straindesign
StrainDesign is a python package for the computational design of metabolic networks and based on COBRApy
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- JN_01_solver.ipynb
- JN_02_analysis.ipynb
- JN_03_plotting.ipynb
- JN_04_strain_design_introduction.ipynb
- JN_05_strain_design_mcs.ipynb
- JN_06_strain_design_nested.ipynb
- JN_07_network_design.ipynb
- JN_08_compression.ipynb
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- optcouple.jpg
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- SmallExample_mcs1.svg
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- 9_cnapy_integration.rst
- api_reference.rst
- conf.py
- developers_guide.md
- index.rst
- doc_requirements.txt
- logo.png
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- make.bat
- Makefile
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- __init__.py
- compression.py
- compute_strain_designs.py
- cplex_interface.py
- glpk_interface.py
- gurobi_interface.py
- indicatorConstraints.py
- lptools.py
- names.py
- networktools.py
- parse_constr.py
- pool.py
- scip_interface.py
- solver_interface.py
- speedy_fva.py
- strainDesignMILP.py
- strainDesignModule.py
- strainDesignProblem.py
- strainDesignSolutions.py
- __init__.py
- conftest.py
- iMLcore.xml
- model_doubleopt.xml
- model_gpr.xml
- model_small_example.xml
- model_weak_coupling.xml
- test_01_load_models_and_solvers.py
- test_02_lp_optimization.py
- test_03_plots.py
- test_04_preprocessing.py
- test_05_straindesign.py
- test_06_multiprocessing.py
- test_07_compression.py
- test_08_gene_ko.py
- test_09_performance.py
- test_10_gene_design_validity.py
- test_11_gene_regulatory_compression.py
- test_12_save_load_embed_model.py
- test_13_public_api.py
- .gitattributes
- .gitignore
- .readthedocs.yaml
- CODE_OF_CONDUCT.md
- CONTRIBUTING.md
- environment.yml
- LICENSE
- pyproject.toml
- README.md
- requirements.txt
- Update_version.md
# Installation Guide
1. Get the code
git clone https://github.com/klamt-lab/straindesign
Downloads the entire project code from GitHub to your computer.
cd straindesign
Moves into the project folder you just downloaded.
2. Official Install Script
Easy RecommendedPrerequisites
- Python 3 Python is required to use pip.
pip install straindesign
Installs the package published on PyPI directly β no need to clone the source.
After installing, open a new terminal and run the program's version command (e.g. --version) to confirm it worked.
Pulled directly from this repo's README.
3. Python
EasyPrerequisites
pip install straindesign
Installs the package published on PyPI directly β no need to clone the source.
pip install -e .
Installs the Python libraries listed in requirements.txt (or similar).
python -m pip install gurobipy
Installs the Python libraries listed in requirements.txt (or similar).
python -m pip install pyscipopt
Installs the Python libraries listed in requirements.txt (or similar).
If it runs without errors and prints output in the terminal, it worked.
Pulled directly from this repo's README.
// repository documentation
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