cdanielmachado / framed Goto Github PK

So that a solution is easy to look at by "print solution", such as:

Status: Optimal
Objective: 9.034

Hi,

Model simplify function would benefit from having argument constraints:

c_model = simplify(c_model, constraints=environmental_conditions, inplace=False)

This would allow to retrieve a context-specific model without changing the original one.

Thanks,

Hi, I am exactly following dfba tutorial for batch fermentation. I have encountered many problems so far:

1- ImportError: cannot import name 'CONSTRAINT_BASED'

If I remove CONSTRAINT_BASED from the script, then I see this error when typing fix_cobra_model(ec_core_model):
2- AttributeError: 'Reaction' object has no attribute 'lb'

Removing fix_cobra_model(ec_core_model), I get this error:

3- AttributeError: 'Model' object has no attribute 'biomass_reaction'

Then, removing ec = Ecoli(ec_core_model, id='ecoli'), I get this error:

4- AttributeError: 'Model' object has no attribute 'update'
This happens when it reaches to : result = dFBAm(bioreactor, t0, tf, dt, initial_conditions, solver, verbose)

I really need help and any advice is greatly appreciated. I have similar problems for fed-batch example.
Thanks

Hi,
In the metabolite class, the value of "constant" parameter present in the SBML files is not saved.
Moreover, when boundaryCondition="true" constant="true" the rate law must be "0" even if the metabolite has a kinetic law associated in the SBML model.

Importing models doesn't support scientific notation yet, but exporting models will generate scientific notation for coefficients below 1e-5.

Reactions with simultaneous reactants and products are not properly supported yet, only the last occurrence of the metabolite in the equation is stored.

This must be fixed, so that this happens instead:

A + B -> C + B => A -> C

A + 2 B -> C + B => A + B -> C

Hi,
While importing our model some of the exchange reactions are being identified as sink reactions.

Thanks,

The metabolites without an associated kinetic law will not have variation. So, in the function "print_balance", when the len of the variable "terms" == 0, the return value zero.

@cdanielmachado I meet error when I try to use framed in my computer. Can you help me solve it?
import carveme
Traceback (most recent call last):
File "/Users/luho/PycharmProjects/python learning/venv/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2910, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "", line 1, in
import framed
File "/Applications/PyCharm CE.app/Contents/helpers/pydev/_pydev_bundle/pydev_import_hook.py", line 20, in do_import
module = self._system_import(name, *args, **kwargs)
File "/Users/luho/PycharmProjects/python learning/venv/lib/python3.6/site-packages/framed/init.py", line 1, in
from .cobra.deletion import reaction_deletion, gene_deletion
File "/Applications/PyCharm CE.app/Contents/helpers/pydev/_pydev_bundle/pydev_import_hook.py", line 20, in do_import
module = self._system_import(name, *args, **kwargs)
File "/Users/luho/PycharmProjects/python learning/venv/lib/python3.6/site-packages/framed/cobra/deletion.py", line 7, in
from simulation import FBA, pFBA, MOMA, lMOMA, ROOM
File "/Applications/PyCharm CE.app/Contents/helpers/pydev/_pydev_bundle/pydev_import_hook.py", line 20, in do_import
module = self._system_import(name, *args, **kwargs)
ModuleNotFoundError: No module named 'simulation'

Then we don't have to pass it through all kinds of function calls

Reference:
http://www.biomedcentral.com/1752-0509/6/42

With a generic interface for parallelizing any sort of problems.

Similar to the Pool.map() function in python's multiprocessing module.

Create a centralized configuration file with common configuration options for all solvers:

• set pre-solve
• set tolerances
• etc...

Default solver preferences can maybe go here as well rather than inside solvers/_ init _.py

Please change "target" to "objRxn" in FBA and pFBA.

Start storing the models with the proper fbc package rather than old style annotations.

For more details:

http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/Flux_Balance_Constraints_(flux)

Framed currently allows creating metabolites without assigned compartment (to facilitate creation of models from plain text). However, this cannot be saved to valid SBML. Must add a default compartment.