LICENSE
README.md
pyproject.toml
src/strainOptimizer/__init__.py
src/strainOptimizer/io.py
src/strainOptimizer.egg-info/PKG-INFO
src/strainOptimizer.egg-info/SOURCES.txt
src/strainOptimizer.egg-info/dependency_links.txt
src/strainOptimizer.egg-info/requires.txt
src/strainOptimizer.egg-info/top_level.txt
src/strainOptimizer/analysis/FCC.py
src/strainOptimizer/analysis/__init__.py
src/strainOptimizer/analysis/dataset.py
src/strainOptimizer/analysis/ecGEM_utils.py
src/strainOptimizer/analysis/enzyme_variety_analysis.py
src/strainOptimizer/analysis/etfl_utils.py
src/strainOptimizer/analysis/flux_variety_analysis.py
src/strainOptimizer/analysis/model_process.py
src/strainOptimizer/analysis/network.py
src/strainOptimizer/analysis/optimal_yield.py
src/strainOptimizer/analysis/protein_process.py
src/strainOptimizer/etfl/__init__.py
src/strainOptimizer/etfl/analysis/__init__.py
src/strainOptimizer/etfl/analysis/dynamic.py
src/strainOptimizer/etfl/analysis/summary.py
src/strainOptimizer/etfl/analysis/utils.py
src/strainOptimizer/etfl/core/__init__.py
src/strainOptimizer/etfl/core/allocation.py
src/strainOptimizer/etfl/core/carbohydrate.py
src/strainOptimizer/etfl/core/dna.py
src/strainOptimizer/etfl/core/enzyme.py
src/strainOptimizer/etfl/core/expression.py
src/strainOptimizer/etfl/core/genes.py
src/strainOptimizer/etfl/core/ion.py
src/strainOptimizer/etfl/core/lipid.py
src/strainOptimizer/etfl/core/macromolecule.py
src/strainOptimizer/etfl/core/memodel.py
src/strainOptimizer/etfl/core/reactions.py
src/strainOptimizer/etfl/core/rna.py
src/strainOptimizer/etfl/core/thermomemodel.py
src/strainOptimizer/etfl/data/__init__.py
src/strainOptimizer/etfl/data/ecoli.py
src/strainOptimizer/etfl/data/ecoli_utils.py
src/strainOptimizer/etfl/debugging/__init__.py
src/strainOptimizer/etfl/debugging/debugging.py
src/strainOptimizer/etfl/integration/__init__.py
src/strainOptimizer/etfl/integration/transcriptomics.py
src/strainOptimizer/etfl/io/__init__.py
src/strainOptimizer/etfl/io/dict.py
src/strainOptimizer/etfl/io/json.py
src/strainOptimizer/etfl/optim/__init__.py
src/strainOptimizer/etfl/optim/config.py
src/strainOptimizer/etfl/optim/constraints.py
src/strainOptimizer/etfl/optim/utils.py
src/strainOptimizer/etfl/optim/variables.py
src/strainOptimizer/etfl/tests/__init__.py
src/strainOptimizer/etfl/tests/small_model.py
src/strainOptimizer/etfl/utils/__init__.py
src/strainOptimizer/etfl/utils/parsing.py
src/strainOptimizer/etfl/utils/utils.py
src/strainOptimizer/manipulation/__init__.py
src/strainOptimizer/manipulation/mainFunction.py
src/strainOptimizer/manipulation/model_process.py
src/strainOptimizer/manipulation/protein_process.py
src/strainOptimizer/manipulation/constraint/__init__.py
src/strainOptimizer/manipulation/constraint/enzyme.py
src/strainOptimizer/manipulation/constraint/reaction.py
src/strainOptimizer/manipulation/constraint/total_resource_allocation.py
src/strainOptimizer/manipulation/integration/__init__.py
src/strainOptimizer/manipulation/integration/gimme.py
src/strainOptimizer/manipulation/integration/proteome.py
src/strainOptimizer/manipulation/integration/transcriptome.py
src/strainOptimizer/manipulation/variable/__init__.py
src/strainOptimizer/manipulation/variable/enzyme.py
src/strainOptimizer/manipulation/variable/metabolite.py
src/strainOptimizer/manipulation/variable/reaction.py
src/strainOptimizer/simulation/FBA.py
src/strainOptimizer/simulation/MOMA.py
src/strainOptimizer/simulation/MOPA.py
src/strainOptimizer/simulation/TFA.py
src/strainOptimizer/simulation/__init__.py
src/strainOptimizer/simulation/ecYeastFlux.py
src/strainOptimizer/simulation/pFBA.py
src/strainOptimizer/simulation/pprotFBA.py
src/strainOptimizer/simulation/utils.py
src/strainOptimizer/strainDesign/__init__.py
src/strainOptimizer/strainDesign/workflow_engine.py
src/strainOptimizer/strainDesign/ecFactory/__init__.py
src/strainOptimizer/strainDesign/ecFactory/ecFactory_other.py
src/strainOptimizer/strainDesign/ecFactory/ecfseof.py
src/strainOptimizer/strainDesign/ecFactory/find_min_sets.py
src/strainOptimizer/strainDesign/ecFactory/run_ecFactory.py
src/strainOptimizer/strainDesign/iBridge/__init__.py
src/strainOptimizer/strainDesign/iBridge/ibridge.py
src/strainOptimizer/visualization/__init__.py
src/strainOptimizer/visualization/phase_plane.py