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bio-systems-biology-context-specific-models

85 / 100 · Low risk

Fine to try.

By lilinji/GeneTind-Life-Skills (GitHub) · coding · 17 stars · scanned at commit 908229c

Builds tissue-, cell-type-, and condition-specific metabolic models by integrating transcriptomic or proteomic data into a generic genome-scale model, using extraction algorithms (GIMME, iMAT, INIT/tINIT, MADE, E-Flux, CORDA, FASTCORE) via troppo and corda in Python or the COBRA Toolbox/RAVEN in MATLAB. Use when pruning a generic model to a context, choosing an extraction method and expression threshold, mapping expression through GPR rules to reactions, deciding whether an objective is require…

Works with any agent that supports SKILL.md skills.

What this skill can do

Install

Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.

if [ -e ~/.agents/skills/'bio-systems-biology-context-specific-models' ] || [ -L ~/.agents/skills/'bio-systems-biology-context-specific-models' ]; then echo 'A skill folder named bio-systems-biology-context-specific-models already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/lilinji/GeneTind-Life-Skills' "$d" && git -C "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/bio-systems-biology-context-specific-models' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bio-systems-biology-context-specific-models' ~/.agents/skills/'bio-systems-biology-context-specific-models' && rm -rf "$d"; fi

Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'bio-systems-biology-context-specific-models' ~/.claude/skills/'bio-systems-biology-context-specific-models' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.

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