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jcrozum / pystablemotifs

Python library for attractor identification and control in Boolean networks
MIT License
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Import support for cell collective format #48

Closed jcrozum closed 3 years ago

jcrozum commented 3 years ago

The cell collective (https://research.cellcollective.org) has an option to export the Boolean expressions of their models. Note that this is not the SMBL format, but a separate "Boolean Expressions" download option.

The rules come in a folder with a bunch of text files. There's a file for each variable with its update rule inside, but, more usefully (for us), there are two files called expressions.ALL.txt and external_components.ALL.txt that have the rules for everything. The rules for everything except source nodes are in expressions.ALL.txt, while the source nodes are simply listed in external_components.ALL.txt (one per line).

The format is like this: RhoGDI = ( NOT ( ( PIP2_45 ) OR ( AA ) OR ( PKC ) ) ) OR NOT ( AA OR PIP2_45 OR PKC )

This format is very similar to the BooleanNet format, so it should be easy to implement an importer. We have several options for how to receive the input, but the simplest would be to take the path to the folder the cell collective gives you.

jcrozum commented 3 years ago

Looks like this is working now. Thanks!