Biodivine logical models library

This project is still WIP. The version available in main is deprecated, as major rewrite has taken place - see branch rewrite.

• Though no new features were introduced, the API has changed. The readability of rewrite should be significantly better. Performance is also slightly improved.

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A Rust library for working with logical models (Boolean/multi-valued networks) in systems biology.

Goals

• Can load/store file formats common in systems biology (sbml, bnet, aeon, bma).
• Can perform basic static analysis on such models (unused variables,  invalid regulations, input inlining or general reduction).
• Can represent unknown/uncertain behaviour within the logical model.
• Can represent and manipulate the state-transition graph of a logical model symbolically (maybe using multiple different encodings?).
• Provides some basic utility algorithms for (a) exploring the structural properties of the model (feedback vertex sets, cycles, etc.) (b) exploring the model dynamics (reachability, fixed-points, trap spaces, etc.).

Running reachability integration test

To test the correctness of the implementation, we now have a simple reachability consistency check. This check compares the results of all symbolic representations on a basic reachability exploration. To run the test, execute the following:

# First argument is a timeout, here 1 minute. This uses standard unix `timeout`.
# Second argument is fwd/bwd to indicate which reachability direction you want to test.
python3 reachability_integration_test.py 1m fwd

The process dumps all results into an appropriate ./data/results-* directory. The script will not overwrite existing results, so you have to delete the directory manually before running the test again.

You should see an output similar to the following:

[PASS] No error discovered in `146_BUDDING-YEAST-FAURE-2009.sbml` in less than 1m.
[PASS] No error discovered in `148_AGS-cell-fate-decision.sbml` in less than 1m.
[PASS] No error discovered in `151_TCR-REDOX-METABOLISM.sbml` in less than 1m.
[PASS] No error discovered in `155_CONTROL-OF-TH1-TH2-TH17-TREG-DIFFERENTATION.sbml` in less than 1m.
[PASS] No error discovered in `157_CONTROL-OF-TH-DIFFERENTATION.sbml` in less than 1m.
...

If you see a [FAIL] somewhere, it means an inconsistency has been detected. You can then check the results to examine the specific case.