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bio-workflows-metabolic-modeling-pipeline

80 / 100 · Low risk

Fine to try.

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

Orchestrates genome-scale metabolic modeling from a protein FASTA to flux predictions, chaining CarveMe/gapseq reconstruction, memote QC, gap-filling, media-constrained FBA/FVA, gene essentiality, and context-specific models. Use when committing the reconstruction tool (which locks the identifier NAMESPACE forever - BiGG vs ModelSEED vs KEGG, no automatic translation), setting the medium BEFORE FBA (the exchange bounds ARE the medium; essentiality and gap-fill are computed relative to it), cura…

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-workflows-metabolic-modeling-pipeline' ] || [ -L ~/.agents/skills/'bio-workflows-metabolic-modeling-pipeline' ]; then echo 'A skill folder named bio-workflows-metabolic-modeling-pipeline 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 "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/bio-workflows-metabolic-modeling-pipeline' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bio-workflows-metabolic-modeling-pipeline' ~/.agents/skills/'bio-workflows-metabolic-modeling-pipeline' && 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-workflows-metabolic-modeling-pipeline' ~/.claude/skills/'bio-workflows-metabolic-modeling-pipeline' (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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