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We are unable to run PySB models from the tutorial or examples that have reversible reactions. E.g., neither hello_pysb.py nor the mymodel.py model runs. Running mymodel.py from the tutorial generates…
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Hi, as someone familiar with Python but not so much earlier biochemical modeling tools, PySB looks really cool!
Can PySB be used to simulate Michaelis-Menten kinetics when only the Michaelis constant…
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We need a unit test suite for `pysb/kappa.py` to increase code coverage, which is currently
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We should crib from bng and look for likely install locations or allow the setting of an environment variable.
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Equality comparisons are needed to manipulate models. Pull this patch (with tests): https://github.com/spgarbet/pysb/commit/53c17abd8fac6e6fc34f22d001e1a76d3037a344
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This fixes the problem, by making the module_name compliant with file naming conventions.
https://github.com/spgarbet/pysb/commit/632848763db1bafe2a8f773679eb72c06be94398
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The PySB unit tests fail with the latest Kappa at time of writing (commit https://github.com/Kappa-Dev/KaSim/commit/9c4b41905123055be4c5334c08744e27de6828b8).
Several "no such file or directory" erro…
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I had some problems with a simple model that turned out to be due to the use of a parameter with the name 's0_to_s1_k'. (referring to Bax in 'state 1' going to Bax in 'state 2'). The errors arise from…
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Hi,
Apologies if this has been addressed previously but I couldn't find it. I've just downloaded and installed run the hello_pysb.py example and I'm getting lots of warning messages of the form below.…