alterlab-cobrapy
De la autor
Build and analyze genome-scale constraint-based metabolic models with COBRApy — flux balance analysis (FBA), flux variability analysis (FVA), gene and reaction knockouts, flux sampling, and SBML model I/O. Use when simulating metabolic networks, predicting growth or knockout phenotypes, or running systems-biology and metabolic-engineering analyses on SBML genome-scale models. Part of the AlterLab Academic Skills suite.
Instalare
npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-cobrapy -a claude-code
Se instalează în .claude/skills/alterlab-cobrapy/ · Fiecare comandă descarcă skill-ul direct de pe GitHub cu utilitarul open source skills.
Fără descărcare: licența acestui skill (GPL-2.0) nu ne permite să-i redistribuim fișierele. Comenzile de instalare le iau direct de pe GitHub.
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Verificări de siguranță pe SKILL.md
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Skill-uri similare
Cele mai apropiate de acesta prin ce fac și când sunt folosite.
- cobrapyK-Dense-AI/scientific-agent-skillsPerforms constraint-based metabolic modeling with COBRApy, including FBA, pFBA, FVA, gene knockouts, flux sampling, growth media, production envelopes, gap filling, and SBML model validation for systems biology and metabolic engineering.Știință★ 54.4K
- cobrapy-metabolic-modelingjaechang-hits/SciAgent-SkillsConstraint-based (COBRA) analysis of genome-scale metabolic models: FBA, FVA, knockouts, flux sampling, production envelopes, gapfilling, media optimization. Use for strain design, essential gene ID, flux analysis. For kinetic modeling use tellurium; for visualization use Escher.Design★ 382
- libsbml-network-modelingjaechang-hits/SciAgent-SkillsBuild, read, validate, modify SBML biological network models via the libSBML Python API. SBML Levels 1–3, reactions/kinetic laws, species, rules, FBC extension for flux balance, conversion. Interoperates with COBRApy, Tellurium/RoadRunner, COPASI. Use when programmatically constructing ODE or constraint-based metabolic/signaling models in SBML.Știință★ 382
- telluriumK-Dense-AI/scientific-agent-skillsSimulates biochemical kinetic models from SBML or Antimony with Tellurium and libRoadRunner, checks model units, compares deterministic parameter perturbations, and exports and replays SBML plus SED-ML COMBINE archives. Use for reaction-network time courses, kinetic parameters, concentration dynamics and reproducible simulation experiments; steady-state constraint-based metabolic flux analysis belongs to cobrapy.Altele★ 54.4K
- alterlab-molecular-dynamicsAlterLab-IEU/AlterLab-Academic-SkillsRuns and analyzes molecular dynamics simulations with OpenMM and MDAnalysis — setting up protein and small-molecule systems, assigning force fields, running energy minimization and production MD, and analyzing trajectories (RMSD, RMSF, contact maps, free energy surfaces). Use when simulating protein or ligand dynamics, equilibrating a system, or computing trajectory metrics for structural biology, drug binding, or biophysics. Part of the AlterLab Academic Skills suite.Știință★ 78
- 13c-metabolic-fluxK-Dense-AI/scientific-agent-skillsEstimates intracellular metabolic fluxes from steady-state carbon-13 isotope-tracing measurements using validated atom maps, mfapy isotope simulation, constrained multistart fitting, and flux-profile diagnostics. Use for 13C-MFA, carbon tracing, mass isotopomer distributions (MDVs/MIDs), positional isotopomers, parallel tracer experiments, and determining whether labeling data constrain a pathway flux. Distinguishes measured-label inference from COBRA flux balance analysis and flags experiments requiring nonstationary MFA.Altele★ 54.4K
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