Team:Alberta/Software

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Latest revision as of 22:42, 27 October 2010

TEAM ALBERTA

Try It!

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

To build our web app, we implemented the following open source technologies:

[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.
[http://jquery.com/ jQuery]
- A javascript library that eases user interface design.
[http://git-scm.com/ git]
- A version control system that we used to share and merge our code.
[http://github.com/ gitHub]
- Free source code hosting that integrates with git. Github is also an online coding community and makes collaboration easy.

GENOMIKON 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, DIY molecular biology community.

The Lab Manual

Get started with your first molecular biology experiments

A page out of the lab manual.

Users can upload photos of their results

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.

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

In silico plasmid designer

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

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.

An Integrated Glossary

The glossary, showing a mouse-over popup for a glossary term.

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.

DIY 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.

@@ Line 9: / Line 9: @@
 ==Try It!==
-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.
+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==
-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]
 **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 25: / Line 25: @@
 {{Team:Alberta/beginMainContent}}
-==Genomikon - Companion Software==
+==GENOMIKON ONLINE - Companion Software==
+<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.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.
+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, DIY molecular biology community.
 ==The Lab Manual==
 ===Get started with your first molecular biology experiments===
+<div id="horiz-line"></div>
 [[Image:Alberta-Screen2.png|thumb|200px|A page out of the lab manual.]]
+[[Image:Alberta-Notepic.png|thumb|Users can upload photos of their results]]
 The lab manual starts with a set of experiments of predefined experiments, selected with several criteria in mind:
 *Fun
@@ Line 41: / Line 42: @@
 We used the Province of Alberta's high school curriculum as a model.
-To see specific examples check out the [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>
-[Image:team-alberta-lab-manual-notes.jpg]
 ==Plasmid Design Tool==
-===design your plasmid before you build===
+===Design your own experimental plasmids===
+<div id="horiz-line"></div>
 [[Image:Alberta-Screen1.png|200px|thumb|In silico plasmid designer]]
-The most exciting feature of our kit is the plasmid design tool.  It has an easy to use drag and drop interface, and has built in validation to catch your errors before your build in the lab.
+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).
 [https://2010.igem.org/Team:Alberta/PartsDesigner Learn more about the plasmid designer here]
@@ Line 55: / Line 59: @@
 [http://www.genomikon.ca/sandbox Try the plasmid designer out for yourself right now]
-== ==
+====Software-Automated Protocol Generation====
-===generate instructions and share your design===
+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.
-After you create a valid plasmid you can save it and a lab protocol will automatically be created.  Then you can edit the instructions, add figures, images and a description.  Once your ready click publish and share your cool experiment for others to try.
+<div style="clear:both"></div>
 ==The Encyclopedia==
 ===Develop a deeper understanding===
+<div id="horiz-line"></div>
 [[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.
-[Image:team-alberta-articles.jpg]
+<div style="clear:both"></div>
 ==An Integrated Glossary==
-===A definition is never further than your pointer===
+<div id="horiz-line"></div>
-We have an integrated glossary throughout the website for easy access to definitions
 [[Image:Alberta-Screen4.png|thumb|200px|The glossary, showing a mouse-over popup for a glossary term.]]
-[[Image:team-alberta-articles.jpg]]
-==Student Groups & Sharing Your Experiments==
+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.
-===share your experiments and communicate with your classmates===
+<div style="clear:both"></div>
+==Student and User Groups==
+===Bringing the classroom online===
+<div id="horiz-line"></div>
+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.
-Teachers can create groups and have their students join it.  This allows classes to communicate with each other
+DIY 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}}