Comparison of SBSCL (https://github.com/draeger-lab/SBSCL) against other simulators for correctness and performance. Comparisons are performed for FBA simulations and ODE simulations.
The BiGG model collections are compared against results from cobrapy (https://github.com/opencobra/cobrapy)
and cameo (https://cameo.bio/index.html).
The bigg database is available from
https://github.com/SBRG/bigg_models
A dump of all models is available from
https://www.dropbox.com/sh/ye05djxrpxy37da/AAD6GrSRTt4MRfuIpprlnLYba?dl=0
The models for comparison are included in this repository in
models/bigg-v1.6
The results of the FBA simulations are available in
results/fba
Objective values are compared between different simulators. Model loading and optimization are benchmarked via repeated execution.
ODE models are compared between different simulators:
roadrunnercopasiAMICI
pip install -r requirements.txt
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