sbmlutils: Python utilities for SBML¶
sbmlutils is a collection of python utilities for working with SBML models
implemented on top of the libSBML python bindings.
Features among others
- HTML reports of SBML models
- helpers for model creation, manipulation, and annotation
- interpolation functions to add experimental data to models
- dynamic flux balance analysis (DFBA)
- file converters (XPP)
The project code is available from https://github.com/matthiaskoenig/sbmlutils.
Installation¶
pip install sbmlutilsSBML report¶
- create HTML reports of SBML files
- easy navigation and filtering
fbcandcompsupport
In [2]:
from sbmlutils.report import sbmlreport
sbmlreport.create_sbml_report('./examples/glucose/Hepatic_glucose_3.xml',
out_dir='./examples/glucose', validate=True)
SBML model creator¶
- helper functions for generation of SBML models
- constructors with all fields
- patterns (like generate
ParametersforAssignmentRules) fbcandcomphelpers- unit support
https://sbmlutils.readthedocs.io/en/latest/notebooks/modelcreator.html#Create-FBA-Model
Misc¶
- Data to splines & piecewise functions
- Model annotation based on flat files and regular expressions
- converters (XPP -> SBML)
Dynamic FBA (DFBA)¶
- implementation of dynamic FBA based on comp and fbc
- model encoding & simulation
In [3]:
from __future__ import absolute_import, print_function
import os
import tempfile
import sbmlutils
from sbmlutils import dfba
from sbmlutils.dfba import utils
from sbmlutils.dfba.toy_wholecell import settings as toysettings
from sbmlutils.dfba.toy_wholecell import model_factory as toyfactory
from sbmlutils.dfba.toy_wholecell import simulate as toysimulate
test_dir = tempfile.mkdtemp()
# create toy model
toyfactory.create_model(test_dir)
sbml_path = os.path.join(utils.versioned_directory(test_dir, toyfactory.version),
toysettings.top_file)
print(sbml_path)
In [4]:
from IPython.display import display, HTML
# simulate
dfs = toysimulate.simulate_toy(sbml_path, test_dir, dts=[1.0], figures=False)
display(dfs[0].head(10))
toysimulate.print_species(dfs=dfs)
toysimulate.print_fluxes(dfs=dfs)
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