<br />
Each lane represents the construction of an octomer at a different ligation efficiency. Each row represents the construct length. The top row represents the 8-Bytes long construct, the next row is the 7-Byte long construct and so on. At 0% efficiency, the only DNA left after construction is anchor so it is the only band seen on a gel after the assembly process. At 100% efficiency, all of the DNA has ligated perfectly and every construct is exactly 8-Bytes long. This results in only one band at the corresponding octamer length. For the intermediate efficiencies, we see a variety of band patterns. For the higher efficiencies, we see the same alternating brightness in the band pattern that was seen in our actual construction of the octamer in the lab.<br />
<br />
==Octamer Efficiency==<br />
<div id="horiz-line"></div><br />
<br />
So how efficient was our construction of the octamer in the laboratory? From the model, and the figure above, we can tell easily that the efficiency k is above 85% since our 8-Byte long construct band was the brightest band. <br />
<br />
Looking closely at our octamer gel, we can say that the band for the 8-Byte long construct is at least three times brighter than the band for the 6-Byte long construct. Since the octamer gel appears to have been over exposed (and saturated the pixels), it is hard to tell, but 3 times seems to be a good estimate. Keeping this in mind and looking at the Matlab output for finer efficiency simulations, we can see that this corresponds to a '''Byte addition efficiency of at least 94.5%'''.<br />
<br />
==The Matlab Code==<br />
<div id="horiz-line"></div><br />
<br />
<div><br />
<pre><br />
% This program will take in the lengths of each of your Bytes and output<br />
% the relative intensities of the bands expected.<br />
<br />
function [Intensities] = findIntensities(nBytes,AnchorLength,OddByteLengths,<br />
EvenByteLengths)<br />
<br />
% The anchor counts as a Byte in this code. So for octamer, nBytes == 9.<br />
<br />
x = 1 ;<br />
<br />
% Create the proportion coefficients<br />
<br />
for g=1:nBytes<br />
<br />
cT(g,1) = nchoosek(nBytes-1-floor((g)/2),floor((g-1)/2)) ;<br />
<br />
end<br />
<br />
% Create the (1-K) exponents<br />
<br />
b = 0.5:0.5:nBytes/2 ;<br />
<br />
exps1_k = floor(b)'; % The (1-k) exponents<br />
<br />
% Create the K exponents<br />
<br />
kExps = (nBytes-1:-1:0)' ; % The k exponents<br />
<br />
% Create the length coefficients<br />
<br />
cL(1:nBytes,1) = EvenByteLengths ;<br />
<br />
cL(1,1) = AnchorLength ;<br />
<br />
cL(2:2:nBytes,1) = OddByteLengths ;<br />
<br />
for h=2:length(cL)<br />
<br />
cL(h) = cL(h) + cL(h-1) ;<br />
<br />
end<br />
<br />
cL = flipud(cL)<br />
<br />
cT<br />
<br />
% Compute the intensities for each length (leaving k as a variable)<br />
<br />
syms k ;<br />
<br />
for R=1:nBytes<br />
<br />
IntenSym(R,1) = cT(R)*((1-k)^exps1_k(R))*(k^kExps(R))*cL(R) ;<br />
<br />
end<br />
<br />
IntenSym<br />
<br />
% Compute the intensities at various values of k. Also normalize<br />
% intensities to the brightest band (per lane)<br />
<br />
for k = 0 : 0.05 : 1 % Being evaluated at every 5% efficiency<br />
<br />
IntensEval(:,x)=eval(IntenSym) ; % Evaluate<br />
<br />
Intensities(:,x)=IntensEval(:,x)/max(IntensEval(:,x)) ; % Normalize<br />
<br />
x = x + 1 ;<br />
<br />
end<br />
<br />
% Now create a picture<br />
<br />
w = 0 ; p = 0 ; t = 3 ;<br />
<br />
for a=1:length(Intensities(1,:))<br />
<br />
<br />
for b = 1 : length(Intensities(:,a)) % cycles through rows in the a'th column<br />
<br />
Pic(b+w,a+p:a+p+t) = Intensities(b,a);<br />
<br />
w = w + 2 ;<br />
<br />
end<br />
<br />
w = 0 ; p = p + 1 + t ;<br />
<br />
end<br />
<br />
set(gcf, 'Position', [0 0 1300 400]) % Stretch image so bands look rectangular <br />
like a real gel<br />
<br />
colormap(gray); imagesc(Pic)<br />
<br />
title('Expected Relative Band Intensities for Variable Efficiency')<br />
<br />
xlabel('Efficiency (%)')<br />
</pre><br />
</div><br />
<br />
For the octamer built in the lab, the anchor was 56 base pairs long, the odd numbered bytes were 976 base pairs long, and the even numbered Bytes were 2083 Bytes long. To run the code for the expected bands for this octomer, the following code must be typed into the command window:<br />
<br />
<code>findIntensities(9,56,976,2083)</code><br />
<br />
{{Team:Alberta/endMainContent}}</div>Stjahnshttp://2010.igem.org/Team:Alberta/modellingTeam:Alberta/modelling2010-10-27T03:30:33Z<p>Stjahns: /* The Matlab Code */</p>
<hr />
<div>{{Team:Alberta/Head}}<br />
<br />
{{Team:Alberta/navbar|project=selected}}<br />
<br />
{{Team:Alberta/beginLeftSideBar}}<br />
{{Team:Alberta/endLeftSideBar}}<br />
{{Team:Alberta/beginMainContent}}<br />
==Goal of the Model==<br />
<div id="horiz-line"></div><br />
<p><br />
Efficiency is the key to the BioByte assembly method. For this reason, it is important to determine the efficiency by which each Byte can be added to a growing construct. Our modeling efforts have made it possible for us to determine assembly efficiency and predict future efficiencies of constructs, which have not yet been attempted.<br />
<br />
After assembling a series of Bytes, the construct can be run on a gel. Multiple bands appear. The top band contains the full construct while all of the bands below contain failed intermediate constructs of lower length. <br />
</p><br />
<br />
[[Image:Cropped_labeled_gel_Alberta.png|300px|center]]<br />
<br />
<p><br><b>Why do the band’s intensities alternate in intensity like that? How can the Byte addition efficiency be calculated from the gel?</b><br />
<br />
To answer these questions, we must consider the assembly process of a construct. If we follow through the assembly process while considering the efficiency k of Byte addition at each step, the expected relative intensities of the bands in the gel can be calculated.<br />
</p><br />
<br />
==Characterizing the Assembly Process==<br />
<div id="horiz-line"></div><br />
<br />
For this model, there are a few points to consider that characterize the assembly process:<br />
<br />
*First, Byte addition occurs with a constant efficiency k, which is the same for AB Byte additions and BA Byte additions. This means that for a given Byte addition, a fraction k of the existing construct is successful in growing in construct size, while (1-k) remains at the same construct size because of no ligation. <br />
<br />
*Secondly, AB Bytes can ligate only to BA Bytes, while BA Bytes can ligate only to AB Bytes.<br> <br />
<br />
Considering these points, we see that during the creation of a 8-Bytes long construct, there will be some intermediate sized constructs that will be visible on a gel. With some thought on the second point, we see that intermediate constructs can be made up of multiple arrangements of Bytes. <br />
<br />
For instance, during the creation of a 8-Bytes long construct, a medium sized 4-Byte long construct will be made up of the following combinations of Bytes:<br />
<div style="float:left; margin-right:30px;"><br />
*1,2,3,4<br />
*1,2,3,6<br />
*1,2,3,8<br />
*1,2,5,6<br />
</div><br />
<div style="float:left; margin-right:30px;"><br />
*1,2,5,8<br />
*1,2,7,8<br />
*1,4,5,6<br />
*1,4,5,8<br />
</div><br />
<div style="float:left; margin-right:30px;"><br />
*1,4,7,8<br />
*1,6,7,8<br />
*3,4,5,6<br />
*3,4,5,8<br />
</div><br />
<div style="float:left; margin-right:30px;"><br />
*3,4,7,8<br />
*3,6,7,8<br />
*5,6,7,8<br />
</div><br />
<div style="clear:both;"></div><br />
<br />
''Note that if all even numbered Bytes are of equal length and if all odd numbered Bytes are of equal length, then all of the aforementioned 4-Bytes long constructs are all of the same length. This means that their corresponding bands on a gel would all be superimposed into one band on the gel.'' <br />
<br />
This occurs for all the intermediate sized (failed) constructs. This concept is important for the derivation of a general set of equations describing the expected relative band intensities for each band in a post-assembly gel.<br />
<br />
==Creating the Model==<br />
<div id="horiz-line"></div><br />
Now imagine the construction process of a 8-Byte long construct. We’ll call it the octamer. It will be made up of alternating 1kbp AB Bytes and 2kbp BA Bytes. We’ll follow the construction of it while keeping track of what fraction of all of the intermediate constructs ends up at particular sizes (as a function of the ligation efficiency k). <br />
<br />
First, the anchor is added to the bead. We’ll say that 100% (k=1) of the construct is at anchor length at this point. Then, Byte 1 is added to the anchor with efficiency k. Now, k of the constructs are made up of anchor and Byte 1, while (1-k) is left as anchor. Adding Byte 2, we see that k squared of the constructs are made up of anchor, Byte 1 and Byte 2, whereas (1-k)k are left as anchor plus Byte 1, and (1-k) is still left as just anchor. It is still (1-k) because Byte 2 could not ligate to the anchor at all (because the ends are not compatible). It becomes more complicated for higher Byte additions. This process can be mapped and placed in the following table.<br><br />
<br />
[[Image:team-alberta-modelling-table-bytes.jpg]]<br />
<br />
<br>Each column represents the addition of a Byte. The “Fraction” column describes the fraction of the corresponding construct in the “Construct” column. “A” refers to anchor, and the numbers beside it refer to the Bytes attached to the anchor. For instance, A34 refers to the construct made up of the anchor, Byte 3 and Byte 4.<br />
<br />
The table can be continued indefinitely (up to Byte 8 in this example).<br />
<br />
The key thing to keep in mind when creating this table is that whenever there is a Byte addition, k constructs are successful, and (1-k) are not, and this can only happen for Bytes with the appropriate sticky ends.<br />
<br />
Now assuming that all even numbered Bytes are of equal length and that all odd numbered Bytes are of equal length, these fractions can be combined. For instance, in the “Byte 4” column, since A12, A14, and A34 are of the same length and would therefore superimpose on a gel, these fractions can be summed together resulting in the total fraction of constructs at the 2-Bytes long construct length. This can be done for each construct size in the “Byte 4” column and repeated for every other “Byte #” column. The results of doing this are shown below in the following table for up to step 8 – where the 8th Byte is added.<br><br />
<br />
[[Image:team-alberta-modelling-table.jpg]]<br />
<br />
<br>From the table, we can see that the k exponents and the (1-k) exponents are easily predictable as the steps continue. The coefficients are not, but it can be shown that the coefficients for the equations in Step n correspond to row n of a special kind of Pascal’s triangle. They follow the integer sequence of [http://www.research.att.com/~njas/sequences/A065941 A065941 from the Encyclopedia of Integer Sequences], which can be created with the following Matlab code:<br />
<br />
<pre lang="matlab"><br />
<br />
g=1; nBytes=8;<br />
for n=1:nBytes<br />
for k=1:g<br />
Triangle(n,k)=nchoosek(n-1-floor((k)/2),floor((k-1)/2));<br />
end<br />
g=g+1;<br />
end<br />
<br />
</pre><br />
<br />
where nBytes is the number of bytes the construct is made up of (including the anchor for this code). For a construct of length n, only the nth column is needed.<br />
<br />
Back to our octomer. Now that construction is complete and now that we have our handy table, we know the theoretical proportions of construct at each length. For our octomer assembly process, the brightness of each band can be predicted with the set of equations in the “Step 8” column and multiplying with the corresponding length. This was done for k values ranging from 0 all the way up to 1 in steps of 0.05. When exposing a gel, usually the brightness is adjusted so that the bands are within a visible range. In the model, the results of each equation evaluated at a given k were normalized to the largest value. This is analogous to adjusting the exposure time of your gel such that the brightest band just about saturates the pixels in the output image. The results were output to an image. Each column is the set of equations (in the “Step 8” column) evaluated at a specific k value, multiplied by the corresponding length, and normalized to the brightest band.<br />
<br />
<div style="position: relative; left: -100px;"><br />
[[Image:team-alberta-computed-lanes.png|750px|center]]<br />
</div><br />
<br />
Each lane represents the construction of an octomer at a different ligation efficiency. Each row represents the construct length. The top row represents the 8-Bytes long construct, the next row is the 7-Byte long construct and so on. At 0% efficiency, the only DNA left after construction is anchor so it is the only band seen on a gel after the assembly process. At 100% efficiency, all of the DNA has ligated perfectly and every construct is exactly 8-Bytes long. This results in only one band at the corresponding octamer length. For the intermediate efficiencies, we see a variety of band patterns. For the higher efficiencies, we see the same alternating brightness in the band pattern that was seen in our actual construction of the octamer in the lab.<br />
<br />
==Octamer Efficiency==<br />
<div id="horiz-line"></div><br />
<br />
So how efficient was our construction of the octamer in the laboratory? From the model, and the figure above, we can tell easily that the efficiency k is above 85% since our 8-Byte long construct band was the brightest band. <br />
<br />
Looking closely at our octamer gel, we can say that the band for the 8-Byte long construct is at least three times brighter than the band for the 6-Byte long construct. Since the octamer gel appears to have been over exposed (and saturated the pixels), it is hard to tell, but 3 times seems to be a good estimate. Keeping this in mind and looking at the Matlab output for finer efficiency simulations, we can see that this corresponds to a '''Byte addition efficiency of at least 94.5%'''.<br />
<br />
==The Matlab Code==<br />
<div id="horiz-line"></div><br />
<br />
<div><br />
<pre><br />
% This program will take in the lengths of each of your Bytes and output<br />
% the relative intensities of the bands expected.<br />
<br />
function [Intensities] = findIntensities(nBytes,AnchorLength,OddByteLengths,<br />
EvenByteLengths)<br />
<br />
% The anchor counts as a Byte in this code. So for octamer, nBytes == 9.<br />
<br />
x = 1 ;<br />
<br />
% Create the proportion coefficients<br />
<br />
for g=1:nBytes<br />
<br />
cT(g,1) = nchoosek(nBytes-1-floor((g)/2),floor((g-1)/2)) ;<br />
<br />
end<br />
<br />
% Create the (1-K) exponents<br />
<br />
b = 0.5:0.5:nBytes/2 ;<br />
<br />
exps1_k = floor(b)'; % The (1-k) exponents<br />
<br />
% Create the K exponents<br />
<br />
kExps = (nBytes-1:-1:0)' ; % The k exponents<br />
<br />
% Create the length coefficients<br />
<br />
cL(1:nBytes,1) = EvenByteLengths ;<br />
<br />
cL(1,1) = AnchorLength ;<br />
<br />
cL(2:2:nBytes,1) = OddByteLengths ;<br />
<br />
for h=2:length(cL)<br />
<br />
cL(h) = cL(h) + cL(h-1) ;<br />
<br />
end<br />
<br />
cL = flipud(cL)<br />
<br />
cT<br />
<br />
% Compute the intensities for each length (leaving k as a variable)<br />
<br />
syms k ;<br />
<br />
for R=1:nBytes<br />
<br />
IntenSym(R,1) = cT(R)*((1-k)^exps1_k(R))*(k^kExps(R))*cL(R) ;<br />
<br />
end<br />
<br />
IntenSym<br />
<br />
% Compute the intensities at various values of k. Also normalize<br />
% intensities to the brightest band (per lane)<br />
<br />
for k = 0 : 0.05 : 1 % Being evaluated at every 5% efficiency<br />
<br />
IntensEval(:,x)=eval(IntenSym) ; % Evaluate<br />
<br />
Intensities(:,x)=IntensEval(:,x)/max(IntensEval(:,x)) ; % Normalize<br />
<br />
x = x + 1 ;<br />
<br />
end<br />
<br />
% Now create a picture<br />
<br />
w = 0 ; p = 0 ; t = 3 ;<br />
<br />
for a=1:length(Intensities(1,:))<br />
<br />
<br />
for b = 1 : length(Intensities(:,a)) % cycles through rows in the a'th column<br />
<br />
Pic(b+w,a+p:a+p+t) = Intensities(b,a);<br />
<br />
w = w + 2 ;<br />
<br />
end<br />
<br />
w = 0 ; p = p + 1 + t ;<br />
<br />
end<br />
<br />
set(gcf, 'Position', [0 0 1300 400]) % Stretch image so bands look rectangular <br />
like a real gel<br />
<br />
colormap(gray); imagesc(Pic)<br />
<br />
title('Expected Relative Band Intensities for Variable Efficiency')<br />
<br />
xlabel('Efficiency (%)')<br />
</pre><br />
</div><br />
<br />
For the octamer built in the lab, the anchor was 56 base pairs long, the odd numbered bytes were 976 base pairs long, and the even numbered Bytes were 2083 Bytes long. To run the code for the expected bands for this octomer, the following code must be typed into the command window:<br />
<br />
<code>findIntensities(9,56,976,2083)</code><br />
<br />
{{Team:Alberta/endMainContent}}</div>Stjahnshttp://2010.igem.org/Team:Alberta/modellingTeam:Alberta/modelling2010-10-27T03:30:19Z<p>Stjahns: /* The Matlab Code */</p>
<hr />
<div>{{Team:Alberta/Head}}<br />
<br />
{{Team:Alberta/navbar|project=selected}}<br />
<br />
{{Team:Alberta/beginLeftSideBar}}<br />
{{Team:Alberta/endLeftSideBar}}<br />
{{Team:Alberta/beginMainContent}}<br />
==Goal of the Model==<br />
<div id="horiz-line"></div><br />
<p><br />
Efficiency is the key to the BioByte assembly method. For this reason, it is important to determine the efficiency by which each Byte can be added to a growing construct. Our modeling efforts have made it possible for us to determine assembly efficiency and predict future efficiencies of constructs, which have not yet been attempted.<br />
<br />
After assembling a series of Bytes, the construct can be run on a gel. Multiple bands appear. The top band contains the full construct while all of the bands below contain failed intermediate constructs of lower length. <br />
</p><br />
<br />
[[Image:Cropped_labeled_gel_Alberta.png|300px|center]]<br />
<br />
<p><br><b>Why do the band’s intensities alternate in intensity like that? How can the Byte addition efficiency be calculated from the gel?</b><br />
<br />
To answer these questions, we must consider the assembly process of a construct. If we follow through the assembly process while considering the efficiency k of Byte addition at each step, the expected relative intensities of the bands in the gel can be calculated.<br />
</p><br />
<br />
==Characterizing the Assembly Process==<br />
<div id="horiz-line"></div><br />
<br />
For this model, there are a few points to consider that characterize the assembly process:<br />
<br />
*First, Byte addition occurs with a constant efficiency k, which is the same for AB Byte additions and BA Byte additions. This means that for a given Byte addition, a fraction k of the existing construct is successful in growing in construct size, while (1-k) remains at the same construct size because of no ligation. <br />
<br />
*Secondly, AB Bytes can ligate only to BA Bytes, while BA Bytes can ligate only to AB Bytes.<br> <br />
<br />
Considering these points, we see that during the creation of a 8-Bytes long construct, there will be some intermediate sized constructs that will be visible on a gel. With some thought on the second point, we see that intermediate constructs can be made up of multiple arrangements of Bytes. <br />
<br />
For instance, during the creation of a 8-Bytes long construct, a medium sized 4-Byte long construct will be made up of the following combinations of Bytes:<br />
<div style="float:left; margin-right:30px;"><br />
*1,2,3,4<br />
*1,2,3,6<br />
*1,2,3,8<br />
*1,2,5,6<br />
</div><br />
<div style="float:left; margin-right:30px;"><br />
*1,2,5,8<br />
*1,2,7,8<br />
*1,4,5,6<br />
*1,4,5,8<br />
</div><br />
<div style="float:left; margin-right:30px;"><br />
*1,4,7,8<br />
*1,6,7,8<br />
*3,4,5,6<br />
*3,4,5,8<br />
</div><br />
<div style="float:left; margin-right:30px;"><br />
*3,4,7,8<br />
*3,6,7,8<br />
*5,6,7,8<br />
</div><br />
<div style="clear:both;"></div><br />
<br />
''Note that if all even numbered Bytes are of equal length and if all odd numbered Bytes are of equal length, then all of the aforementioned 4-Bytes long constructs are all of the same length. This means that their corresponding bands on a gel would all be superimposed into one band on the gel.'' <br />
<br />
This occurs for all the intermediate sized (failed) constructs. This concept is important for the derivation of a general set of equations describing the expected relative band intensities for each band in a post-assembly gel.<br />
<br />
==Creating the Model==<br />
<div id="horiz-line"></div><br />
Now imagine the construction process of a 8-Byte long construct. We’ll call it the octamer. It will be made up of alternating 1kbp AB Bytes and 2kbp BA Bytes. We’ll follow the construction of it while keeping track of what fraction of all of the intermediate constructs ends up at particular sizes (as a function of the ligation efficiency k). <br />
<br />
First, the anchor is added to the bead. We’ll say that 100% (k=1) of the construct is at anchor length at this point. Then, Byte 1 is added to the anchor with efficiency k. Now, k of the constructs are made up of anchor and Byte 1, while (1-k) is left as anchor. Adding Byte 2, we see that k squared of the constructs are made up of anchor, Byte 1 and Byte 2, whereas (1-k)k are left as anchor plus Byte 1, and (1-k) is still left as just anchor. It is still (1-k) because Byte 2 could not ligate to the anchor at all (because the ends are not compatible). It becomes more complicated for higher Byte additions. This process can be mapped and placed in the following table.<br><br />
<br />
[[Image:team-alberta-modelling-table-bytes.jpg]]<br />
<br />
<br>Each column represents the addition of a Byte. The “Fraction” column describes the fraction of the corresponding construct in the “Construct” column. “A” refers to anchor, and the numbers beside it refer to the Bytes attached to the anchor. For instance, A34 refers to the construct made up of the anchor, Byte 3 and Byte 4.<br />
<br />
The table can be continued indefinitely (up to Byte 8 in this example).<br />
<br />
The key thing to keep in mind when creating this table is that whenever there is a Byte addition, k constructs are successful, and (1-k) are not, and this can only happen for Bytes with the appropriate sticky ends.<br />
<br />
Now assuming that all even numbered Bytes are of equal length and that all odd numbered Bytes are of equal length, these fractions can be combined. For instance, in the “Byte 4” column, since A12, A14, and A34 are of the same length and would therefore superimpose on a gel, these fractions can be summed together resulting in the total fraction of constructs at the 2-Bytes long construct length. This can be done for each construct size in the “Byte 4” column and repeated for every other “Byte #” column. The results of doing this are shown below in the following table for up to step 8 – where the 8th Byte is added.<br><br />
<br />
[[Image:team-alberta-modelling-table.jpg]]<br />
<br />
<br>From the table, we can see that the k exponents and the (1-k) exponents are easily predictable as the steps continue. The coefficients are not, but it can be shown that the coefficients for the equations in Step n correspond to row n of a special kind of Pascal’s triangle. They follow the integer sequence of [http://www.research.att.com/~njas/sequences/A065941 A065941 from the Encyclopedia of Integer Sequences], which can be created with the following Matlab code:<br />
<br />
<pre lang="matlab"><br />
<br />
g=1; nBytes=8;<br />
for n=1:nBytes<br />
for k=1:g<br />
Triangle(n,k)=nchoosek(n-1-floor((k)/2),floor((k-1)/2));<br />
end<br />
g=g+1;<br />
end<br />
<br />
</pre><br />
<br />
where nBytes is the number of bytes the construct is made up of (including the anchor for this code). For a construct of length n, only the nth column is needed.<br />
<br />
Back to our octomer. Now that construction is complete and now that we have our handy table, we know the theoretical proportions of construct at each length. For our octomer assembly process, the brightness of each band can be predicted with the set of equations in the “Step 8” column and multiplying with the corresponding length. This was done for k values ranging from 0 all the way up to 1 in steps of 0.05. When exposing a gel, usually the brightness is adjusted so that the bands are within a visible range. In the model, the results of each equation evaluated at a given k were normalized to the largest value. This is analogous to adjusting the exposure time of your gel such that the brightest band just about saturates the pixels in the output image. The results were output to an image. Each column is the set of equations (in the “Step 8” column) evaluated at a specific k value, multiplied by the corresponding length, and normalized to the brightest band.<br />
<br />
<div style="position: relative; left: -100px;"><br />
[[Image:team-alberta-computed-lanes.png|750px|center]]<br />
</div><br />
<br />
Each lane represents the construction of an octomer at a different ligation efficiency. Each row represents the construct length. The top row represents the 8-Bytes long construct, the next row is the 7-Byte long construct and so on. At 0% efficiency, the only DNA left after construction is anchor so it is the only band seen on a gel after the assembly process. At 100% efficiency, all of the DNA has ligated perfectly and every construct is exactly 8-Bytes long. This results in only one band at the corresponding octamer length. For the intermediate efficiencies, we see a variety of band patterns. For the higher efficiencies, we see the same alternating brightness in the band pattern that was seen in our actual construction of the octamer in the lab.<br />
<br />
==Octamer Efficiency==<br />
<div id="horiz-line"></div><br />
<br />
So how efficient was our construction of the octamer in the laboratory? From the model, and the figure above, we can tell easily that the efficiency k is above 85% since our 8-Byte long construct band was the brightest band. <br />
<br />
Looking closely at our octamer gel, we can say that the band for the 8-Byte long construct is at least three times brighter than the band for the 6-Byte long construct. Since the octamer gel appears to have been over exposed (and saturated the pixels), it is hard to tell, but 3 times seems to be a good estimate. Keeping this in mind and looking at the Matlab output for finer efficiency simulations, we can see that this corresponds to a '''Byte addition efficiency of at least 94.5%'''.<br />
<br />
==The Matlab Code==<br />
<div id="horiz-line"></div><br />
<br />
<div><br />
<pre style="width:550px;"><br />
% This program will take in the lengths of each of your Bytes and output<br />
% the relative intensities of the bands expected.<br />
<br />
function [Intensities] = findIntensities(nBytes,AnchorLength,OddByteLengths,<br />
EvenByteLengths)<br />
<br />
% The anchor counts as a Byte in this code. So for octamer, nBytes == 9.<br />
<br />
x = 1 ;<br />
<br />
% Create the proportion coefficients<br />
<br />
for g=1:nBytes<br />
<br />
cT(g,1) = nchoosek(nBytes-1-floor((g)/2),floor((g-1)/2)) ;<br />
<br />
end<br />
<br />
% Create the (1-K) exponents<br />
<br />
b = 0.5:0.5:nBytes/2 ;<br />
<br />
exps1_k = floor(b)'; % The (1-k) exponents<br />
<br />
% Create the K exponents<br />
<br />
kExps = (nBytes-1:-1:0)' ; % The k exponents<br />
<br />
% Create the length coefficients<br />
<br />
cL(1:nBytes,1) = EvenByteLengths ;<br />
<br />
cL(1,1) = AnchorLength ;<br />
<br />
cL(2:2:nBytes,1) = OddByteLengths ;<br />
<br />
for h=2:length(cL)<br />
<br />
cL(h) = cL(h) + cL(h-1) ;<br />
<br />
end<br />
<br />
cL = flipud(cL)<br />
<br />
cT<br />
<br />
% Compute the intensities for each length (leaving k as a variable)<br />
<br />
syms k ;<br />
<br />
for R=1:nBytes<br />
<br />
IntenSym(R,1) = cT(R)*((1-k)^exps1_k(R))*(k^kExps(R))*cL(R) ;<br />
<br />
end<br />
<br />
IntenSym<br />
<br />
% Compute the intensities at various values of k. Also normalize<br />
% intensities to the brightest band (per lane)<br />
<br />
for k = 0 : 0.05 : 1 % Being evaluated at every 5% efficiency<br />
<br />
IntensEval(:,x)=eval(IntenSym) ; % Evaluate<br />
<br />
Intensities(:,x)=IntensEval(:,x)/max(IntensEval(:,x)) ; % Normalize<br />
<br />
x = x + 1 ;<br />
<br />
end<br />
<br />
% Now create a picture<br />
<br />
w = 0 ; p = 0 ; t = 3 ;<br />
<br />
for a=1:length(Intensities(1,:))<br />
<br />
<br />
for b = 1 : length(Intensities(:,a)) % cycles through rows in the a'th column<br />
<br />
Pic(b+w,a+p:a+p+t) = Intensities(b,a);<br />
<br />
w = w + 2 ;<br />
<br />
end<br />
<br />
w = 0 ; p = p + 1 + t ;<br />
<br />
end<br />
<br />
set(gcf, 'Position', [0 0 1300 400]) % Stretch image so bands look rectangular <br />
like a real gel<br />
<br />
colormap(gray); imagesc(Pic)<br />
<br />
title('Expected Relative Band Intensities for Variable Efficiency')<br />
<br />
xlabel('Efficiency (%)')<br />
</pre><br />
</div><br />
<br />
For the octamer built in the lab, the anchor was 56 base pairs long, the odd numbered bytes were 976 base pairs long, and the even numbered Bytes were 2083 Bytes long. To run the code for the expected bands for this octomer, the following code must be typed into the command window:<br />
<br />
<code>findIntensities(9,56,976,2083)</code><br />
<br />
{{Team:Alberta/endMainContent}}</div>Stjahnshttp://2010.igem.org/Team:Alberta/modellingTeam:Alberta/modelling2010-10-27T03:30:05Z<p>Stjahns: /* The Matlab Code */</p>
<hr />
<div>{{Team:Alberta/Head}}<br />
<br />
{{Team:Alberta/navbar|project=selected}}<br />
<br />
{{Team:Alberta/beginLeftSideBar}}<br />
{{Team:Alberta/endLeftSideBar}}<br />
{{Team:Alberta/beginMainContent}}<br />
==Goal of the Model==<br />
<div id="horiz-line"></div><br />
<p><br />
Efficiency is the key to the BioByte assembly method. For this reason, it is important to determine the efficiency by which each Byte can be added to a growing construct. Our modeling efforts have made it possible for us to determine assembly efficiency and predict future efficiencies of constructs, which have not yet been attempted.<br />
<br />
After assembling a series of Bytes, the construct can be run on a gel. Multiple bands appear. The top band contains the full construct while all of the bands below contain failed intermediate constructs of lower length. <br />
</p><br />
<br />
[[Image:Cropped_labeled_gel_Alberta.png|300px|center]]<br />
<br />
<p><br><b>Why do the band’s intensities alternate in intensity like that? How can the Byte addition efficiency be calculated from the gel?</b><br />
<br />
To answer these questions, we must consider the assembly process of a construct. If we follow through the assembly process while considering the efficiency k of Byte addition at each step, the expected relative intensities of the bands in the gel can be calculated.<br />
</p><br />
<br />
==Characterizing the Assembly Process==<br />
<div id="horiz-line"></div><br />
<br />
For this model, there are a few points to consider that characterize the assembly process:<br />
<br />
*First, Byte addition occurs with a constant efficiency k, which is the same for AB Byte additions and BA Byte additions. This means that for a given Byte addition, a fraction k of the existing construct is successful in growing in construct size, while (1-k) remains at the same construct size because of no ligation. <br />
<br />
*Secondly, AB Bytes can ligate only to BA Bytes, while BA Bytes can ligate only to AB Bytes.<br> <br />
<br />
Considering these points, we see that during the creation of a 8-Bytes long construct, there will be some intermediate sized constructs that will be visible on a gel. With some thought on the second point, we see that intermediate constructs can be made up of multiple arrangements of Bytes. <br />
<br />
For instance, during the creation of a 8-Bytes long construct, a medium sized 4-Byte long construct will be made up of the following combinations of Bytes:<br />
<div style="float:left; margin-right:30px;"><br />
*1,2,3,4<br />
*1,2,3,6<br />
*1,2,3,8<br />
*1,2,5,6<br />
</div><br />
<div style="float:left; margin-right:30px;"><br />
*1,2,5,8<br />
*1,2,7,8<br />
*1,4,5,6<br />
*1,4,5,8<br />
</div><br />
<div style="float:left; margin-right:30px;"><br />
*1,4,7,8<br />
*1,6,7,8<br />
*3,4,5,6<br />
*3,4,5,8<br />
</div><br />
<div style="float:left; margin-right:30px;"><br />
*3,4,7,8<br />
*3,6,7,8<br />
*5,6,7,8<br />
</div><br />
<div style="clear:both;"></div><br />
<br />
''Note that if all even numbered Bytes are of equal length and if all odd numbered Bytes are of equal length, then all of the aforementioned 4-Bytes long constructs are all of the same length. This means that their corresponding bands on a gel would all be superimposed into one band on the gel.'' <br />
<br />
This occurs for all the intermediate sized (failed) constructs. This concept is important for the derivation of a general set of equations describing the expected relative band intensities for each band in a post-assembly gel.<br />
<br />
==Creating the Model==<br />
<div id="horiz-line"></div><br />
Now imagine the construction process of a 8-Byte long construct. We’ll call it the octamer. It will be made up of alternating 1kbp AB Bytes and 2kbp BA Bytes. We’ll follow the construction of it while keeping track of what fraction of all of the intermediate constructs ends up at particular sizes (as a function of the ligation efficiency k). <br />
<br />
First, the anchor is added to the bead. We’ll say that 100% (k=1) of the construct is at anchor length at this point. Then, Byte 1 is added to the anchor with efficiency k. Now, k of the constructs are made up of anchor and Byte 1, while (1-k) is left as anchor. Adding Byte 2, we see that k squared of the constructs are made up of anchor, Byte 1 and Byte 2, whereas (1-k)k are left as anchor plus Byte 1, and (1-k) is still left as just anchor. It is still (1-k) because Byte 2 could not ligate to the anchor at all (because the ends are not compatible). It becomes more complicated for higher Byte additions. This process can be mapped and placed in the following table.<br><br />
<br />
[[Image:team-alberta-modelling-table-bytes.jpg]]<br />
<br />
<br>Each column represents the addition of a Byte. The “Fraction” column describes the fraction of the corresponding construct in the “Construct” column. “A” refers to anchor, and the numbers beside it refer to the Bytes attached to the anchor. For instance, A34 refers to the construct made up of the anchor, Byte 3 and Byte 4.<br />
<br />
The table can be continued indefinitely (up to Byte 8 in this example).<br />
<br />
The key thing to keep in mind when creating this table is that whenever there is a Byte addition, k constructs are successful, and (1-k) are not, and this can only happen for Bytes with the appropriate sticky ends.<br />
<br />
Now assuming that all even numbered Bytes are of equal length and that all odd numbered Bytes are of equal length, these fractions can be combined. For instance, in the “Byte 4” column, since A12, A14, and A34 are of the same length and would therefore superimpose on a gel, these fractions can be summed together resulting in the total fraction of constructs at the 2-Bytes long construct length. This can be done for each construct size in the “Byte 4” column and repeated for every other “Byte #” column. The results of doing this are shown below in the following table for up to step 8 – where the 8th Byte is added.<br><br />
<br />
[[Image:team-alberta-modelling-table.jpg]]<br />
<br />
<br>From the table, we can see that the k exponents and the (1-k) exponents are easily predictable as the steps continue. The coefficients are not, but it can be shown that the coefficients for the equations in Step n correspond to row n of a special kind of Pascal’s triangle. They follow the integer sequence of [http://www.research.att.com/~njas/sequences/A065941 A065941 from the Encyclopedia of Integer Sequences], which can be created with the following Matlab code:<br />
<br />
<pre lang="matlab"><br />
<br />
g=1; nBytes=8;<br />
for n=1:nBytes<br />
for k=1:g<br />
Triangle(n,k)=nchoosek(n-1-floor((k)/2),floor((k-1)/2));<br />
end<br />
g=g+1;<br />
end<br />
<br />
</pre><br />
<br />
where nBytes is the number of bytes the construct is made up of (including the anchor for this code). For a construct of length n, only the nth column is needed.<br />
<br />
Back to our octomer. Now that construction is complete and now that we have our handy table, we know the theoretical proportions of construct at each length. For our octomer assembly process, the brightness of each band can be predicted with the set of equations in the “Step 8” column and multiplying with the corresponding length. This was done for k values ranging from 0 all the way up to 1 in steps of 0.05. When exposing a gel, usually the brightness is adjusted so that the bands are within a visible range. In the model, the results of each equation evaluated at a given k were normalized to the largest value. This is analogous to adjusting the exposure time of your gel such that the brightest band just about saturates the pixels in the output image. The results were output to an image. Each column is the set of equations (in the “Step 8” column) evaluated at a specific k value, multiplied by the corresponding length, and normalized to the brightest band.<br />
<br />
<div style="position: relative; left: -100px;"><br />
[[Image:team-alberta-computed-lanes.png|750px|center]]<br />
</div><br />
<br />
Each lane represents the construction of an octomer at a different ligation efficiency. Each row represents the construct length. The top row represents the 8-Bytes long construct, the next row is the 7-Byte long construct and so on. At 0% efficiency, the only DNA left after construction is anchor so it is the only band seen on a gel after the assembly process. At 100% efficiency, all of the DNA has ligated perfectly and every construct is exactly 8-Bytes long. This results in only one band at the corresponding octamer length. For the intermediate efficiencies, we see a variety of band patterns. For the higher efficiencies, we see the same alternating brightness in the band pattern that was seen in our actual construction of the octamer in the lab.<br />
<br />
==Octamer Efficiency==<br />
<div id="horiz-line"></div><br />
<br />
So how efficient was our construction of the octamer in the laboratory? From the model, and the figure above, we can tell easily that the efficiency k is above 85% since our 8-Byte long construct band was the brightest band. <br />
<br />
Looking closely at our octamer gel, we can say that the band for the 8-Byte long construct is at least three times brighter than the band for the 6-Byte long construct. Since the octamer gel appears to have been over exposed (and saturated the pixels), it is hard to tell, but 3 times seems to be a good estimate. Keeping this in mind and looking at the Matlab output for finer efficiency simulations, we can see that this corresponds to a '''Byte addition efficiency of at least 94.5%'''.<br />
<br />
==The Matlab Code==<br />
<div id="horiz-line"></div><br />
<br />
<div><br />
<pre style="width:600px;"><br />
% This program will take in the lengths of each of your Bytes and output<br />
% the relative intensities of the bands expected.<br />
<br />
function [Intensities] = findIntensities(nBytes,AnchorLength,OddByteLengths,<br />
EvenByteLengths)<br />
<br />
% The anchor counts as a Byte in this code. So for octamer, nBytes == 9.<br />
<br />
x = 1 ;<br />
<br />
% Create the proportion coefficients<br />
<br />
for g=1:nBytes<br />
<br />
cT(g,1) = nchoosek(nBytes-1-floor((g)/2),floor((g-1)/2)) ;<br />
<br />
end<br />
<br />
% Create the (1-K) exponents<br />
<br />
b = 0.5:0.5:nBytes/2 ;<br />
<br />
exps1_k = floor(b)'; % The (1-k) exponents<br />
<br />
% Create the K exponents<br />
<br />
kExps = (nBytes-1:-1:0)' ; % The k exponents<br />
<br />
% Create the length coefficients<br />
<br />
cL(1:nBytes,1) = EvenByteLengths ;<br />
<br />
cL(1,1) = AnchorLength ;<br />
<br />
cL(2:2:nBytes,1) = OddByteLengths ;<br />
<br />
for h=2:length(cL)<br />
<br />
cL(h) = cL(h) + cL(h-1) ;<br />
<br />
end<br />
<br />
cL = flipud(cL)<br />
<br />
cT<br />
<br />
% Compute the intensities for each length (leaving k as a variable)<br />
<br />
syms k ;<br />
<br />
for R=1:nBytes<br />
<br />
IntenSym(R,1) = cT(R)*((1-k)^exps1_k(R))*(k^kExps(R))*cL(R) ;<br />
<br />
end<br />
<br />
IntenSym<br />
<br />
% Compute the intensities at various values of k. Also normalize<br />
% intensities to the brightest band (per lane)<br />
<br />
for k = 0 : 0.05 : 1 % Being evaluated at every 5% efficiency<br />
<br />
IntensEval(:,x)=eval(IntenSym) ; % Evaluate<br />
<br />
Intensities(:,x)=IntensEval(:,x)/max(IntensEval(:,x)) ; % Normalize<br />
<br />
x = x + 1 ;<br />
<br />
end<br />
<br />
% Now create a picture<br />
<br />
w = 0 ; p = 0 ; t = 3 ;<br />
<br />
for a=1:length(Intensities(1,:))<br />
<br />
<br />
for b = 1 : length(Intensities(:,a)) % cycles through rows in the a'th column<br />
<br />
Pic(b+w,a+p:a+p+t) = Intensities(b,a);<br />
<br />
w = w + 2 ;<br />
<br />
end<br />
<br />
w = 0 ; p = p + 1 + t ;<br />
<br />
end<br />
<br />
set(gcf, 'Position', [0 0 1300 400]) % Stretch image so bands look rectangular <br />
like a real gel<br />
<br />
colormap(gray); imagesc(Pic)<br />
<br />
title('Expected Relative Band Intensities for Variable Efficiency')<br />
<br />
xlabel('Efficiency (%)')<br />
</pre><br />
</div><br />
<br />
For the octamer built in the lab, the anchor was 56 base pairs long, the odd numbered bytes were 976 base pairs long, and the even numbered Bytes were 2083 Bytes long. To run the code for the expected bands for this octomer, the following code must be typed into the command window:<br />
<br />
<code>findIntensities(9,56,976,2083)</code><br />
<br />
{{Team:Alberta/endMainContent}}</div>Stjahnshttp://2010.igem.org/Team:Alberta/modellingTeam:Alberta/modelling2010-10-27T03:29:14Z<p>Stjahns: /* The Matlab Code */</p>
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==Goal of the Model==<br />
<div id="horiz-line"></div><br />
<p><br />
Efficiency is the key to the BioByte assembly method. For this reason, it is important to determine the efficiency by which each Byte can be added to a growing construct. Our modeling efforts have made it possible for us to determine assembly efficiency and predict future efficiencies of constructs, which have not yet been attempted.<br />
<br />
After assembling a series of Bytes, the construct can be run on a gel. Multiple bands appear. The top band contains the full construct while all of the bands below contain failed intermediate constructs of lower length. <br />
</p><br />
<br />
[[Image:Cropped_labeled_gel_Alberta.png|300px|center]]<br />
<br />
<p><br><b>Why do the band’s intensities alternate in intensity like that? How can the Byte addition efficiency be calculated from the gel?</b><br />
<br />
To answer these questions, we must consider the assembly process of a construct. If we follow through the assembly process while considering the efficiency k of Byte addition at each step, the expected relative intensities of the bands in the gel can be calculated.<br />
</p><br />
<br />
==Characterizing the Assembly Process==<br />
<div id="horiz-line"></div><br />
<br />
For this model, there are a few points to consider that characterize the assembly process:<br />
<br />
*First, Byte addition occurs with a constant efficiency k, which is the same for AB Byte additions and BA Byte additions. This means that for a given Byte addition, a fraction k of the existing construct is successful in growing in construct size, while (1-k) remains at the same construct size because of no ligation. <br />
<br />
*Secondly, AB Bytes can ligate only to BA Bytes, while BA Bytes can ligate only to AB Bytes.<br> <br />
<br />
Considering these points, we see that during the creation of a 8-Bytes long construct, there will be some intermediate sized constructs that will be visible on a gel. With some thought on the second point, we see that intermediate constructs can be made up of multiple arrangements of Bytes. <br />
<br />
For instance, during the creation of a 8-Bytes long construct, a medium sized 4-Byte long construct will be made up of the following combinations of Bytes:<br />
<div style="float:left; margin-right:30px;"><br />
*1,2,3,4<br />
*1,2,3,6<br />
*1,2,3,8<br />
*1,2,5,6<br />
</div><br />
<div style="float:left; margin-right:30px;"><br />
*1,2,5,8<br />
*1,2,7,8<br />
*1,4,5,6<br />
*1,4,5,8<br />
</div><br />
<div style="float:left; margin-right:30px;"><br />
*1,4,7,8<br />
*1,6,7,8<br />
*3,4,5,6<br />
*3,4,5,8<br />
</div><br />
<div style="float:left; margin-right:30px;"><br />
*3,4,7,8<br />
*3,6,7,8<br />
*5,6,7,8<br />
</div><br />
<div style="clear:both;"></div><br />
<br />
''Note that if all even numbered Bytes are of equal length and if all odd numbered Bytes are of equal length, then all of the aforementioned 4-Bytes long constructs are all of the same length. This means that their corresponding bands on a gel would all be superimposed into one band on the gel.'' <br />
<br />
This occurs for all the intermediate sized (failed) constructs. This concept is important for the derivation of a general set of equations describing the expected relative band intensities for each band in a post-assembly gel.<br />
<br />
==Creating the Model==<br />
<div id="horiz-line"></div><br />
Now imagine the construction process of a 8-Byte long construct. We’ll call it the octamer. It will be made up of alternating 1kbp AB Bytes and 2kbp BA Bytes. We’ll follow the construction of it while keeping track of what fraction of all of the intermediate constructs ends up at particular sizes (as a function of the ligation efficiency k). <br />
<br />
First, the anchor is added to the bead. We’ll say that 100% (k=1) of the construct is at anchor length at this point. Then, Byte 1 is added to the anchor with efficiency k. Now, k of the constructs are made up of anchor and Byte 1, while (1-k) is left as anchor. Adding Byte 2, we see that k squared of the constructs are made up of anchor, Byte 1 and Byte 2, whereas (1-k)k are left as anchor plus Byte 1, and (1-k) is still left as just anchor. It is still (1-k) because Byte 2 could not ligate to the anchor at all (because the ends are not compatible). It becomes more complicated for higher Byte additions. This process can be mapped and placed in the following table.<br><br />
<br />
[[Image:team-alberta-modelling-table-bytes.jpg]]<br />
<br />
<br>Each column represents the addition of a Byte. The “Fraction” column describes the fraction of the corresponding construct in the “Construct” column. “A” refers to anchor, and the numbers beside it refer to the Bytes attached to the anchor. For instance, A34 refers to the construct made up of the anchor, Byte 3 and Byte 4.<br />
<br />
The table can be continued indefinitely (up to Byte 8 in this example).<br />
<br />
The key thing to keep in mind when creating this table is that whenever there is a Byte addition, k constructs are successful, and (1-k) are not, and this can only happen for Bytes with the appropriate sticky ends.<br />
<br />
Now assuming that all even numbered Bytes are of equal length and that all odd numbered Bytes are of equal length, these fractions can be combined. For instance, in the “Byte 4” column, since A12, A14, and A34 are of the same length and would therefore superimpose on a gel, these fractions can be summed together resulting in the total fraction of constructs at the 2-Bytes long construct length. This can be done for each construct size in the “Byte 4” column and repeated for every other “Byte #” column. The results of doing this are shown below in the following table for up to step 8 – where the 8th Byte is added.<br><br />
<br />
[[Image:team-alberta-modelling-table.jpg]]<br />
<br />
<br>From the table, we can see that the k exponents and the (1-k) exponents are easily predictable as the steps continue. The coefficients are not, but it can be shown that the coefficients for the equations in Step n correspond to row n of a special kind of Pascal’s triangle. They follow the integer sequence of [http://www.research.att.com/~njas/sequences/A065941 A065941 from the Encyclopedia of Integer Sequences], which can be created with the following Matlab code:<br />
<br />
<pre lang="matlab"><br />
<br />
g=1; nBytes=8;<br />
for n=1:nBytes<br />
for k=1:g<br />
Triangle(n,k)=nchoosek(n-1-floor((k)/2),floor((k-1)/2));<br />
end<br />
g=g+1;<br />
end<br />
<br />
</pre><br />
<br />
where nBytes is the number of bytes the construct is made up of (including the anchor for this code). For a construct of length n, only the nth column is needed.<br />
<br />
Back to our octomer. Now that construction is complete and now that we have our handy table, we know the theoretical proportions of construct at each length. For our octomer assembly process, the brightness of each band can be predicted with the set of equations in the “Step 8” column and multiplying with the corresponding length. This was done for k values ranging from 0 all the way up to 1 in steps of 0.05. When exposing a gel, usually the brightness is adjusted so that the bands are within a visible range. In the model, the results of each equation evaluated at a given k were normalized to the largest value. This is analogous to adjusting the exposure time of your gel such that the brightest band just about saturates the pixels in the output image. The results were output to an image. Each column is the set of equations (in the “Step 8” column) evaluated at a specific k value, multiplied by the corresponding length, and normalized to the brightest band.<br />
<br />
<div style="position: relative; left: -100px;"><br />
[[Image:team-alberta-computed-lanes.png|750px|center]]<br />
</div><br />
<br />
Each lane represents the construction of an octomer at a different ligation efficiency. Each row represents the construct length. The top row represents the 8-Bytes long construct, the next row is the 7-Byte long construct and so on. At 0% efficiency, the only DNA left after construction is anchor so it is the only band seen on a gel after the assembly process. At 100% efficiency, all of the DNA has ligated perfectly and every construct is exactly 8-Bytes long. This results in only one band at the corresponding octamer length. For the intermediate efficiencies, we see a variety of band patterns. For the higher efficiencies, we see the same alternating brightness in the band pattern that was seen in our actual construction of the octamer in the lab.<br />
<br />
==Octamer Efficiency==<br />
<div id="horiz-line"></div><br />
<br />
So how efficient was our construction of the octamer in the laboratory? From the model, and the figure above, we can tell easily that the efficiency k is above 85% since our 8-Byte long construct band was the brightest band. <br />
<br />
Looking closely at our octamer gel, we can say that the band for the 8-Byte long construct is at least three times brighter than the band for the 6-Byte long construct. Since the octamer gel appears to have been over exposed (and saturated the pixels), it is hard to tell, but 3 times seems to be a good estimate. Keeping this in mind and looking at the Matlab output for finer efficiency simulations, we can see that this corresponds to a '''Byte addition efficiency of at least 94.5%'''.<br />
<br />
==The Matlab Code==<br />
<div id="horiz-line"></div><br />
<br />
<div><br />
<pre style="width:650px;"><br />
% This program will take in the lengths of each of your Bytes and output<br />
% the relative intensities of the bands expected.<br />
<br />
function [Intensities] = findIntensities(nBytes,AnchorLength,OddByteLengths,<br />
EvenByteLengths)<br />
<br />
% The anchor counts as a Byte in this code. So for octamer, nBytes == 9.<br />
<br />
x = 1 ;<br />
<br />
% Create the proportion coefficients<br />
<br />
for g=1:nBytes<br />
<br />
cT(g,1) = nchoosek(nBytes-1-floor((g)/2),floor((g-1)/2)) ;<br />
<br />
end<br />
<br />
% Create the (1-K) exponents<br />
<br />
b = 0.5:0.5:nBytes/2 ;<br />
<br />
exps1_k = floor(b)'; % The (1-k) exponents<br />
<br />
% Create the K exponents<br />
<br />
kExps = (nBytes-1:-1:0)' ; % The k exponents<br />
<br />
% Create the length coefficients<br />
<br />
cL(1:nBytes,1) = EvenByteLengths ;<br />
<br />
cL(1,1) = AnchorLength ;<br />
<br />
cL(2:2:nBytes,1) = OddByteLengths ;<br />
<br />
for h=2:length(cL)<br />
<br />
cL(h) = cL(h) + cL(h-1) ;<br />
<br />
end<br />
<br />
cL = flipud(cL)<br />
<br />
cT<br />
<br />
% Compute the intensities for each length (leaving k as a variable)<br />
<br />
syms k ;<br />
<br />
for R=1:nBytes<br />
<br />
IntenSym(R,1) = cT(R)*((1-k)^exps1_k(R))*(k^kExps(R))*cL(R) ;<br />
<br />
end<br />
<br />
IntenSym<br />
<br />
% Compute the intensities at various values of k. Also normalize<br />
% intensities to the brightest band (per lane)<br />
<br />
for k = 0 : 0.05 : 1 % Being evaluated at every 5% efficiency<br />
<br />
IntensEval(:,x)=eval(IntenSym) ; % Evaluate<br />
<br />
Intensities(:,x)=IntensEval(:,x)/max(IntensEval(:,x)) ; % Normalize<br />
<br />
x = x + 1 ;<br />
<br />
end<br />
<br />
% Now create a picture<br />
<br />
w = 0 ; p = 0 ; t = 3 ;<br />
<br />
for a=1:length(Intensities(1,:))<br />
<br />
<br />
for b = 1 : length(Intensities(:,a)) % cycles through rows in the a'th column<br />
<br />
Pic(b+w,a+p:a+p+t) = Intensities(b,a);<br />
<br />
w = w + 2 ;<br />
<br />
end<br />
<br />
w = 0 ; p = p + 1 + t ;<br />
<br />
end<br />
<br />
set(gcf, 'Position', [0 0 1300 400]) % Stretch image so bands look rectangular <br />
like a real gel<br />
<br />
colormap(gray); imagesc(Pic)<br />
<br />
title('Expected Relative Band Intensities for Variable Efficiency')<br />
<br />
xlabel('Efficiency (%)')<br />
</pre><br />
</div><br />
<br />
For the octamer built in the lab, the anchor was 56 base pairs long, the odd numbered bytes were 976 base pairs long, and the even numbered Bytes were 2083 Bytes long. To run the code for the expected bands for this octomer, the following code must be typed into the command window:<br />
<br />
<code>findIntensities(9,56,976,2083)</code><br />
<br />
{{Team:Alberta/endMainContent}}</div>Stjahnshttp://2010.igem.org/Team:Alberta/biobyte2Team:Alberta/biobyte22010-10-27T03:26:42Z<p>Stjahns: /* BioBytes v.2 */</p>
<hr />
<div>{{Team:Alberta/Head}}<br />
{{Team:Alberta/navbar|project=selected}}<br />
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<br />
==Overview==<br />
<div id="horiz-line"></div><br />
<br />
BioBytes 2.0 is the heart of the GENOMIKON kit. BioBytes 2.0 is a method of creating novel plasmids through the sequential addition of functional units of DNA. It is designed to be used in a high school setting but has potential to be used in professional settings as well. The assembly method we have created has some conceptual similarities to the original BioBytes Assembly System developed from the 2009 Alberta iGEM project. However, there are some striking differences between the two systems.<br />
<br />
==Traditional Methods==<br />
<div id="horiz-line"></div><br />
The current assembly standard is the BioBrick method. While the registry of parts and the assembly standard has allowed for effective construction of plasmids in a laboratory setting, it has numerous limitations prohibiting its use in high schools. For example, common laboratory protocols such as transformation, ligation, and restriction digestion require materials and equipment not available to high schools. Not only does this require expensive reagents and equipment, it also takes days to weeks to assemble a complicated construct. An experiment of such length far surpasses the average high school student’s attention span and the time a curriculum can spend on a particular subject.<br />
<br />
<br />
[[Image:team-alberta-biobrick-tour.jpg|center|frame|Figure 1.1. Traditional BioBrick construction which takes approximately 3 days to complete the addition of one part; from the cutting of the original constructs to transformation and confirmation.]]<br />
<br />
====Comparison====<br />
<br />
The BioBytes Assembly System 2.0 has provided a solution to these issues. The GENOMIKON kit is fast allowing for assembly of a novel plasmid in an afternoon rather than over the course of several days. The kit is completely self-contained, requiring no other equipment or reagents that does not come with the kit. This eliminates the need for the expensive equipment and reagents common place in a University laboratory setting. <br />
The addition of one part to a construct takes under 10 minutes. So creating a plasmid of your desired specifications can happen in an afternoon, rather than the 3 or more days to create a plasmid through the traditional BioBrick methods.<br />
[[Image:team-alberta-building-tour.jpg|center|frame|BioByte version 2.0 construction.]] <br />
<br />
==Components of the System==<br />
<div id="horiz-line"></div><br />
<br />
The Assembly Method 2.0 is composed of three main components. An <b>anchor</b> byte attached to an iron micro bead is the beginning of a construct. Because of the magnetic nature of these beads, they can be positioned by using a simple magnet. The <b>BioBytes</b> are added to the anchor-byte one at a time in sequence. This is possible due to the alternating overhang structure of the <b>BioBytes</b>. Finally, a <b>cap</b> is added allowing for circularization of the construct. The construct is now ready to transform<br />
<br />
<br />
<br />
====Anchor Byte====<br />
<br />
The Anchor-byte begins the process of assembly. It is composed of:<br />
<br />
*a poly-A tail<br />
*a BsaI recognition site<br />
*an A or B overhang<br />
<br />
[[Image:team-alberta-anchor-tour.jpg|center|frame|The two components of the anchoring system.]] <br />
<br />
Iron micro beads purchased from New England Biolabs have covalently attached poly-T tails. The bead allows us to manipulate the DNA with magnets making washing and subsequent attachments easier.<br />
<br />
We have designed an anchor byte which begins the process of assembly. The anchor-byte is comprised of an Anchor piece ligated to the first byte of the assembly. Construction begins by ligating a selectable marker to the anchor. This first step allows for complete constructs to be selected for. As well, the incorporation of a BsaI cut site into the Anchor, before the first byte, gives versatility to the construct because the first byte and the rest of the construct can be removed from the anchor, and used as a Byte in and of itself. <br />
<br />
Once the selectable marker is ligated to the first byte, we anneal the anchor-byte to the poly-T tails on the iron micro bead. We have created anchors with both varieties of ends so that assemblies can begin with any type of byte.<br />
The results of one of our experiments is shown here. Note that the interaction between the anchor and the bead is non-covalent. The anchor along with the construct can be separated from the bead with heat. The gel shows the process of anchoring a construct. A anchor-byte construct of 1kb is allowed to anneal to the magnetic beads. This is done in excess, and the supernatant is shown in the first lane. A subsequent wash step showed the absence of DNA, indicating that DNA construct is stably bound. The construct can be melted from the scaffold at 70 degrees Celsius. The melted construct can be seen in the last lane.<br />
<br />
[[Image:Alberta_AnchorPiece.png|500px|center|frame|Figure]]<br />
<br />
The BsaI cut site found in the anchor allows for constructs to be created in parallel and then utilized as large Bytes in the assembly in the same way. <br />
<br />
====BioBytes 2.0====<br />
<br />
This year's BioByte design has a number of unique features. Each Byte has 4 base 5' overhangs on each side. These overhangs have be engineered to serve a number of purposes. The overhangs allow for ordered and sequential addition of parts to growing assemblies. <br />
[[Image:team-alberta-bytes-tour.jpg|500px|center|thumb|BioBytes come in two flavors: 'AB' and 'BA'.]]<br />
<br />
The addition of each byte to a growing assembly takes about 7 minutes.<br />
<br />
====Cap====<br />
The <b>cap</b> is analogous to the anchor. The cap finishes the construct, where the anchor starts a construct. The cap is comprised of a poly-T tail, complimentary to the poly-A tail of the anchor piece. The cap also contains a BsaI cut site which allows it's removal from the construct. The cap also comes in both applicable flavors with an A or B overhang. <br />
<br />
[[Image:team-alberta-cap-tour.jpg|center|The cap. The poly-T anneals to the poly-A of the anchor component to circularize the complete plasmid.]]<br />
<br />
When finishing a construct, the cap is added and ligated to the growing construct, in the same manner as another byte. The completed construct is the heated, to melt the anchor piece from the iron micro bead. The solution is removed from the beads and allowed to cool. The cap and anchor then have opportunity to anneal to each other. The construct is now ready for transformation without ligation.<br />
<br />
==The Assembly Process==<br />
<div id="horiz-line"></div><br />
<br />
[[Image:team-alberta-biobyteprocess-tour.jpg|center|frame|The entire construction process can be completed in an afternoon.]]<br />
<br />
Starting with an anchor, add the first piece and ligate.<br />
<br />
Then anneal the anchor-byte construct to the iron micro beads by incubating at room temperature for 30 minutes, mixing every 5 minutes. Now you can wash away the excess of the anchor-byte. This is done by putting the tube in the magnetic rack, allowing the magnet to pull all the beads with your anchor-byte attached to one side, and removing the supernatant.<br />
<br />
Before another part is added, wash the beads twice with Wash Buffer. This is done by adding wash buffer, mixing the iron micro beads into the solution, pulling the beads to the side and pulling out the supernatant. Add the next piece in an equimolar amount to the anchor-byte and ligate for 5 minutes with Quick Ligation <sup>TM</sup> Kit purchased from NEB. Ensure that the beads have been distributed into the solution during the ligation. Again remove the supernatant and wash twice before adding the next part. <br />
<br />
Then when you have added all the parts you want, add the cap in exactly the same way as any other byte except add it in 20 times molar excess. After you add the cap, remove the supernatant, and wash twice again with wash buffer. Wash the beads a third time with room temperature elution buffer.<br />
<br />
Now just heat to release the construct, add hot (75<sup>o</sup>C) elution buffer and incubate the solution at 75<sup>o</sup>C for 10 minutes. Move the beads to the side, and remove the supernatant to a second tube and put it on ice. Your construct should be in the supernatant. The cold allows the cap and the anchor to anneal and the plasmid is circularized and ready for transformation. <br />
<br />
Easy!<br />
<br />
Using this process we were able to assemble eight pieces in an afternoon!<br />
<br />
<br />
==Byte Construction==<br />
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New Biobytes are constructed with the aid of our Base Plasmids v.2. The Base Plasmids v.2 have an RFP coding cassette (j04450) flanked by BsaI cut sites that leave the appropriate overhangs to create either a AB part or a BA part. Because the BsaI restriction enzyme cuts at a site downstream of the recognition sequence, the overhang sequence can be engineered to be unique. We have designed our own overhangs that define the AB and the BA parts. To create a new part, PCR the part of interest incorporating BsaI cut sites with appropriate overhangs onto each side. Then cut the Base Plasmid v.2 and the PCR product with BsaI. Ligate it together. Again, because the overhangs are unique, the plasmid backbone can not re-ligate without an insert. The insert can only be the new part of interest, or the RFP coding cassette that was originally in the base plasmid, leading to a total of 2 possible ligation products. When transformed, the ligation products can appear red (if the original RFP cassette is reinserted) or white (if the part of interest is inserted). This provides a selection method for plasmids that have the part of interest in it. <br />
<br />
[[Image:Alberta_pAB_Plasmid.png|350px|center|frame|Figure Base Plasmid v.2. The Base plasmids can be cut leaving unique overhangs so that directional cloning of new parts can be inserted. The lack of the RFP coding cassette provides a selection method for colonies containing new parts]]<br />
<br />
Because all the parts are created in the same plasmid, mass production of parts for the kit is also a straight forward matter. Using universal primers of our own design, which start about 100 base before the BsaI cut sites. The PCR is then digested with BsaI. Starting the PCR 100 bases outside the part allows for us to check that the part is completely digested. Before parts are used in assembly, they are purified using weak anion exchange column through HPLC (high performance liquid chromatography). <br />
<br />
[[Image:Alberta_PCR.png|350px|center|frame|Figure Part Mass Production. New parts are PCRed, Digested with BsaI, then purified through an HPLC before being used in assembly]]<br />
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==BioBytes 2.0 vs. BioBytes==<br />
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For those of you that have followed the Alberta team for the last few years, there are a few similarities between original BioByte system and the new BioBytes v.2 system that we have put forward this year. However, if you look closely there are a number of profound differences between the systems. <br />
<br />
The similarities in the systems reside in the theory of alternating and complimentary ends. The AB and BA parts can only ligate to each other, and AB parts can not ligate to themselves and BA parts can not ligate to themselves. <br />
<br />
The "BioBytes Version 2.0" construction method has been shown to create (insert actual data here) plasmids from up to 8 separate parts in <br />
an afternoon's work. This is a vast improvement.<br />
<br />
<br />
<br />
<br />
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[[Image:Alberta Plate highschool.jpg|center|frame|A high school student shows off his colonies transformed with his plasmid constructed with GENOMIKON.]]<br />
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==Project Overview==<br />
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''GENOMIKON: an Educational Toolkit for Rapid Genetic Construction''<br />
<br />
Genetic manipulation using synthetic biology is a technology with unlimited potential. Unfortunately, its teaching is currently confined to universities, where students have chosen to specialize in science. Recognizing that many of the basic principles and methods are easily explained, the University of Alberta sought to expand the accessibility of synthetic biology by creating a teaching package capable of working within a high school environment, which exposes young minds to genetic technology. To construct the kit, known as GENOMIKON, we first optimized the BioBytes 2.0 assembly method created by the University of Alberta 2009 team. The experiments of the kit were then designed to be done quickly, reliably, and with very limited equipment. To make GENOMIKON useful as a classroom resource, an interactive lab manual was created to guide students through their experiments. Lastly, we looked at how best to distribute this kit into students’ hands. GENOMIKON is a major advancement for synthetic biology because it shows the next generation of students how biology can work as an engineering discipline and functional technology, even before they enter post-secondary education.<br />
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==[[Team:Alberta/biobyte2 |BioByte Theory]]==<br />
<br />
The DNA components of the GENOMIKON kit will be provided in linear pieces called BioBytes. These Bytes have 4 base 5' overhangs on both ends, which gives specificity to the Bytes that can neighbor it. BioBytes come in two flavors: 'AB Bytes' and 'BA Bytes', which are defined by the composition of the overhangs it has. The result is that AB Bytes can only be ligated to BA Bytes and vice versa. This leads to a construct alternating in AB and BA Bytes. The specificity in absolute order of a construct is given by an anchor, which restricts ligation to only one side.<br />
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==[[Team:Alberta/Kit |The GENOMIKON Kit]]==<br />
<br />
The GENOMIKON kit was designed for a high school environment. The major challenge facing the GENOMIKON kit was that high schools lack most lab equipment traditionally needed for molecular biology. Creating a sterile environment to avoid contamination was another challenge that had to be overcome. Fortunately, the BioByte 2.0 assembly method does not require centrifuges, thermocyclers or extreme accuracy with regards to volume and temperature. The only equipment a high school must supply then is a hot plate, thermometer, and a beaker. The issue of sterility is addressed by sending reagents in individual sterilized packages. The kit sends everything that a high school would need to perform the transformations using synthetic parts.<br />
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==[[Team:Alberta/Software |GENOMIKON ONLINE]]==<br />
<br />
For the GENOMIKON kit to be functional, students and teachers need access to a lab manual that can accommodate the many different experiments possible. The GENOMIKON lab manual was designed to act as a teaching resource, giving students background information for the experiments they design. GENOMIKON ONLINE was created as the lab manual complementary to the GENOMIKON kit. GENOMIKON ONLINE is found at the website, www.GENOMIKON.ca. Features include: descriptions of the different parts used to construct a plasmid, a toolkit where students can engineer their own creative expressions by dragging and dropping different parts into sequence to automatically generate a protocol to follow. Students can also do predetermined experiments outlined and collect background information by reading articles. Lastly, the teacher can coordinate the class experiments by working through the groups feature.<br />
<br />
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{{Team:Alberta/endMainContent}}</div>Stjahnshttp://2010.igem.org/Template:Team:Alberta/tourbarTemplate:Team:Alberta/tourbar2010-10-27T03:21:44Z<p>Stjahns: </p>
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