sbrg / ecolime Goto Github PK

Trying to run prototype 41.

ipython nbconvert --to script prototype_41.ipynb
# comment out TODOs that converted incorrectly
python prototype_41.py

I get the following error:

Traceback (most recent call last):
  File "prototype_41.py", line 461, in <module>
    me.prune()
  File "/Users/zaking/sharedrepos/minime/minime/core/MEModel.py", line 144, in prune
    raise e
TypeError: cannot determine truth value of
-0.0224722222222222*mu + 1 < 0

From original model:

• biotin biosynthesis

Newly blocked:

When solving the model, the objective function is to maximize the dummy-protein(CPLX-dummy). Can we change the objective function, such as setting the maximum acetate production? Is it possible to achieve functions like optknock, maximizing the target product with maximized biomass?

Similar to #9, there seem to be some import errors and missing functions. I found add_modification_data missing; mentioned in ribosome.py.

Apply growth rate dependent DNA demand as reaction bounds, not metabolite coefficients

Confirm coefficients are calculated correctly

can we remove dashes from complex names for tab-completion of ME reactions?

e.g. model.reactions.GAPD_FWD_GAPDH-A-CPLX

At /ecolime/ecolime/init.py line 1
"import scripts" raises error when running build_ME_model.ipynb, no module named scripts
Removing this line does not affect the model creation process

Hi，I want to build other organism genome-model of metabolism and expression (ME-model). I don’t know how to obtain accurate effective turnover rate (Keff) for metabolic enzymes. When you reconstructed E.coli ME-model, how did you get the Keff for each enzyme.
Thank you!

Hi, I've been trying to use the make_composition_piechart from the ecolime/ecolime/characterization/biomass_allocation.py scrip but I keep geting a KeyError: 'SA_demand_Inner_Membrane' and I was hoping that you could help me figure out why.

This key isn't in my x_dict nor any of the "SA_demand". To make my model I used the build_ME_model.ipynb script.

Do I need to use another script before the make_composition_piechart function?

Thank you.

def getGC_content(genbank_file):
for seqrecord in SeqIO.parse(genbank_file, 'genbank'):
sequence = str(seqrecord.seq)
GC_fraction = (sequence.count('G')+sequence.count('C'))/float(sequence.count('G')+sequence.count('C')+sequence.count('T')+sequence.count('A'))
return GC_fraction

• ManXYZ complex stoichiometry it incorrect

EG10544-MONOMER_mod_palmitate cannot be made?

for rxn in me.metabolites.get_by_id('EG10544-MONOMER_mod_palmitate').reactions:
print rxn.id, ':', rxn.reaction
print

ALPATG160pp1_FWD_EG10168-MONOMER : pg160_p + EG10544-MONOMER_mod_palmitate + 6.3610692415329e-6*mu EG10168-MONOMER --> 2agpg160_p + EG10544-MONOMER

ALPATE160pp1_FWD_EG10168-MONOMER : EG10544-MONOMER_mod_palmitate + 6.3610692415329e-6*mu EG10168-MONOMER + pe160_p --> 2agpe160_p + EG10544-MONOMER

Hi! I tried to use the get_protein_distribution from the ecolime/ecolime/characterization/biomass_allocation.py scrip but I get the next error:

AttributeError: 'generator' object has no attribute 'get_by_id'

from the line

--> 185 protein_mass = model.translation_data.get_by_id(protein).mass

Thank you!

Looks like you have a circular import. If I run from minime.core.MEReactions import MetabolicReaction:

In [1]: from minime.core.MEReactions import MetabolicReaction
cobra/io/sbml3.py:23 UserWarning: Install lxml for faster SBML I/O
cobra/io/__init__.py:10 UserWarning: cobra.io.sbml requires libsbml
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-1-15aa313e9471> in <module>()
----> 1 from minime.core.MEReactions import MetabolicReaction

/Users/zaking/sharedrepos/minime/minime/__init__.py in <module>()
      1 from core.Components import *
----> 2 from core.MEModel import *
      3 from core.MEReactions import *
      4 from core.ProcessData import *

/Users/zaking/sharedrepos/minime/minime/core/MEModel.py in <module>()
      4 from cobra import Model, DictList
      5
----> 6 from minime.core.MEReactions import *
      7 from minime.util import mu
      8

/Users/zaking/sharedrepos/minime/minime/core/MEReactions.py in <module>()
     12 from minime.core.Components import *
     13
---> 14 from ecolime.ribosome import translation_stop_dict
     15
     16

/Users/zaking/sharedrepos/ecolime/ecolime/__init__.py in <module>()
----> 1 from flat_files import get_m_model

/Users/zaking/sharedrepos/ecolime/ecolime/flat_files.py in <module>()
      6
      7
----> 8 from minime.core.MEReactions import MetabolicReaction
      9 import cobra
     10 import pandas

ImportError: cannot import name MetabolicReaction

At build_ME_model.ipynb, part 8, corrections, changing PFL info (#this reaction was edited based on iJO1366 GPR) does not update me.stoichiometric_data.PFL.parent_reactions. This causes error when trying to knockout PFL metabolic reactions using parent_reactions call.