execute some experiments using command line tool

[tomvej]

Try exporting SBML from Copasi. Can parasim read it?

[tomvej]

Need real-life model (Lazár -- photosynthesis?). It would be also good to have real-life data.

[papousek]

• make sure there is a SBML editor producing files compatible with Parasim
• compare parasim results to other tools like Biocham and Breach

[papousek]

only SBML level 2 version 4 supported

SBMLeditor 2.0-b1

• produces invalid SBML file
• parasim updated to skip invalid species, parameters and species references
• compatible now

[papousek]

compartments in kinetic laws aren't supported (skipped with warning)

Copasi 48 (Build 35)

• parameters are placed locally in kinetic laws - have to be referenced via {reaction name}:{parameter name} from other files
• parasim skips compartment references in kinetic laws
• compatible now

[papousek]

Added Lorenz 84 model and compared its analysis to Breach.