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BuildACell / bioCRNpyler

A modular compiler for biological chemical reaction networks
BSD 3-Clause "New" or "Revised" License
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Colab: 'biocrnpyler' is not defined, 'CRN.simulate_with_bioscrape_via_sbml()' returns 'NoneType' object #280

Open HengyuWangWHY opened 1 week ago

HengyuWangWHY commented 1 week ago

When I run the 'Lecture 2 Compiling CRNs Colab Notebook.ipynb' downloaded from YouTube, the 'CRN.simulate_with_bioscrape_via_sbml()' returns 'NoneType' object, which is not subscriptable.

The file contains more information about the bugs: https://colab.research.google.com/drive/1032AsF34S4XggarQvWx8qHu_pJytFrwA?usp=sharing

murrayrm commented 1 week ago

I was able to get the simulation examples in BioCRNpyler working under Python 3.12 (with Numpy 2.0) using BioSCRAPE PR #173.

@HengyuWangWHY: You might try installing that version of BioSCRAPE locally (or in Colab via a pip install of the branch used for the PR) and see if it solves your problem.

ayush9pandey commented 3 days ago

With https://github.com/biocircuits/bioscrape/pull/173 now merged, you can now clone the latest Bioscrape code from https://github.com/biocircuits/bioscrape/

Can you confirm if this fixes your error @HengyuWangWHY ?