.coveragerc
.gitignore
LICENSE
MANIFEST.in
PKG-INFO
README.md
pyproject.toml
requirements.txt
setup.cfg
setup.py
tox.ini
.github/workflows/main.yaml
docs/Makefile
docs/conf.py
docs/doc_gen.sh
docs/envelope.png
docs/evaluation.md
docs/germ.md
docs/germ_overview.png
docs/index.rst
docs/install.md
docs/main.md
docs/make.bat
docs/mewpy-2.png
docs/mewpy-3.png
docs/mewpy-arch.png
docs/mewpy.io.rst
docs/mewpy.model.data.rst
docs/mewpy.model.rst
docs/mewpy.optimization.inspyred.rst
docs/mewpy.optimization.jmetal.rst
docs/mewpy.optimization.rst
docs/mewpy.problems.rst
docs/mewpy.regulation.rst
docs/mewpy.rst
docs/mewpy.simulation.rst
docs/mewpy.utils.rst
docs/mewpy.visualization.rst
docs/modules.rst
docs/optimization.md
docs/options.md
docs/problems.md
docs/requirements.txt
docs/simulation.md
docs/_static/default.css
examples/01-simulation.ipynb
examples/02-optimization.ipynb
examples/03-kinetic.ipynb
examples/04-ROUproblem.ipynb
examples/05-GOUproblem.ipynb
examples/06-GeckoKOProblem.ipynb
examples/07-CoFactorSwap.ipynb
examples/08-community.ipynb
examples/09-crossfeeding.ipynb
examples/GERM_Models.ipynb
examples/GERM_Models_analysis.ipynb
examples/README.md
examples/models/ec-protein-gene.csv
examples/models/yeast-protein-gene.csv
examples/models/autopacmen/iJO1366_2019_06_25_GECKO.xml
examples/models/autopacmen/iJO1366_sMOMENT_2019_06_25.xml
examples/models/autopacmen/iJO1366_sMOMENT_2019_06_25_GECKO_ANALOGON.xml
examples/models/autopacmen/iJO1366_sMOMENT_2019_06_25_STANDARD_EXCHANGE_SCENARIO.xml
examples/models/ec/e_coli_core.xml.gz
examples/models/ec/eciML1515_batch.xml
examples/models/ec/iJO1366.xml
examples/models/ec/iJO1366SL.xml
examples/models/ec/iML1515.xml
examples/models/ec/nontargets#RK#iJO1366SL#[lim-aerobic#glucose].txt
examples/models/ec/nontargets#ROU#iJO1366SL#[lim-aerobic#glucose].txt
examples/models/germ/SampleNet.xml
examples/models/germ/SampleRegNet.csv
examples/models/germ/e_coli_core.xml
examples/models/germ/e_coli_core_trn.csv
examples/models/germ/e_coli_core_trn_original.csv
examples/models/germ/iJR904.xml
examples/models/germ/iMC1010.csv
examples/models/germ/iMC1010_original.csv
examples/models/germ/iMM904.xml
examples/models/germ/iMM904_experiments.csv
examples/models/germ/iMM904_gene_expression.csv
examples/models/germ/iMM904_gene_expression_prediction.csv
examples/models/germ/iMM904_influence.csv
examples/models/germ/iMM904_trn.csv
examples/models/germ/iNJ661.xml
examples/models/germ/iNJ661_gene_expression.csv
examples/models/germ/iNJ661_trn.csv
examples/models/kinetic/Jahan2016_chemostat_fixed.xml
examples/models/kinetic/chassagnole2002.xml
examples/models/optram/TFnames.csv
examples/models/optram/mgene.csv
examples/models/optram/regnet.csv
examples/models/optram/yeast-essential.xlsx
examples/models/optram/yeast_7.6-optram.xml
examples/models/yeast/iMM904.xml.gz
examples/models/yeast/iMM904SL_v6.xml
examples/models/yeast/nontargets#RK#iMM904SL_v6#[lim-aerobic#glucose].txt
examples/models/yeast/nontargets#ROU#iMM904SL_v6#[lim-aerobic#glucose].txt
examples/models/yeast/yeast_7.6.xml
examples/scripts/cobra_geckoopt.py
examples/scripts/eacomparison.py
examples/scripts/geckoopt.py
examples/scripts/geckosimulation.py
examples/scripts/geneopt.py
examples/scripts/germ_models_analysis.py
examples/scripts/gpr_eval.py
examples/scripts/ids-mapping.csv
examples/scripts/kinetic.py
examples/scripts/load.py
examples/scripts/optorf.py
examples/scripts/optram.py
examples/scripts/sddb.py
examples/scripts/smoment.py
src/mewpy/__init__.py
src/mewpy.egg-info/PKG-INFO
src/mewpy.egg-info/SOURCES.txt
src/mewpy.egg-info/dependency_links.txt
src/mewpy.egg-info/requires.txt
src/mewpy.egg-info/top_level.txt
src/mewpy.egg-info/zip-safe
src/mewpy/cobra/__init__.py
src/mewpy/cobra/medium.py
src/mewpy/cobra/parsimonious.py
src/mewpy/cobra/util.py
src/mewpy/com/__init__.py
src/mewpy/com/analysis.py
src/mewpy/com/com.py
src/mewpy/com/regfba.py
src/mewpy/com/similarity.py
src/mewpy/com/steadycom.py
src/mewpy/germ/__init__.py
src/mewpy/germ/algebra/__init__.py
src/mewpy/germ/algebra/algebra_constants.py
src/mewpy/germ/algebra/algebra_utils.py
src/mewpy/germ/algebra/expression.py
src/mewpy/germ/algebra/parsing.py
src/mewpy/germ/algebra/symbolic.py
src/mewpy/germ/analysis/__init__.py
src/mewpy/germ/analysis/analysis_utils.py
src/mewpy/germ/analysis/coregflux.py
src/mewpy/germ/analysis/fba.py
src/mewpy/germ/analysis/integrated_analysis.py
src/mewpy/germ/analysis/metabolic_analysis.py
src/mewpy/germ/analysis/pfba.py
src/mewpy/germ/analysis/prom.py
src/mewpy/germ/analysis/regulatory_analysis.py
src/mewpy/germ/analysis/rfba.py
src/mewpy/germ/analysis/srfba.py
src/mewpy/germ/lp/__init__.py
src/mewpy/germ/lp/linear_containers.py
src/mewpy/germ/lp/linear_problem.py
src/mewpy/germ/lp/linear_utils.py
src/mewpy/germ/models/__init__.py
src/mewpy/germ/models/metabolic.py
src/mewpy/germ/models/model.py
src/mewpy/germ/models/regulatory.py
src/mewpy/germ/models/serialization.py
src/mewpy/germ/solution/__init__.py
src/mewpy/germ/solution/model_solution.py
src/mewpy/germ/solution/multi_solution.py
src/mewpy/germ/solution/summary.py
src/mewpy/germ/variables/__init__.py
src/mewpy/germ/variables/gene.py
src/mewpy/germ/variables/interaction.py
src/mewpy/germ/variables/metabolite.py
src/mewpy/germ/variables/reaction.py
src/mewpy/germ/variables/regulator.py
src/mewpy/germ/variables/target.py
src/mewpy/germ/variables/variable.py
src/mewpy/germ/variables/variables_utils.py
src/mewpy/io/__init__.py
src/mewpy/io/builder.py
src/mewpy/io/director.py
src/mewpy/io/dto.py
src/mewpy/io/reader.py
src/mewpy/io/sbml.py
src/mewpy/io/writer.py
src/mewpy/io/engines/__init__.py
src/mewpy/io/engines/boolean_csv.py
src/mewpy/io/engines/co_expression_csv.py
src/mewpy/io/engines/cobra_model.py
src/mewpy/io/engines/engine.py
src/mewpy/io/engines/engines_utils.py
src/mewpy/io/engines/json.py
src/mewpy/io/engines/metabolic_sbml.py
src/mewpy/io/engines/reframed_model.py
src/mewpy/io/engines/regulatory_sbml.py
src/mewpy/io/engines/target_regulator_csv.py
src/mewpy/model/__init__.py
src/mewpy/model/gecko.py
src/mewpy/model/kinetic.py
src/mewpy/model/smoment.py
src/mewpy/model/data/__init__.py
src/mewpy/model/data/ecYeastGEM_multi-pool.xml
src/mewpy/model/data/ecYeastGEM_single-pool.xml
src/mewpy/model/data/proteins.txt
src/mewpy/omics/__init__.py
src/mewpy/omics/expression.py
src/mewpy/omics/integration/__init__.py
src/mewpy/omics/integration/eflux.py
src/mewpy/omics/integration/gimme.py
src/mewpy/omics/integration/imat.py
src/mewpy/optimization/__init__.py
src/mewpy/optimization/ea.py
src/mewpy/optimization/settings.py
src/mewpy/optimization/evaluation/__init__.py
src/mewpy/optimization/evaluation/base.py
src/mewpy/optimization/evaluation/community.py
src/mewpy/optimization/evaluation/evaluator.py
src/mewpy/optimization/evaluation/phenotype.py
src/mewpy/optimization/inspyred/__init__.py
src/mewpy/optimization/inspyred/ea.py
src/mewpy/optimization/inspyred/observers.py
src/mewpy/optimization/inspyred/operators.py
src/mewpy/optimization/inspyred/problem.py
src/mewpy/optimization/inspyred/settings.py
src/mewpy/optimization/inspyred/terminator.py
src/mewpy/optimization/jmetal/__init__.py
src/mewpy/optimization/jmetal/ea.py
src/mewpy/optimization/jmetal/observers.py
src/mewpy/optimization/jmetal/operators.py
src/mewpy/optimization/jmetal/problem.py
src/mewpy/optimization/jmetal/settings.py
src/mewpy/problems/__init__.py
src/mewpy/problems/cofactor.py
src/mewpy/problems/com.py
src/mewpy/problems/etfl.py
src/mewpy/problems/gecko.py
src/mewpy/problems/genes.py
src/mewpy/problems/hybrid.py
src/mewpy/problems/kinetic.py
src/mewpy/problems/optorf.py
src/mewpy/problems/optram.py
src/mewpy/problems/problem.py
src/mewpy/problems/reactions.py
src/mewpy/simulation/__init__.py
src/mewpy/simulation/cobra.py
src/mewpy/simulation/environment.py
src/mewpy/simulation/germ.py
src/mewpy/simulation/hybrid.py
src/mewpy/simulation/kinetic.py
src/mewpy/simulation/reframed.py
src/mewpy/simulation/sglobal.py
src/mewpy/simulation/simulation.py
src/mewpy/simulation/simulator.py
src/mewpy/solvers/__init__.py
src/mewpy/solvers/cplex_solver.py
src/mewpy/solvers/gurobi_solver.py
src/mewpy/solvers/ode.py
src/mewpy/solvers/odespy_solver.py
src/mewpy/solvers/optlang_solver.py
src/mewpy/solvers/scikits_solver.py
src/mewpy/solvers/scipy_solver.py
src/mewpy/solvers/sglobal.py
src/mewpy/solvers/solution.py
src/mewpy/solvers/solver.py
src/mewpy/util/__init__.py
src/mewpy/util/constants.py
src/mewpy/util/crossmodel.py
src/mewpy/util/graph.py
src/mewpy/util/history.py
src/mewpy/util/parsing.py
src/mewpy/util/process.py
src/mewpy/util/request.py
src/mewpy/util/utilities.py
src/mewpy/visualization/__init__.py
src/mewpy/visualization/envelope.py
src/mewpy/visualization/escher.py
src/mewpy/visualization/plot.py
tests/test_a_simulator.py
tests/test_b_problem.py
tests/test_c_optimization.py
tests/test_d_models.py
tests/test_e_germ_problem.py
tests/test_f_omics.py
tests/test_g_com.py
tests/test_h_kin.py
tests/data/SampleNet.xml
tests/data/SampleRegNet.csv
tests/data/TFnames.csv
tests/data/chassagnole2002.xml
tests/data/e_coli_core.json
tests/data/e_coli_core.xml
tests/data/e_coli_core.xml.gz
tests/data/e_coli_core_trn.csv
tests/data/e_coli_lac.xml
tests/data/mgene.csv
tests/data/regnet.csv
tests/data/yeast-essential.xlsx
tests/data/yeast_7.6-optram.xml