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sybila / biodivine-boolean-models

A collection of 230+ Boolean networks from various sources useful for benchmarking or testing.
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[Problem] Some larger models time out on static analysis. #1

Open daemontus opened 3 years ago

daemontus commented 3 years ago

Very large models (10.000+ variables, or ones using very complex update functions) are represented using very large SBML files which our parser can't handle at the moment.

See for example: https://www.ebi.ac.uk/biomodels/MODEL2007020001#Overview (this one is "only" 3000 variables, but still quite large)

The solution is to use a different parser that does not need to store the whole abstract-syntax-tree of the XML document in memory at the same time. However, this requires a substantial change in biodivine-lib-param-bn.

daemontus commented 2 years ago

Correction: It seems that the SBML parser itself is mostly ok (it's not super fast, but its fine). However, static analysis is the real bottleneck in the pipeline.