Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-cobrapygit clone --depth 1 https://github.com/AlterLab-IEU/AlterLab-Academic-SkillsWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/alterlab-ieu/alterlab-academic-skills/alterlab-cobrapy)<a href="https://agentmods.dev/skills/alterlab-ieu/alterlab-academic-skills/alterlab-cobrapy"><img src="https://agentmods.dev/badge/skills/alterlab-ieu/alterlab-academic-skills/alterlab-cobrapy/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/alterlab-ieu/alterlab-academic-skills/alterlab-cobrapy"><img src="https://agentmods.dev/badge/skills/alterlab-ieu/alterlab-academic-skills/alterlab-cobrapy.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector pass
What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00091 | $0.03940 |
| Opus 5.5 | $0.00036 | $0.01576 |
| Sonnet 5.5 | $0.00018 | $0.00788 |
| Haiku 4.5 | $0.00009 | $0.00394 |
Grade A, and why
alterlab-cobrapy scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 1mo ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 507 lines — stays where its author put it; the contents beside it link to each section on GitHub.
COBRApy - Constraint-Based Reconstruction and Analysis
Overview
COBRApy is a Python library for constraint-based reconstruction and analysis (COBRA) of metabolic models, essential for systems biology research. Work with genome-scale metabolic models, perform computational simulations of cellular metabolism, conduct metabolic engineering analyses, and predict phenotypic behaviors.
When to Use This Skill
Use this skill when the user wants to:
- Load a genome-scale metabolic model (SBML/JSON/YAML) and simulate growth with FBA/pFBA.
- Predict knockout phenotypes, essential genes, or minimal media.
- Explore flux space with FVA, flux sampling, or production envelopes.
- Build, gapfill, or curate a constraint-based model.
Does NOT Trigger
| Scenario | Use Instead |
|---|---|
| Looking up a pathway or reaction annotation rather than simulating | alterlab-kegg, alterlab-reactome |
| Enzyme kinetic parameters (kcat, Km) for a reaction | alterlab-brenda |
| Graph analysis of the metabolic network (centrality, communities) rather than flux | alterlab-networkx |
| Metabolomics measurements and their identification | alterlab-metabolomics-wb, alterlab-hmdb |
| Multi-objective optimization that is not a flux-balance problem | alterlab-pymoo |
Installation and Requirements
uv pip install cobra # 0.32.x as of 2026-09
uv pip install 'cobra[array]' # scipy extra, for array-based model handling
uv pip install 'cobra[chrr]' # hopsy, enables the fast CHRR sampler
Requirements: depends on optlang and a solver — GLPK ships by default via swiglpk, while CPLEX and Gurobi are optional and considerably faster on genome-scale models. pandas is a hard dependency (pinned < 3); matplotlib/seaborn only for plots. Flux sampling and parallel deletions use multiprocessing, so guard scripts with if __name__ == "__main__": on Windows/macOS spawn.
Bundled model names.
load_modelonly recognizes three bundled aliases:"textbook"(the E. coli core model,e_coli_core),"iJO1366"(full E. coli genome-scale), and"salmonella". Any other identifier (e.g."ecoli","e_coli_core") is not a bundled alias and triggers a remote lookup against BiGG/BioModels, which requires network access and may fail. Useread_sbml_model("path.xml")for your own models.
What ships with it
3 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 1mo ago Changed · +25 lines 1b07237ae0d9
- 1mo ago First seen · 482 lines · 91 tokens per session scan A 53d99cca26fc
alterlab-cobrapy is a skill published in the GitHub repository AlterLab-IEU/AlterLab-Academic-Skills (78 stars, last pushed 4d ago), licensed MIT. It adds 91 tokens to every session and 3,940 once invoked, about $0.0004 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
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