.gitignore
LICENSE
README.md
README.rst
logo_300px.png
setup.cfg
setup.py
doc/Makefile
doc/cobra.rst
doc/conf.py
doc/index.rst
doc/install.rst
doc/kinetic.rst
doc/requirements.txt
doc/start.rst
doc/apidoc/framed.bioreactor.rst
doc/apidoc/framed.cobra.rst
doc/apidoc/framed.community.rst
doc/apidoc/framed.experimental.rst
doc/apidoc/framed.io.rst
doc/apidoc/framed.kinetic.rst
doc/apidoc/framed.model.rst
doc/apidoc/framed.omics.rst
doc/apidoc/framed.rst
doc/apidoc/framed.solvers.rst
doc/apidoc/framed.unittests.rst
doc/apidoc/modules.rst
doc/images/flux_envelope.png
doc/images/sampling.png
doc/images/time_course.png
examples/bioreactor/ex_dfba1.py
examples/bioreactor/ex_dfba2.py
examples/bioreactor/ex_dyssco.py
examples/bioreactor/ex_envelope.py
examples/models/BIOMD0000000051.xml
examples/models/Ec_iAF1260_flux1.xml
examples/models/cbmodel_copy.txt
examples/models/cbmodel_copy.xml
examples/models/cbmodel_copy2.xml
examples/models/cbmodel_copy3.xml
examples/models/ecoli_core_bigg2.0.xml
examples/models/ecoli_core_model.xml
examples/models/odemodel_copy.xml
examples/models/prey_predator.xml
examples/models/toy/A.xml
examples/models/toy/B.xml
examples/models/toy/C.xml
examples/models/toy/D.xml
framed.egg-info/PKG-INFO
framed.egg-info/SOURCES.txt
framed.egg-info/dependency_links.txt
framed.egg-info/requires.txt
framed.egg-info/top_level.txt
scripts/framed-deletions
src/framed/__init__.py
src/framed.egg-info/PKG-INFO
src/framed.egg-info/SOURCES.txt
src/framed.egg-info/dependency_links.txt
src/framed.egg-info/requires.txt
src/framed.egg-info/top_level.txt
src/framed/bioreactor/__init__.py
src/framed/bioreactor/base.py
src/framed/bioreactor/bioreactors.py
src/framed/bioreactor/dfba.py
src/framed/bioreactor/dyssco.py
src/framed/cobra/__init__.py
src/framed/cobra/deletion.py
src/framed/cobra/ensemble.py
src/framed/cobra/essentiality.py
src/framed/cobra/genewise.py
src/framed/cobra/phaseplane.py
src/framed/cobra/plotting.py
src/framed/cobra/reconstruction.py
src/framed/cobra/simulation.py
src/framed/cobra/strain_design.py
src/framed/cobra/thermodynamics.py
src/framed/cobra/variability.py
src/framed/community/__init__.py
src/framed/community/model.py
src/framed/experimental/__init__.py
src/framed/experimental/benchmark.py
src/framed/experimental/elements.py
src/framed/experimental/fluxutils.py
src/framed/experimental/marge.py
src/framed/experimental/mass_conservation.py
src/framed/experimental/medium.py
src/framed/experimental/metanetx.py
src/framed/experimental/reduction.py
src/framed/experimental/sampling.py
src/framed/experimental/visualization/KEGG.py
src/framed/experimental/visualization/__init__.py
src/framed/experimental/visualization/escher_maps.py
src/framed/experimental/visualization/iPATH.py
src/framed/io/__init__.py
src/framed/io/bioopt.py
src/framed/io/cache.py
src/framed/io/plaintext.py
src/framed/io/sbml.py
src/framed/kinetic/__init__.py
src/framed/kinetic/fitting.py
src/framed/kinetic/plotting.py
src/framed/kinetic/sampling.py
src/framed/kinetic/simulation.py
src/framed/model/__init__.py
src/framed/model/cbmodel.py
src/framed/model/environment.py
src/framed/model/fixes.py
src/framed/model/model.py
src/framed/model/odemodel.py
src/framed/model/parser.py
src/framed/model/transformation.py
src/framed/omics/__init__.py
src/framed/omics/dataset.py
src/framed/omics/simulation.py
src/framed/solvers/__init__.py
src/framed/solvers/cplex_interface.py
src/framed/solvers/gurobi_interface.py
src/framed/solvers/solver.py
src/framed/unittests/__init__.py
src/framed/unittests/kinetic.py
src/framed/unittests/tests_cobra.py
src/framed/unittests/tests_sbml.py