Gigabase: Synthetic Biology Cell Modeling Project
GitHub Pages: http://sleeplessbyte.github.io/programming-life
Life/Live Application: http://life.jstfy.com/
Developing a visual environment for designing and simulating virtual cells.
- Substrate, s.
- Metabolism converting substrate s into product p.
- Substrate and product transporter.
- DNA synthesis.
- Protein synthesis and degratation.
- Lipid synthesis.
The lipid membrane separates the inside of the cell from the outside environment, allowing for unequal substrate and product concentrations inside and outside the cell (s#in, p#in and s#ext, p#ext respectively). Each of the components is associated with a cellular process (e.g. molecule synthesis or substrate conversion), which is modeled by one or more differential equations. The proposed model describes an av- erage cell in a growing population of cells. Ordinary Differential Equations (ODEs) in this model describe the change of molecule concentrations in time.
Gigabase runs on Rails. You can load this repository onto your hard drive and directly use
it as a rails app. Just run bundle install and rake db:setup and you are good to go.
For windows users, some gems might not install and display a message such as not native build.
Download the Ruby Devkit and run the bundle install command in mysys terminal. All the
gems will then perfectly build. Don't forget you might need administrator rights.
After June 2013 the project will no longer have constraints so we could go any direction. We do not allow pull requests on master or release branches. Fork the repository, create a patch/feature/issue branch and merge to develop.
Your code should be rdoc or codo/coffeedoc commented, assets should be /spec/ tested
and when applied should have /test/functional integration tests. Server side code should
also be /test/ unit tested.