libsbml-network-modeling
CommunityBuild and manage SBML biological models.
Education & Research#systems biology#model building#metabolic modeling#sbml#libsbml#network modeling#fbc
Authorjaechang-hits
Version1.0.0
Installs0
System Documentation
What problem does it solve?
This Skill addresses the need for programmatic creation, modification, validation, and analysis of biological network models encoded in the Systems Biology Markup Language (SBML) standard.
Core Features & Use Cases
- Model Construction: Programmatically build SBML models from scratch, defining compartments, species, reactions, and kinetic laws.
- Model Manipulation: Read existing SBML files, modify parameters, species concentrations, or reaction stoichiometry.
- Validation & Interoperability: Validate SBML files against specifications and ensure compatibility with other simulation tools like COBRApy, Tellurium, and COPASI.
- FBC Extension: Support for the Flux Balance Constraints (FBC) extension for genome-scale metabolic modeling.
- Use Case: A researcher needs to build a new metabolic model for a specific bacterium, define its flux bounds, and set an objective function for flux balance analysis. This Skill allows them to generate the SBML file programmatically, which can then be loaded into COBRApy.
Quick Start
Use the libsbml-network-modeling skill to build a simple enzymatic reaction model in SBML format.
Dependency Matrix
Required Modules
python-libsbmlnumpypandascobratellurium
Components
scriptsreferencesassets
💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: libsbml-network-modeling Download link: https://github.com/jaechang-hits/SciAgent-Skills/archive/main.zip#libsbml-network-modeling Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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