"
Team:Alberta/Software
From 2010.igem.org
(→Genomikon - Companion Software) |
|||
| Line 9: | Line 9: | ||
==Try It!== | ==Try It!== | ||
| - | Head to [http://www.genomikon.ca GENOMIKON. | + | Head to [http://www.genomikon.ca GENOMIKON.ca] and start designing your own plasmids right away! Or, create an account and sign in to check out the lab manual. |
==Technology== | ==Technology== | ||
| - | To build our web app we implemented the following open source technologies: | + | To build our web app, we implemented the following open source technologies: |
*[http://rubyonrails.org/ Ruby on Rails] | *[http://rubyonrails.org/ Ruby on Rails] | ||
**A web server back-end framework that uses the Ruby programming language. Implements a [http://en.wikipedia.org/wiki/Model%E2%80%93View%E2%80%93Controller MVC] architecture, and is easily customizable and extendable. | **A web server back-end framework that uses the Ruby programming language. Implements a [http://en.wikipedia.org/wiki/Model%E2%80%93View%E2%80%93Controller MVC] architecture, and is easily customizable and extendable. | ||
| Line 27: | Line 27: | ||
==GENOMIKION ONLINE - Companion Software== | ==GENOMIKION ONLINE - Companion Software== | ||
<div id="horiz-line"></div> | <div id="horiz-line"></div> | ||
| - | To assist students in performing their very first molecular biology experiments, we created an online, electronic lab manual to walk them through the process. At [http://www.genomikon.ca GENOMIKON. | + | To assist students in performing their very first molecular biology experiments, we created an online, electronic lab manual to walk them through the process. At [http://www.genomikon.ca GENOMIKON.ca], users of the kit will find an electronic, interactive lab manual. Bringing the lab manual into the twenty-first century, GENOMIKON.ca compliments the kit. It will not only inform students, but also empower them to create their own experiments and share them with the world in an online, DYI molecular biology community. |
==The Lab Manual== | ==The Lab Manual== | ||
| Line 44: | Line 44: | ||
To see specific examples check out the [https://2010.igem.org/Team:Alberta/Experiments experiments] page. | To see specific examples check out the [https://2010.igem.org/Team:Alberta/Experiments experiments] page. | ||
| - | As the students progress through the experiments they can take notes and even upload images of their results. | + | As the students progress through the experiments, they can take notes and even upload images of their results. |
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
| Line 54: | Line 54: | ||
To expand the beyond the traditional "recipe in a cookbook" model of the high school science lab, students | To expand the beyond the traditional "recipe in a cookbook" model of the high school science lab, students | ||
| - | are encouraged to design their own plasmids and experiments. With GENOMIKON. | + | are encouraged to design their own plasmids and experiments. With GENOMIKON.ca's intuitive Plasmid Designer, |
| - | designing their own unique plasmids is as simple as dragging and dropping parts together on a screen. Students can stick together | + | designing their own unique plasmids is as simple as dragging and dropping parts together on a screen. Students can stick together any combination of the parts available in the kit ''in silico'' with the guidance of the software to ensure certain specifications are met (ie, the plasmid has an origin of replication, it has some sort of selectable marker, incompatible ends have not been stuck together, etc). |
| - | any combination of the parts available in the kit ''in silico'' with the guidance of the software to ensure | + | |
| - | certain specifications are met (ie the plasmid has an origin of replication, it has some sort of selectable marker, incompatible ends have not been stuck together, etc). | + | |
[https://2010.igem.org/Team:Alberta/PartsDesigner Learn more about the plasmid designer here] | [https://2010.igem.org/Team:Alberta/PartsDesigner Learn more about the plasmid designer here] | ||
| Line 64: | Line 62: | ||
====Software-Automated Protocol Generation==== | ====Software-Automated Protocol Generation==== | ||
| - | After students design a valid plasmid for an experiment, the software automatically generates a protocol to create that plasmid and transform into cells using only materials that are available in the kit. Afterwards, the student can add further instructions and descriptions to the experimental plan to show how the transformed cells are to be used. Then, the experimental plan can be published and let loose into the online community at GENOMIKON. | + | After students design a valid plasmid for an experiment, the software automatically generates a protocol to create that plasmid and transform into cells using only materials that are available in the kit. Afterwards, the student can add further instructions and descriptions to the experimental plan to show how the transformed cells are to be used. Then, the experimental plan can be published and let loose into the online community at GENOMIKON.ca, where other students and molecular biology experiments can try the experiment themselves. |
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
| Line 71: | Line 69: | ||
<div id="horiz-line"></div> | <div id="horiz-line"></div> | ||
[[Image:Alberta-Screen3.png|thumb|200px|The encyclopaedia index]] | [[Image:Alberta-Screen3.png|thumb|200px|The encyclopaedia index]] | ||
| - | To offer some extra context to the experiments we have included a selection of articles about synthetic biology and various biology concepts relating to the kit and the high school curriculum. They are integrated with the experiments and also available separately for review. | + | To offer some extra context to the experiments, we have included a selection of articles about synthetic biology and various biology concepts relating to the kit and the high school curriculum. They are integrated with the experiments and also available separately for review. |
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
| Line 85: | Line 83: | ||
<div id="horiz-line"></div> | <div id="horiz-line"></div> | ||
| - | High | + | High school teachers can create and administer user groups and have their students join it. This brings the classroom together online, and gives teachers control over their students' online activities at GENOMIKON.ca. |
DYI Bio enthusiasts are also encouraged to create and join user groups, giving them the ability to network, communicate, and collaborate with other enthusiasts around the world. | DYI Bio enthusiasts are also encouraged to create and join user groups, giving them the ability to network, communicate, and collaborate with other enthusiasts around the world. | ||
{{Team:Alberta/endMainContent}} | {{Team:Alberta/endMainContent}} | ||
Revision as of 01:02, 27 October 2010
GENOMIKION ONLINE - Companion Software
To assist students in performing their very first molecular biology experiments, we created an online, electronic lab manual to walk them through the process. At [http://www.genomikon.ca GENOMIKON.ca], users of the kit will find an electronic, interactive lab manual. Bringing the lab manual into the twenty-first century, GENOMIKON.ca compliments the kit. It will not only inform students, but also empower them to create their own experiments and share them with the world in an online, DYI molecular biology community.
The Lab Manual
Get started with your first molecular biology experiments
The lab manual starts with a set of experiments of predefined experiments, selected with several criteria in mind:
- Fun
- Completable using only materials available in the kit
- Teach concepts that inline with a high school biology curriculum
- Extend beyond the traditional curriculum to inspire students
We used the Province of Alberta's high school curriculum as a model.
To see specific examples check out the experiments page.
As the students progress through the experiments, they can take notes and even upload images of their results.
Plasmid Design Tool
Design your own experimental plasmids
To expand the beyond the traditional "recipe in a cookbook" model of the high school science lab, students are encouraged to design their own plasmids and experiments. With GENOMIKON.ca's intuitive Plasmid Designer, designing their own unique plasmids is as simple as dragging and dropping parts together on a screen. Students can stick together any combination of the parts available in the kit in silico with the guidance of the software to ensure certain specifications are met (ie, the plasmid has an origin of replication, it has some sort of selectable marker, incompatible ends have not been stuck together, etc).
Learn more about the plasmid designer here
[http://www.genomikon.ca/sandbox Try the plasmid designer out for yourself right now]
Software-Automated Protocol Generation
After students design a valid plasmid for an experiment, the software automatically generates a protocol to create that plasmid and transform into cells using only materials that are available in the kit. Afterwards, the student can add further instructions and descriptions to the experimental plan to show how the transformed cells are to be used. Then, the experimental plan can be published and let loose into the online community at GENOMIKON.ca, where other students and molecular biology experiments can try the experiment themselves.
The Encyclopedia
Develop a deeper understanding
To offer some extra context to the experiments, we have included a selection of articles about synthetic biology and various biology concepts relating to the kit and the high school curriculum. They are integrated with the experiments and also available separately for review.
An Integrated Glossary
We have an integrated glossary throughout the website for easy access to definitions. Any glossary terms that appear in the experimental protocols and descriptions can be defined by simply hovering the mouse over a term and reading the popup text.
Student and User Groups
Bringing the classroom online
High school teachers can create and administer user groups and have their students join it. This brings the classroom together online, and gives teachers control over their students' online activities at GENOMIKON.ca.
DYI Bio enthusiasts are also encouraged to create and join user groups, giving them the ability to network, communicate, and collaborate with other enthusiasts around the world.
