carrascomj on devel
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ShortestElementaryFluxModes. Sorry no documentation yet. But this unit test probably helps https://github.com/biosustain/cameo/blob/6babaffb50ea1c5f342fec255574f36e9350fa0e/tests/test_flux_analysis.py#L303. This is really experimental though. We were planning to use this for http://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1003378 but so far we have not got it completely right I think (need to talk Kristian). I think the application of real EFM software is fairly limited in both cobrapy and cameo. Calculating the shortest EFMs (like described in the paper) has some value though. You mentioned that you had nice wrappers for some of the better EFM tools in your cobrapy fork. Why not just make nice separate packages since they come with some heavy dependencies? I think we should try to avoid making cobrapy larger. With Python packaging being slightly less traumatic now, I think it makes sense to have many packages that do certain things very well. Of course we could highlight those on http://opencobra.github.io/.
ShortestElementaryFluxModes(model)and iterate over this object. This will return all flux modes ordered by length. I'm fairly certain this method in cameo works correctly. The MinimalCutSetsEnumerator is based on http://bioinformatics.oxfordjournals.org/content/28/3/381.short , but there still seems to be some issues with our implementation
efmtoolfrom marco terzer (doi:10.1093/bioinformatics/btn401) for EFMs and the berge algorithm from Christian Jungreuthmayer (http://www.biomedcentral.com/1471-2105/14/318) for minimum cut sets. Java / C++, respectively, though.
with model: ...(like here https://twitter.com/DDDeCaF/status/841974326526128128). The latest cobrapy release also uses optlang. We're going to migrate cameo soon to the latest cobrapy release too.
Can one add reactions to cameo models in a single line? Like in model.add("a + b -> c") ?
You can build a reaction from a string and then add that to your model. https://cobrapy.readthedocs.io/en/latest/cobra.core.html#cobra.core.reaction.Reaction.build_reaction_from_string
I have a problem with cameo, specifically OptGene, and would be very delighted about your help.
After importing OptGene, my model, and fba as simulation method, I tried to run OptGene:
result = optgene.run(target='r_4054',
Upon this, Jupiter stops and throws me the error "show() got an unexpected keyword argument 'notebook_handle'". Do you know how to fix that?
If I try the same in the terminal to avoid the Jupiter Notebook the process finishes without error, but the result seems to be empty?
# Empty DataFrame # Columns: [reactions, genes, size, fva_min, fva_max, target_flux, biomass_flux, yield, fitness] # Index: 
I would be very happy about your ideas where the problem is.
Many thanks and kind regards,