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Using the attached .faa file and through the ModelSEED platform I built the also attached .sbml growing model.
I am now trying to reproduce that through the CLI and here is what I have done so far:
# modelseedpyfrommodelseedpyimportKBaseMediaPkgfrommodelseedpyimportMSBuilder, MSGenome# cobrakbase importcobrakbasegenome=MSGenome.from_fasta('data/genomes/s_infantis/s_inf_all_contigs_default.faa')
kbase_api=cobrakbase.KBaseAPI()
kb_template=kbase_api.get_from_ws("GramNegModelTemplateV4","NewKBaseModelTemplates")
model=MSBuilder.build_metabolic_model('salmonella infantis', genome, template=kb_template, allow_all_non_grp_reactions=True)
#Pulling a KBase media to specify an environment for gapfillingmedia=kbase_api.get_from_ws("Complete","KBaseMedia")
#Gapfilling the model in the specified mediamodel=MSBuilder.gapfill_model(model, "bio1", kb_template, media)
#Applying the same media to the resulting modelkmp=KBaseMediaPkg(model)
kmp.build_package(media)
However, my media is just empty and therefore, my new model is not growing.
Hi!
Using the attached
.faa
file and through the ModelSEED platform I built the also attached.sbml
growing model.I am now trying to reproduce that through the CLI and here is what I have done so far:
However, my
media
is just empty and therefore, my new model is not growing.I would like to ask you:
Thank you very much for your time and help!
p.s. I have a
.txt
suffix on the files so GitHub allows them as attacheds_inf_all_contigs_default.faa.txt
s_inf_from_modelseed.sbml.txt
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