BioNetGen

The software we primarily modelled with, BioNetGen, is very intuitive to work with and very powerful. However prior to this year it has only been used by one other iGEM team. Therefore we gave a workshop on using BioNetGen to the other UK iGEM teams. This inspired another team to use the software. We also recorded an introductory video for modelling in BioNetGen using the GUI rulebender, which can be found below. This video was also for a collaboration with the Manchester iGEM team for their introduction to modelling project.

BioNetGen is an example of rule based modelling (the only other commonly used example being Kappa). In this we state a series of 'reaction rules' which specify what reactions can occur and at what rates. Molecules are given 'domains'. These represent binding sites to other domains, allowing the formation of complexes. A domain can also represent a site that can exist in multiple states, for example a site which can be phosphorylated and dephosphorylated. These features are unique to rule based modelling, and reduce the number of reactions that need to be written without sacrificing complexity.

The Manchester iGEM teams introduction to modelling project can be found here