PyFBA
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linsalrob
A python implementation of flux balance analysis to model microbial metabolism
I recently installed pyfba v 2.62 (using python3) and I was running through the "How to create and run a gap-filled FBA from PATRIC" iPython notebook. I kept receiving an...
I have followed the instructions in creating the ModelSEEDDatabase variable as shown below; thomas@Kiwi:~/PyFBA$ echo $ModelSEEDDatabase /home/thomas/PyFBA/ModelSEEDDatabase However when I test the setup.py code the following occurs; thomas@Kiwi:~/PyFBA$ python setup.py...
Hi, I am trying to run the model_seed.py and it is depended to ComplexRoles.tsv and TemplateReactions.tsv files. Yet I could not figure out how I will dump/extract these files. I...
Hi Rob, I have successfully installed PyFBA using python2. However, I failed to update to python3 after following the instructions (recompile pyglpk). The output is "SyntaxError: Missing parentheses in call...
The [ModelSEEDDatabase](https://github.com/ModelSEED/ModelSEEDDatabase) has been completely refactored and cleaned up but is now incompatible with PyFBA parsing scripts. One of the latest versions that is currently compatible with PyFBA is `c4ba1c6...
We need to implement a mechanism to correct role mapping from RAST to the biochemistry tables. This file [role_corrections.txt](https://github.com/linsalrob/PyFBA/files/272439/role_corrections.txt) has a two column table with RAST role and Biochemistry role....
Hey there! I recently installed PyFBA v2.62 and ran the tests (sudo python3 setup.py test). The tests ended up with an Type Error (argument of type 'module' is not iterable)...
