README.txt
setup.cfg
setup.py
doc/Makefile
doc/make.bat
doc/source/ChangeLog.rst
doc/source/applications.rst
doc/source/authors.rst
doc/source/biblio.rst
doc/source/conf.py
doc/source/contribute.rst
doc/source/index.rst
doc/source/quickstart.rst
doc/source/references.rst
doc/source/todo.rst
doc/source/userguide.rst
doc/source/_static/copybutton.js
share/data/MD-MultipleCellLines.csv
share/data/MD-Test.csv
share/data/MD-Test2.csv
share/data/MD-ToyMMB.csv
share/data/MD-one_exp.csv
share/data/MD-one_inhibitor.csv
share/data/MD-one_stimulus.csv
share/data/MD-unnorm.csv
share/data/PKN-Test.sif
share/data/PKN-ToyMMB.net
share/data/PKN-ToyMMB.sif
share/data/README.txt
share/data/adjacency_matrix.csv
share/data/adjacency_names.csv
share/data/data.sop
share/data/kinetic.csv
share/data/metabolites
share/data/midas.xml
share/data/reactions
share/data/metabolites_samples/ExampleNetwIdent/app_para.m
share/data/metabolites_samples/ExampleNetwIdent/assembly
share/data/metabolites_samples/ExampleNetwIdent/examplenetwident.png
share/data/metabolites_samples/ExampleNetwIdent/examplenetwident_layout.dat
share/data/metabolites_samples/ExampleNetwIdent/macromolecule_synthesis
share/data/metabolites_samples/ExampleNetwIdent/macromolecules
share/data/metabolites_samples/ExampleNetwIdent/metabolites
share/data/metabolites_samples/ExampleNetwIdent/metabolites.simp
share/data/metabolites_samples/ExampleNetwIdent/metabolites.simplest
share/data/metabolites_samples/ExampleNetwIdent/reactions
share/data/metabolites_samples/ExampleNetwIdent/reactions.nocrosst
share/data/metabolites_samples/ExampleNetwIdent/reactions.simp
share/data/metabolites_samples/ExampleNetwIdent/reactions.simplest
share/data/metabolites_samples/ExampleNetwIdent/reactions2CreateData
share/data/metabolites_samples/ExampleNetwIdent/reactions2Optimize
share/data/metabolites_samples/ExampleNetwIdentNoCrossT/app_para.m
share/data/metabolites_samples/ExampleNetwIdentNoCrossT/assembly
share/data/metabolites_samples/ExampleNetwIdentNoCrossT/examplenetwident.png
share/data/metabolites_samples/ExampleNetwIdentNoCrossT/examplenetwident_layout.dat
share/data/metabolites_samples/ExampleNetwIdentNoCrossT/macromolecule_synthesis
share/data/metabolites_samples/ExampleNetwIdentNoCrossT/macromolecules
share/data/metabolites_samples/ExampleNetwIdentNoCrossT/metabolites
share/data/metabolites_samples/ExampleNetwIdentNoCrossT/reactions
share/data/metabolites_samples/ExampleNetwIdentNoCrossT/reactions2CreateData
share/data/metabolites_samples/ExampleNetwIdentNoCrossT/reactions2Optimize
share/data/metabolites_samples/FasTnfTrail/app_para.m
share/data/metabolites_samples/FasTnfTrail/assembly
share/data/metabolites_samples/FasTnfTrail/fastnftrail.png
share/data/metabolites_samples/FasTnfTrail/fastnftrail_layout.dat
share/data/metabolites_samples/FasTnfTrail/macromolecule_synthesis
share/data/metabolites_samples/FasTnfTrail/macromolecules
share/data/metabolites_samples/FasTnfTrail/metabolites
share/data/metabolites_samples/FasTnfTrail/reactions
share/data/metabolites_samples/FusedLDPSN/metabolites
share/data/metabolites_samples/FusedLDPSN/reactions
share/data/metabolites_samples/HepatHCCs/app_para.m
share/data/metabolites_samples/HepatHCCs/assembly
share/data/metabolites_samples/HepatHCCs/hepatingenuity.png
share/data/metabolites_samples/HepatHCCs/hepatingenuity_layout.dat
share/data/metabolites_samples/HepatHCCs/macromolecule_synthesis
share/data/metabolites_samples/HepatHCCs/macromolecules
share/data/metabolites_samples/HepatHCCs/metabolites
share/data/metabolites_samples/HepatHCCs/reactions
share/data/metabolites_samples/HepatHCCs/reactions.OK
share/data/metabolites_samples/HepatHCCs/reactions.notimes
share/data/metabolites_samples/HepatHCCs/reactions.notimescales
share/data/metabolites_samples/HepatHCCs/reactions.searchinsilicogenerator
share/data/metabolites_samples/HepatHCCs/reactions.var1
share/data/metabolites_samples/HepatHCCs/reactions.ver1
share/data/metabolites_samples/HepatHCCs/reactions_notes
share/data/metabolites_samples/LDPSN-DREAM/metabolites
share/data/metabolites_samples/LDPSN-DREAM/reactions
share/data/metabolites_samples/LDPSN-DREAM-simpler/metabolites
share/data/metabolites_samples/LDPSN-DREAM-simpler/reactions
share/data/metabolites_samples/LDPSN-Ingenuity/metabolites
share/data/metabolites_samples/LDPSN-Ingenuity/reactions
share/data/metabolites_samples/LDPSN-Ingenuity-NoNeg/metabolites
share/data/metabolites_samples/LDPSN-Ingenuity-NoNeg/reactions
share/data/metabolites_samples/LDPSN-Ingenuity-NoNeg-Extend/metabolites
share/data/metabolites_samples/LDPSN-Ingenuity-NoNeg-Extend/reactions
share/data/metabolites_samples/LDPSN-Ingenuity-NoNeg-Extend1b/metabolites
share/data/metabolites_samples/LDPSN-Ingenuity-NoNeg-Extend1b/reactions
share/data/metabolites_samples/LDPSN-Ingenuity-NoNegIns/metabolites
share/data/metabolites_samples/LDPSN-Ingenuity-NoNegIns/reactions
share/data/metabolites_samples/LDPSN-Ingenuity-NoNegIns4Rec/metabolites
share/data/metabolites_samples/LDPSN-Ingenuity-NoNegIns4Rec/reactions
share/data/metabolites_samples/LDPSN-IngenuityFourHCC/metabolites
share/data/metabolites_samples/LDPSN-IngenuityFourHCC/reactions
share/data/metabolites_samples/LDPSN-IngenuityNeg/metabolites
share/data/metabolites_samples/LDPSN-IngenuityNeg/reactions
share/data/metabolites_samples/LDPSN-IngenuityNeg/reactions (Autosaved)
share/data/metabolites_samples/LDPSN-IngenuityOldMod/metabolites
share/data/metabolites_samples/LDPSN-IngenuityOldMod/reactions
share/data/metabolites_samples/SchlatterApopt/metabolites
share/data/metabolites_samples/SchlatterApopt/reactions
share/data/metabolites_samples/SchlatterApopt/readme
share/data/metabolites_samples/TcellReduced/.__afsB7EB
share/data/metabolites_samples/TcellReduced/app_para.m
share/data/metabolites_samples/TcellReduced/metabolites
share/data/metabolites_samples/TcellReduced/metabolites_notes
share/data/metabolites_samples/TcellReduced/reactions
share/data/metabolites_samples/TcellReduced/reactions_notes
share/data/metabolites_samples/TcellReduced/tcr_map_diamodel.png
share/data/metabolites_samples/TcellSmall/00readme.txt
share/data/metabolites_samples/TcellSmall/TCR_Struct_klein.png
share/data/metabolites_samples/TcellSmall/app_para.m
share/data/metabolites_samples/TcellSmall/assembly
share/data/metabolites_samples/TcellSmall/macromolecule_synthesis
share/data/metabolites_samples/TcellSmall/macromolecules
share/data/metabolites_samples/TcellSmall/metabolites
share/data/metabolites_samples/TcellSmall/noinputs
share/data/metabolites_samples/TcellSmall/reactions
share/data/metabolites_samples/TcellSmall/timescale0.val
share/data/metabolites_samples/TcellSmall/timescale1.val
share/data/metabolites_samples/TcellSmall/timescale2.val
share/data/metabolites_samples/U937Signaling/app_para.m
share/data/metabolites_samples/U937Signaling/assembly
share/data/metabolites_samples/U937Signaling/macromolecule_synthesis
share/data/metabolites_samples/U937Signaling/macromolecules
share/data/metabolites_samples/U937Signaling/metabolites
share/data/metabolites_samples/U937Signaling/metabolites.bak1
share/data/metabolites_samples/U937Signaling/metabolites.bak2
share/data/metabolites_samples/U937Signaling/metabolites.bak3
share/data/metabolites_samples/U937Signaling/metabolites.bak4
share/data/metabolites_samples/U937Signaling/metabolites_notes
share/data/metabolites_samples/U937Signaling/reactions
share/data/metabolites_samples/U937Signaling/reactions.bak3
share/data/metabolites_samples/U937Signaling/reactions.bak4
share/data/metabolites_samples/U937Signaling/reactions_notes
share/data/metabolites_samples/U937Signaling/u937signaling.png
share/data/metabolites_samples/U937Signaling/u937signaling_layout.dat
share/data/metabolites_samples/U937Signaling/u937signaling_prev.png
share/data/metabolites_samples/sigtoynet/00readme.txt
share/data/metabolites_samples/sigtoynet/app_para.m
share/data/metabolites_samples/sigtoynet/assembly
share/data/metabolites_samples/sigtoynet/macromolecule_synthesis
share/data/metabolites_samples/sigtoynet/macromolecules
share/data/metabolites_samples/sigtoynet/metabolites
share/data/metabolites_samples/sigtoynet/reactions
share/data/metabolites_samples/sigtoynet/toynet.gif
share/data/metabolites_samples/sigtoynet/toynet.pcx
share/data/metabolites_samples/sigtoynet/toynet_logical.fig
share/data/metabolites_samples/sigtoynet/toynet_logical.gif
src/cellnopt/__init__.py
src/cellnopt.core.egg-info/PKG-INFO
src/cellnopt.core.egg-info/SOURCES.txt
src/cellnopt.core.egg-info/dependency_links.txt
src/cellnopt.core.egg-info/namespace_packages.txt
src/cellnopt.core.egg-info/requires.txt
src/cellnopt.core.egg-info/top_level.txt
src/cellnopt/core/__init__.py
src/core/XMLMidas.py
src/core/__init__.py
src/core/adj2sif.py
src/core/analysis.py
src/core/asp.py
src/core/cnograph.py
src/core/converter.py
src/core/graphviz_tools.py
src/core/makecnolist.py
src/core/matfun.py
src/core/metabolites.py
src/core/midas.py
src/core/models.py
src/core/normalisation.py
src/core/plot.py
src/core/reactions.py
src/core/sbml.py
src/core/sif.py
src/core/sif2asp.py
src/core/sop2sif.py
src/core/tools.py
src/core/io/__init__.py
src/core/io/csv2pd.py
src/core/io/eda.py
src/core/io/kinexus.py
test/MCP_HepG2mod4.csv
test/MCP_HepG2mod4_norm.csv
test/test_adj2sif.py
test/test_asp.py
test/test_cnograph.py
test/test_cnolist.py
test/test_converter.py
test/test_eda.py
test/test_kinexus.py
test/test_metabolites.py
test/test_midas.py
test/test_normalisation.py
test/test_reactions.py
test/test_sif.py
test/test_sif2asp_net.py
test/test_sop2sif.py
test/test_xmlmidas.py