This is (1) work in progress (2) going to be a set of examples showcasing how (extended) SED-ML can be applied to SBML Qual models. The idea of a github-based, fully featured showcase is taken from the CombineArchiveShowcase.
We use four examples to demonstrate how SED-ML would be used for experiments run on SBML Qual models:
- Toy model: taken from the SBML Qual Specification Section 4.1
- Petri net model: taken from the SBML Qual Specification Section 4.2
- Lambda phage model: taken from the GinSim tutorial
- MAPK model: taken from the GinSim repository
The files in each of the four example folders are organised as follows:
/models: Files that describe and encode the biological system, using SBML L3 with SBML Qual extension.
/simulations: Files that encode the simulation setup, using SED-ML L1V2 plus the proposed extensions necessary for discrete simulations
/figures: Graphical representations of the models and of the results obtained from the simulation experiments, using png format.
I chose this structure because it is a convenient way for me to organise my COMBINE Archive. However, the structure is not mandatory.