search

jcrozum / pystablemotifs

Python library for attractor identification and control in Boolean networks
MIT License
28 stars 7 forks source link

MPBN Support #50

Closed jcrozum closed 2 years ago

jcrozum commented 3 years ago

To do: implement proper support for MPBN update. See "Reconciling qualitative, abstract, and scalable modeling of biological networks" Loïc Paulevé, Juraj Kolčák, Thomas Chatain & Stefan Haar Nat. Com. vol. 11, no. 4256 (2020) https://www.nature.com/articles/s41467-020-18112-5

This entails 1) skipping completeness checks for "ghost branches" and 2) adding MPBN STG-building functions. The MPBN STG should have the option include nodes corresponding to intermediate states (4^N total) or not (2^N total).

jcrozum commented 3 years ago

Partial support added in #64. Still need to implement STG functions for full support. This is implemented here: https://github.com/pauleve/mpbn, so maybe we don't have to write our own.

jcrozum commented 2 years ago

Since the projected STGs restricted to attractors are always complete, further STG support seems like overkill at this point. I will close this issue for now, and we can reassess when if/when we add more simulation tools.