|
|
(54 intermediate revisions not shown) |
Line 86: |
Line 86: |
| padding-bottom: 10px; | | padding-bottom: 10px; |
| background-color: black; | | background-color: black; |
- | background-image: url('https://static.igem.org/mediawiki/2010/4/44/Metu-background.png'); | + | background-image: url('https://static.igem.org/mediawiki/2010/d/de/Metu-bg3.jpg'); |
| background-attachment: fixed; | | background-attachment: fixed; |
| + | background-position:center top; |
| + | background-repeat:no-repeat; |
| font: 13px Tahoma, Arial, Helvetica, sans-serif; | | font: 13px Tahoma, Arial, Helvetica, sans-serif; |
| position: absolute; | | position: absolute; |
- | top: 0;
| |
- | left: 0;
| |
| overflow: hidden; | | overflow: hidden; |
| margin: 0 auto; | | margin: 0 auto; |
Line 139: |
Line 139: |
| line-height: 1em; | | line-height: 1em; |
| color: navy; | | color: navy; |
| + | } |
| + | .content2 .text a{ |
| + | color:#A4C4EB; |
| } | | } |
| .content2 .text strong { | | .content2 .text strong { |
Line 146: |
Line 149: |
| .homepage { | | .homepage { |
| width: 900px; | | width: 900px; |
- | height: 500px; | + | height: 365px; |
- | top: 50px;
| + | |
| margin: 0 auto; | | margin: 0 auto; |
- | background: url('https://static.igem.org/mediawiki/2010/1/13/Metu-home.png') no-repeat; | + | background: url('1https://static.igem.org/mediawiki/2010/1/13/Metu-home.png') no-repeat; |
| position: relative; | | position: relative; |
- | padding: 50px 0px 50px 0; | + | } |
| + | #homecontainer{ |
| + | padding: 10px 30px 10px 20px; |
| + | width:800px; |
| + | height:300px; |
| + | position: absolute; |
| + | bottom: 40px; |
| + | left:40px; |
| + | text-align:justify; |
| + | opacity:0.85; |
| + | background-color:#000; |
| } | | } |
| #smallwrap { | | #smallwrap { |
Line 236: |
Line 248: |
| font-weight: bold; | | font-weight: bold; |
| } | | } |
| + | #sponsorlist li{float:left; text-decoration:none; margin:20px;} |
| .black { | | .black { |
| color: black; | | color: black; |
Line 298: |
Line 311: |
| z-index: 20; | | z-index: 20; |
| } | | } |
| + | #introvideo {width:480px; length:360px; margin:20px auto; margin-bottom:0;} |
| + | #home {overflow:auto;} |
| img[src*="/wiki/skins/common/images/wiki.png"] { | | img[src*="/wiki/skins/common/images/wiki.png"] { |
| width: 0; | | width: 0; |
Line 310: |
Line 325: |
| </div> | | </div> |
| <div id="home" class="item"> | | <div id="home" class="item"> |
- | <div class="homepage"> | + | <div id="introvideo"> |
| + | <embed width="480" height="360" quality="high" bgcolor="#000000" name="main" id="main" allowfullscreen="true" allowscriptaccess="always" src="http://www.dnatube.com/nvlab/player/player.swf?config=http://www.dnatube.com/nvlab/econfig.php?key=ddbdf3eff0f505975b6a" type="application/x-shockwave-flash" /></div><div class="homepage"> |
| + | <div id="homecontainer"><h3>Abstract</h3> |
| + | <p>As Synthetic Biology field is on the rise, iGEM also grows up and number of parts in parts registry increase with submission of more complex constructs each year. Our first milestone was to perform more efficient standardization on parts entry due to facing some difficulty while running our algorithms on the parts registry. We also used Software Requirements Specification, Software Design Description and Quality Plan approaches to define requirements for each part and building blocks, risks and design art elements of the designed software program.</p> |
| + | <p>Next, we have used graph theoretic modeling to visualize relations between parts and to standardize representation of the parts as much as possible. It will help us when we try to find input-output relations between either biobrick parts or constructs. By this way, our program BIOGUIDE will act as a guide for searhing biobricks and will provide alternative pathway choices to users for construction of the most reliable devices with respect to given inputs and expected outputs.</p> |
| + | </div> |
| </div> | | </div> |
| </div> | | </div> |
Line 325: |
Line 345: |
| <img alt="" src="https://static.igem.org/mediawiki/2010/b/be/Metu-team6.jpg"> | | <img alt="" src="https://static.igem.org/mediawiki/2010/b/be/Metu-team6.jpg"> |
| </div> | | </div> |
- | <p>METU Turkey Software is an interdisciplinary team of 8 students and | + | <p>METU Turkey Software is an interdisciplinary team of 7 students and |
- | 3 advisors from various backgrounds such as Molecular Biology, Bioinformatics, | + | 4 advisors from various backgrounds such as Molecular Biology, Bioinformatics, |
| Computer Engineering and Computer Education and Instructional Technology. | | Computer Engineering and Computer Education and Instructional Technology. |
| We have put our knowledge and experience in our fields together to bring | | We have put our knowledge and experience in our fields together to bring |
Line 404: |
Line 424: |
| <div class="smallbox" style="margin: 0 auto; float: none"> | | <div class="smallbox" style="margin: 0 auto; float: none"> |
| <h2 class="black">Muhammed Akif Ağca</h2> | | <h2 class="black">Muhammed Akif Ağca</h2> |
- | <img src=""> | + | <img src="https://static.igem.org/mediawiki/2010/1/10/Metu-akif2.jpg"> |
| <div class="smalltext"> | | <div class="smalltext"> |
- | <p>Content here</p> | + | <p>In bachelor he has worked on Software Development, Database Management, Instructional Technologies, and Bioinformatics. He was developing the software and leading the team. |
| + | A new page to his life is starting at 2011 after becoming a graduate of Computer Education and Instructional Technologies. He says that " If we can use technology and science efficiently we can solve too many problems in the world, but if can use. That is if we can manage those we can solve the problems and organize the world with minimum problems " which is a study field Science Technology and Management ( STM ) which is the field he will start to work in 2011 ".</p> |
| </div> | | </div> |
| </div> | | </div> |
Line 990: |
Line 1,011: |
| </div> | | </div> |
| </div> | | </div> |
- | </div> | + | </div><h3>Follow our discussion topic at <a href="http://groups.google.com.tr/group/software_MetuTurkey/topics">our googlegroups</a></h3> |
| + | |
| </div> | | </div> |
| </div> | | </div> |
Line 996: |
Line 1,018: |
| <div class="content2"> | | <div class="content2"> |
| <div class="text"> | | <div class="text"> |
- | <h2>Download</h2> | + | <h2>Download Executable and Code</h2> |
| + | <p>You can download BioGUIDE at <a href="http://sourceforge.net/projects/bioguide">http://sourceforge.net/projects/bioguide</a></p> |
| + | <p>Download & install it and feel it's power!!</p> |
| </div> | | </div> |
| </div> | | </div> |
Line 1,371: |
Line 1,395: |
| <div class="text"> | | <div class="text"> |
| <h2>Design</h2> | | <h2>Design</h2> |
| + | <a href="https://static.igem.org/mediawiki/2010/6/6a/Metu_Turkey_Software_ER3.jpg"><img src="https://static.igem.org/mediawiki/igem.org/7/71/Metu_Software_ER3.png" /></a> |
| + | |
| </div> | | </div> |
| </div> | | </div> |
Line 1,379: |
Line 1,405: |
| <div class="content2"> | | <div class="content2"> |
| <div class="text"> | | <div class="text"> |
- | <h2>Code</h2> | + | <h2>User Guide</h2> |
| + | <object width="425" height="344"><param name="movie" value="http://www.youtube.com/v/Znb1o7cr5dc?hl=en&fs=1"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/Znb1o7cr5dc?hl=en&fs=1" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="425" height="344"></embed></object><object width="425" height="344"><param name="movie" value="http://www.youtube.com/v/Fk7eJ-Ig_IQ?hl=en&fs=1"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/Fk7eJ-Ig_IQ?hl=en&fs=1" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="425" height="344"></embed></object><p>For new users whom want to interest with synthetic biology and for experienced scientists, in our program you have two options for Input Output properties ;</p> |
| + | <p>To find input-output related biobrick parts or larger constructs! If you want to provide specific chemical or physical inputs from external environment, you may choose these inputs from the list. if you want other specific inputs which will be expressed from a coding sequence, the list can provide these specified protein names.</p> |
| + | <img src="https://static.igem.org/mediawiki/2010/6/60/Metu-guide1.jpg"> |
| + | <p>Wanted features of outputs can be selected by either from list or entering individually into text boxes.</p> |
| + | <img src="https://static.igem.org/mediawiki/2010/c/c0/Metu-guide2.jpg"> |
| + | <p>Then click on the “Show Parts ” button.</p> |
| + | <img src="https://static.igem.org/mediawiki/2010/9/95/Metu-guide3.jpg"> |
| + | <p>Then the program will show you the parts have specified I/O properties</p> |
| + | <img src="https://static.igem.org/mediawiki/2010/7/7f/Metu-guide4.jpg"> |
| + | <p>To see the properties of a part just click on it.</p> |
| + | <img src="https://static.igem.org/mediawiki/2010/3/33/Metu-guide5.jpg"> |
| + | <img src="https://static.igem.org/mediawiki/2010/2/27/Metu-guide6.jpg"> |
| + | <p>After clicking, you will see a highlighted pathway on the 2nd graph. Which are the subparts of the clicked part. Showing the sub graph in network.</p> |
| </div> | | </div> |
| </div> | | </div> |
Line 1,387: |
Line 1,426: |
| <div class="text"> | | <div class="text"> |
| <h2>Human Practices</h2> | | <h2>Human Practices</h2> |
| + | <p>iGEM’s parts registry is the only current database that holds information |
| + | and DNA for over 3000 standard parts for the use of synthetic biology |
| + | community. BioGUIDE is the first designed software that organizes the |
| + | parts in iGEM spring 2010 distribution as possible atomics parts to |
| + | build new biological device and systems for specific input and outputs |
| + | based on graph theory. We are the first group who has applied a novel |
| + | algorithm to search for input/output relations between the parts to |
| + | reveal possible construct assemblies. This new approach will chance |
| + | how the parts registry is used by the scientific community. And the |
| + | availability of software implementing our algorithm with a very user |
| + | friendly graphical user interface will allow all the users of the parts |
| + | registry to explore new and novel constructs according to their parameter |
| + | with ease. Additionally as the BioGUIDE software is an open source ware |
| + | , any user can contribute to the development of the application. So, |
| + | BioGUIDE will be improving with a collaborative effort, which will make |
| + | it even more widely used among the synthetic biologists. </p> |
| + | <p>We also had many collabrations with the teams such as, INSA-Lyon, |
| + | Lethbridge, WashU through our survey and WARSAW as we have participated |
| + | in their survey. Also our sister team METU_TURKEY is our main collaborator. |
| + | They have provided feedback BioGUIDE at different stages of the development. |
| + | And they had the chance to analyze their constructs input/output relations |
| + | throughout this collaboration. </p> |
| + | <p><strong>ALL TEAMS</strong>: The Parts Registry Survey that has been |
| + | developed by METU_TURKEY_SOFTWARE got response from 253 of participant |
| + | from 94 teams. Analysis of the survey results we have received so far |
| + | indicates that we were able outreach to the iGEM community and help |
| + | them verbalize their concerns and suggestions for the parts registry |
| + | standards and the maintenance of the database.</p> |
| + | <p><strong>WARSAW</strong>: Our team members have participated in their |
| + | survey abour iGEM participants profile. </p> |
| + | <p><strong>METU_TURKEY</strong>: Beta testing of the algorithm developed |
| + | and the BioGUIDE software has been performed by METU_TURKEY on few case |
| + | studies. Additionally they have tested their construct for 2010 competition |
| + | with our algorithm. </p> |
| </div> | | </div> |
| </div> | | </div> |
Line 1,405: |
Line 1,478: |
| <div class="text"> | | <div class="text"> |
| <h2>Material</h2> | | <h2>Material</h2> |
| + | <p>Our main data source for BIO Guide Software Program was the available |
| + | background information of parts distributed in 2010 iGEM plates (Total |
| + | of three384-well plates of dried DNA) to the wetlab teams. This data |
| + | was available through both the parts registry main website (<a href="http://partsregistry.org/Main_Page">http://partsregistry.org/Main_Page</a>) |
| + | in XML format and parts registry libraries (http://partsregistry.org/assembly/libraries.cgi?id=31) |
| + | in Excel format. Data from parts with specific part IDs have been parsed |
| + | with a custom code developed to modify SAX Parser. Then, the rest of |
| + | the data which needs to be standardized according to biological importance |
| + | have been extracted from the Registry of Parts Page manually. The chemical |
| + | (IPTG, galactose etc.) or physical (UV irradiation, temperature etc) |
| + | external inputs and proteins synthesized from a biobrick coding sequence |
| + | can affect promoters on the parts. These effectors are identified under |
| + | the title “Input”. And the “Output” s of these effectors are classified |
| + | as inducers (a molecule that starts gene expression), repressors (blocker |
| + | of attachment of RNA polymerase to promoter), activators (increasing |
| + | the rate of transcription) and inhibitor s(decreasing the rate of transcription). |
| + | These standardizations on the database helped us to build the algorithm |
| + | based on input/output relationships. MySQL Server is used for Database |
| + | development and organization. All of our illustrations for ER and algorithm |
| + | is created in SmartDraw (trial version). Java Programming Language, |
| + | and NetBeans Development environment is used or for software development. |
| + | The graphical visualization of the software is done with Cyctoscape |
| + | and yfiles libraries (trial version) are used for the presentation of |
| + | graphical events. We have utilized css Javascripts for our webdesign. |
| + | Autodesk Maya 2011 with Academic Licence, Adobe Creative Suite 5 Master |
| + | Collection (Trial Version) have been used for animations and illustrations. |
| + | Video tutorial for the BioGUIDE has been created by camstudio and trial |
| + | versions of Flash and After Effects are also used for the videos. |
| + | </p> |
| </div> | | </div> |
| </div> | | </div> |
Line 1,413: |
Line 1,515: |
| <div class="content2"> | | <div class="content2"> |
| <div class="text"> | | <div class="text"> |
- | <h2>User Guide</h2> | + | <h2>Supporting Tools</h2> |
| + | <ul> |
| + | <li>SAX Parser ( modified )to parse XML files</li> |
| + | <li>Java ProramingLanguage, NetBeans Developement environment for |
| + | software developement</li> |
| + | <li>MySQL Server for DataBase</li> |
| + | <li>cystoscape for graph visualization</li> |
| + | <li>yfiles library for graph events</li> |
| + | <li>SmartDraw for illutration of ER and Algorithm</li> |
| + | <li>maya & Cinema 4D for 3D animation, Adobe Master Collection and |
| + | Microsoft Expression Studio for design</li> |
| + | <li>CSS, Java Script for web</li> |
| + | </ul> |
| </div> | | </div> |
| </div> | | </div> |
Line 1,421: |
Line 1,535: |
| <div class="text"> | | <div class="text"> |
| <h2>Safety</h2> | | <h2>Safety</h2> |
| + | <p>Synthetic biology has the potential to impact many areas of society. |
| + | Synthetic biologists may use artificial molecules to reproduce emergent |
| + | behavior from natural biology, with the goal of creating artificial |
| + | life or seeking interchangeable biological parts to assemble them into |
| + | devices and systems that function in a manner not found in nature (Benner |
| + | and Sismour 2005, Endy 2005, Heinemann and Panke 2006, Luisi 2007, Serrano |
| + | 2007).There is possibility of causing intentional or accidental harm |
| + | to humans, agriculture or the environment. While deliberate damage is |
| + | dealt with under the heading biosecurity, the potential unintended consequences |
| + | have to be considered under the term biosafety. As a software developer |
| + | , we have to consider all possible maliciously use of synthetic biology |
| + | tools. However, it is diffucult to understand for which purposesour |
| + | tools will be used, bestway avoiding garage bioterrorism is all parts |
| + | before adding to partsregistry must be checked , looked for toxic affect |
| + | and any environmental or human harmness. After scanning possible candidate |
| + | parts, a committe should decide whether novel part can be added parts |
| + | registry or not.And we can only warn the user about our intention while |
| + | building the application: </p> |
| + | <p>“BioGUIDE v1.0 software is <strong>FOR RESEARCH USE ONLY</strong>, |
| + | no medical or diagnostic use for applications of the novel Biobrick |
| + | constructs generated through our software has been described “</p> |
| + | <p>“No military (defense or combat) applications will be allowed in |
| + | future”</p> |
| </div> | | </div> |
| </div> | | </div> |
Line 1,481: |
Line 1,618: |
| <div class="content2"> | | <div class="content2"> |
| <div class="text"> | | <div class="text"> |
- | <h2>Supporting Tools</h2> | + | <h2>Contact</h2> |
- | <ul> | + | <p>For critics, suggestion, or appraisal, you can contact us on |
- | <li>SAX Parser ( modified )to parse XML files</li>
| + | <a href="mailto:software_metuturkey@googlegroups.com">software_metuturkey@googlegroups.com</a></p> |
- | <li>Java ProramingLanguage, NetBeans Developement environment for
| + | |
- | software developement</li>
| + | |
- | <li>MySQL Server for DataBase</li>
| + | |
- | <li>cystoscape for graph visualization</li>
| + | |
- | <li>yfiles library for graph events</li>
| + | |
- | <li>SmartDraw for illutration of ER and Algorithm</li>
| + | |
- | <li>maya & Cinema 4D for 3D animation, Adobe Master Collection and
| + | |
- | Microsoft Expression Studio for design</li>
| + | |
- | <li>CSS, Java Script for web</li>
| + | |
- | </ul>
| + | |
| </div> | | </div> |
| </div> | | </div> |
Line 1,932: |
Line 2,059: |
| <div class="item"> | | <div class="item"> |
| </div> | | </div> |
- | <div id="download5" class="item"> | + | <div class="item"> |
- | <div class="content2">
| + | </div> |
- | <div class="text">
| + | <div id="miscellaneous5" class="item"> |
- | <h2>Contact</h2>
| + | <div class="content2"> |
- | <p>For critics, suggestion, or appraisal, you can contact us on
| + | <div class="text"> |
- | <a href="mailto:software_metuturkey@googlegroups.com">software_metuturkey@googlegroups.com</a></p>
| + | <h2>Sponsors</h2> |
- | </div>
| + | <ul id="sponsorlist"> |
- | </div>
| + | <li><img src="http://tecrubem.net/wp-content/uploads/2009/09/tubitak.jpg" width="200" height="200"></li> |
| + | <li><img src="https://static.igem.org/mediawiki/igem.org/0/06/METU-Surat.jpg"></li> |
| + | <li><img src="https://static.igem.org/mediawiki/igem.org/6/64/Teknokent.jpg"></li> |
| + | <li><img src="https://static.igem.org/mediawiki/igem.org/d/d8/Sentegen.jpg"></li> |
| + | </ul> |
| + | </div> |
| </div> | | </div> |
- | <div class="item">
| |
| </div> | | </div> |
| <div class="clear"> | | <div class="clear"> |
Line 2,028: |
Line 2,159: |
| <div class="content2"> | | <div class="content2"> |
| <div class="text"> | | <div class="text"> |
- | <h2>Modeling</h2> | + | <h2>Graph Modeling</h2> |
| <h3>Graphical Modeling for Bio-Guide</h3> | | <h3>Graphical Modeling for Bio-Guide</h3> |
| <h4>Introduction</h4> | | <h4>Introduction</h4> |
Line 2,120: |
Line 2,251: |
| <div id="project8" class="item"> | | <div id="project8" class="item"> |
| <div class="content2"> | | <div class="content2"> |
- | <div class="text" style:"padding-bottom:20px"> | + | <div class="text"> |
| <h2>Results</h2> | | <h2>Results</h2> |
| <ul> | | <ul> |
- | <li>In order to develop BioGuide algoritm, there is a need to reorganize | + | <li>In order to develop BioGuide algorithm, there was a need to |
- | and normalize parts information database in partsregistry.org. information | + | reorganize and normalize parts information database in partsregistry.org. |
- | of the parts was processed and developed from partsregistry.org | + | Information of the parts was processed and developed from partsregistry.org |
- | which includes the PartID, PartName, RFC values, , designer and | + | which includes the PartID, PartName, RFC values, etc , designer |
- | contact information and parameters to build standardized template. | + | and contact information and parameters to build a standardized template |
- | </li> | + | for our algorithm to run smoothly. </li> |
- | <li>Database standardization is done by additional gathered unstandardized | + | <li>Database standardization is done by analyzing iGEM Spring 2010 |
- | information manually by hand , most of the distributed parts are | + | distribution and collecting information needed for the standardized |
- | analyzed and new parameters are assigned according to parts input-output | + | parts. Also new parameters are assigned according to parts input-output |
- | model like : Inducer, Activator, Repressor, Inhibitor </li> | + | model like : Inducer, Activator, Repressor, Inhibitor</li> |
- | <li>For each promoters we assigned their inducers or repressors | + | <li>For each promoter we have assigned their inducers or repressors |
- | as input and for protein generator parts we assigned generated proteins | + | as input and for protein generator parts we have assigned generated |
- | as output which maybe activator or repressor of other devices. | + | proteins as output which maybe activator or repressor of other devices. |
| </li> | | </li> |
| <li>iGEM devices are depicted in pictorial forms called flowcharts, | | <li>iGEM devices are depicted in pictorial forms called flowcharts, |
| encapsulation of implementations , decision branching and direction | | encapsulation of implementations , decision branching and direction |
- | are milestones of our algoritm. The subprogram at the head of the | + | are milestones of our algorithm. Following flowcharts are the high |
- | arrow starts executing after the termination of the subprogram at
| + | level representations of our algorithms developed for the BioGuide |
- | the tail of the arrow. Following flowcharts are the high level representations
| + | software.</li> |
- | of our algorithms developed for the BioGuide software. </li>
| + | <li>We run our algorithm on the real combination dataset in order |
- | <li>We run our algorithm on the real combination dataset to build | + | to build our input/output relations graphs. We also collected the |
- | our input/output relations graphs . We also collected the subpart | + | subpart assembly order, such as 1st: promoter, 2nd:rbs, 3rd:coding |
- | assembly order, such as 1st: promoter, 2nd:rbs, 3rd:coding seq, | + | seq, any internal parts and the Last: terminator. Each specific |
- | any internal parts and the Last: terminator. Each specific Biobrick
| + | Biobrick type has been assigned a number as a unique image ID from |
- | type has been assigned a number as a unique image ID from 1 to 19. | + | 1 to 19. </li> |
- | </li>
| + | <li>ImageID assembly orders for each construct have been used to |
- | <li>ImageID assembly orders for each construct has been used to | + | |
| extract the type information for each subpart with that construct. | | extract the type information for each subpart with that construct. |
| This innovative approach helped us to reveal 400 possible brick | | This innovative approach helped us to reveal 400 possible brick |
| combinations present within the 3x384 well plates distributed by | | combinations present within the 3x384 well plates distributed by |
- | iGEM in Spring 2010 </li> | + | iGEM in Spring 2010</li> |
- | <li>Four different graphs were constructed Graphical Modeling Theory | + | <li>Four different graphs were constructed based on graphical modeling |
- | where relations of atomic parts, devices and systems and the functional | + | theory where relations of atomic parts, devices and systems and |
- | combinations that can build new constructs are presented for the | + | the functional combinations that can build new constructs are presented |
- | iGEMs parts registry database. Three graphs are composed of iGEM | + | for the iGEMs parts registry database. Three graphs are composed |
- | devices and one graph is based on Biobricks. </li> | + | of iGEM devices and one graph is based on Biobricks.</li> |
| <li>Each graph comprises a set of vertices or nodes and a set of | | <li>Each graph comprises a set of vertices or nodes and a set of |
| edges. In the set of nodes each node represents a device, while | | edges. In the set of nodes each node represents a device, while |
| in the set of edges each edge represents the input-output combination | | in the set of edges each edge represents the input-output combination |
- | of the nodes. </li> | + | of the nodes.</li> |
| <li>We arrange a survey to analyze user needs and response, According | | <li>We arrange a survey to analyze user needs and response, According |
- | to our survey results,244 participants are completed our survey | + | to our survey results, 244 participants are completed our survey |
| between 10 to 22.10.2010, 57% of the participant had scientific | | between 10 to 22.10.2010, 57% of the participant had scientific |
| degrees from B.Sc to Professor and 18% had graduate degrees. 18% | | degrees from B.Sc to Professor and 18% had graduate degrees. 18% |
| of participants are enrolled in their teams as either Instructors | | of participants are enrolled in their teams as either Instructors |
| or Advisors.INSA-Lyon, Lethbridge, WashU are dedicated as collaborators | | or Advisors.INSA-Lyon, Lethbridge, WashU are dedicated as collaborators |
- | with more than 60% team participation. </li> | + | with more than 60% team participation. You can learn more on survey |
| + | results on our collaboration page</li> |
| </ul> | | </ul> |
| </div> | | </div> |
Line 2,181: |
Line 2,312: |
| </div> | | </div> |
| <div class="clear"> | | <div class="clear"> |
| + | </div> |
| + | <!-- 9th row --> |
| + | <div class="item"> |
| + | </div> |
| + | <div class="item"> |
| + | </div> |
| + | <div class="item"> |
| + | </div> |
| + | <div class="item"> |
| + | </div> |
| + | <div id="project9" class="item"> |
| + | <div class="content2"> |
| + | <div class="text"> |
| + | <h2>Attribution and Contributions</h2> |
| + | <p>The BioGUIDE software is a proud product of METU_TURKEY_SOFTWARE group where the students have presented the problem and come up with the solution with minor advising. This project was not a part of an ongoing project in any of the advisors.</p> |
| + | <p>The biologist of the team have done the preliminary database standardization by analyzing and collected data from the iGEM Spring 2010 distribution. All the algorithms have been developed by the soon-to-be computer scientist in the group. The Parts registry survey and standardization of the database information on parts have been developed through a colloborotative effort within the group. </p> |
| + | <p>Additionally all the logo, illustrations, animations, video and other visual media and web design has been created by the design team in the group.</p> |
| + | </div> |
| + | </div> |
| + | </div> |
| + | <div class="item"> |
| + | </div> |
| + | <div class="item"> |
| + | </div> |
| + | <div class="item"> |
| + | </div> |
| + | <div class="clear"> |
| + | </div> |
| + | <!-- 10th row --> |
| + | <div class="item"> |
| + | </div> |
| + | <div class="item"> |
| + | </div> |
| + | <div class="item"> |
| + | </div> |
| + | <div class="item"> |
| + | </div> |
| + | <div id="project10" class="item"> |
| + | <div class="content2"> |
| + | <div class="text"> |
| + | <h2>Development Plans and Project Management</h2> |
| + | <p>The application we are developing can be used by all iGEM members and it’s data is increasing very fast as the iGEM becomes a bigger organization. Moreover, other data resources like NCBI can be imported to this application, hence the user group of application is gets bigger and bigger. In such a situation, extendibility of the application is vital. New data resources and new functions should be added easily. </p> |
| + | <p>Before starting to think about those, first we have to ask to other teams and iGEM headquarters about the BioGuide 1.0 to see the missing points in our idea, and to check our theories. Until developing this idea we were not using professional software approaches. We were planning our weekly tasks and doing those as in the notebook. </p> |
| + | <p>After finding a novel software project we have to change our approach. We have to use professional software development approaches to develop such an application to be able to state the requirements exactly and to use a common language between software oriented and biology oriented members in the team.</p> |
| + | <p>As we mentioned above, our software can be extended, and new data resources can be imported. The requirements are changing and the problem can be understood better in time. Extreme Programming Approach is developed for such software projects. That is the approach we are going to use in BioGuide2.0</p> |
| + | </div> |
| + | </div> |
| + | </div> |
| + | <div class="item"> |
| + | </div> |
| + | <div class="item"> |
| + | </div> |
| + | <div class="item"> |
| + | </div> |
| + | <div class="clear"> |
| + | </div> |
| + | <!-- 9th row --> |
| + | <div class="item"> |
| + | </div> |
| + | <div class="item"> |
| + | </div> |
| + | <div class="item"> |
| + | </div> |
| + | <div class="item"> |
| + | </div> |
| + | <div class="item"> |
| + | </div> |
| + | <div class="item"> |
| + | </div> |
| + | <div class="item"> |
| + | </div> |
| + | <div class="item"> |
| </div> | | </div> |
| <script type="text/javascript">if (window.runOnloadHook) runOnloadHook();</script> | | <script type="text/javascript">if (window.runOnloadHook) runOnloadHook();</script> |
Line 2,213: |
Line 2,416: |
| <li><a class="panel" href="#project5">Database Standardization</a></li> | | <li><a class="panel" href="#project5">Database Standardization</a></li> |
| <li><a class="panel" href="#project6">Algorithm</a></li> | | <li><a class="panel" href="#project6">Algorithm</a></li> |
- | <li><a class="panel" href="#project7">Modeling</a></li> | + | <li><a class="panel" href="#project7">Graph Modeling</a></li> |
| <li><a class="panel" href="#project8">Results</a></li> | | <li><a class="panel" href="#project8">Results</a></li> |
| + | <li><a class="panel" href="#project9">Attribution and Contributions</a></li> |
| + | <li><a class="panel" href="#project10">Development Plans</a></li> |
| </ul> | | </ul> |
| </li> | | </li> |
Line 2,227: |
Line 2,432: |
| </div> | | </div> |
| <ul class="submenu"> | | <ul class="submenu"> |
- | <li><a class="panel" href="#download">Executable</a></li> | + | <li><a class="panel" href="#download">Executable and Code</a></li> |
- | <li><a class="panel" href="#download2">Code</a></li> | + | <li><a class="panel" href="#download2">User Guide</a></li> |
- | <li><a class="panel" href="#download3">User Guide</a></li>
| + | <li><a class="panel" href="#download3">Supporting Tools</a></li> |
- | <li><a class="panel" href="#download4">Supporting Tools</a></li> | + | <li><a class="panel" href="#download4">Contact</a></li> |
- | <li><a class="panel" href="#download5">Contact</a></li> | + | |
| </ul> | | </ul> |
| </li> | | </li> |
Line 2,244: |
Line 2,448: |
| <li><a class="panel" href="#miscellaneous3">Safety</a></li> | | <li><a class="panel" href="#miscellaneous3">Safety</a></li> |
| <li><a class="panel" href="#miscellaneous4">Future Plan</a></li> | | <li><a class="panel" href="#miscellaneous4">Future Plan</a></li> |
| + | <li><a class="panel" href="#miscellaneous5">Sponsors</a></li> |
| </ul> | | </ul> |
| </li> | | </li> |