We put here a list of softwares that could be useful in the development of iGEM in silico work:
- Mathematica: A general program much oriented to work with algebraic equations.
- Matlab: Matlab is a numerical computing environment which is quite easy to use compared with other programming languages like C.
- Simulink: developed by Matlab's team, is a tool for modeling, simulating and analyzing multidomain dynamic systems. Its primary interface is a graphical block diagramming tool and a customizable set of block libraries. It offers tight integration with the rest of the MATLAB environment and hence the functions of the subrutines available in matlab can be used in simulink and viceversa. Simulink is widely used in control theory and digital signal processing for multidomain simulation and design.
- COPASI: COPASI is a software application for simulation and analysis of biochemical networks.
- Small knowledge about mark up lenguages like xml (sbml): SBML is a mark up language in which a lot of biological models has been written in and it is modular in nature.
As COPASI allows to read sbml models, it is quite interesting from the point of view of students preparation, to run some developed models in sbml like repressilator in COPASI to get introduced in the dynamics of this kind of systems.
Some other programs are also available that could be useful for other iGEM teams although we are not going to use them:
- SimBiology (This software looks quite interesting to our purposes but we do not have the licence in our university)