cobrame
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SBRG
A COBRApy extension for genome-scale models of metabolism and expression (ME-models)
I am running into an error with the `build_me_model.ipynb`: ``` --------------------------------------------------------------------------- TypeError Traceback (most recent call last) /Users/bsp/unix/ecolime/ecolime/build_me_model.ipynb Cell 5' in () 2 ijo_directory = join(flat_files.ecoli_files_dir, 'iJO1366.json') 3 ijo =...
Hi,I would like to change the objective function from maximize biomass to ATPM in COBRAME. Just changing the objective_coefficient as follows results in a an error where me.solution is NOTYPE....
Hi, when you built Escherichia coli ME-model, why did you divide the iJO1366 biomass equations into several different equations such as biomass_constituent_demand, lipid components and DNA demand requirements.
Hi folks, I am trying to load [iJL965_ME.pickle](https://www.editorialmanager.com/pcompbiol/download.aspx?id=965746&guid=0fa8a190-12ef-4dd3-b527-fa15dfe77246&scheme=1) in python2 and I am unable to because I don't have access to the minime library. ```python from cPickle import dump,load me...
Dear all, Is there any planned COBRAme workshop for this year? For sure the user community will beneficit from it. Best and thanks, Fair.
Hi folks, If you do the following in the Docker image: ```python import pickle, cobrame with open('/home/meuser/me_models/iJL1678b.pickle', 'rb') as f: me = pickle.load(f) me.remove_genes_from_model( ['b0002'] ) ``` Then I get...
Using lowercase nucleotide sequences when creating a translation reactions gives an unclear error message.
The full ComplexData instance doesn't need to be linked to the MetabolicReaction. The complex id is all that is required