cobrapy SKILL.md skillA
cobrapy from k-dense-ai/scientific-agent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add k-dense-ai/scientific-agent-skills/cobrapy@v1.5Pins v1.5 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- k-dense-ai/scientific-agent-skills
- Path
skills/cobrapy/SKILL.md- Versions recorded
- 6
- Latest version
- v1.5, committed Oct 1, 2026
- First version recorded
- Jun 11, 2026
- Size
- 11,690 bytes
- Repository stars
- 56,497
- License
- MIT
Performs 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.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# COBRApy - Constraint-Based Reconstruction and Analysis ## When to use Use for loading/building metabolic networks, optimizing their steady-state fluxes, knockout screens, medium design, feasible-space sampling, and gap-filling hypotheses. FBA is a constraint-based prediction; it does not infer kinetic rates or establish experimental growth, thermodynamic feasibility, or flux identifiability. ## Setup and reproducibility Targets **cobra 0.32.1** (import `cobra`), checked against its released source and [current documentation](https://cobrapy.readthedocs.io/en/latest/). ```bash uv pip install "cobra==0.32.1" # Optional SciPy support for MATLAB I/O and array operations: uv pip install "cobra[array]==0.32.1" ``` Plotting examples additionally require matplotlib, pandas, and seaborn. The `cobra[chrr]` extra supplies hopsy for the new CHRR sampler; that optional backend was documentation-reviewed, not executed in this refresh. In 0.32.1, `sample()` defaults to `method="auto"` (CHRR when hopsy is installed, otherwise OptGP). Choose the method explicitly to avoid environment-dependent changes. Record model source/version/checksum, cobra and solver versions, objective, …
Read the whole file at its exact version.
How to install
mdr add k-dense-ai/scientific-agent-skills/cobrapy@sha256:b11365507e183d8eThe line at the top of this page pins the label v1.5, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_wpoqeivg7ocknk3w)
4 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 6 versions of this file, between Jun 11, 2026 and Oct 1, 2026, about one every 22 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| v1.5 latest | 2026-10-01 | a92663a | 11,690 B | A | view · diff |
| v1.4 | 2026-09-30 | ce9e6e9 | 14,640 B | A | view · diff |
| v1.3 | 2026-09-10 | 27e3483 | 14,525 B | A | view · diff |
| v1.2 | 2026-09-02 | 1e5eeff | 15,439 B | A | view · diff |
| v1.1 | 2026-07-26 | b085e11 | 14,482 B | A | view · diff |
| git:20260611.1b8fae3 | 2026-06-11 | 1b8fae3 | 14,487 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (11690 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
k-dense-ai/scientific-agent-skills · 56,497 stars · license MIT · pushed 2026-11-02 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_wpoqeivg7ocknk3w GET https://markdownregistry.com/api/v1/resolve?ref=k-dense-ai/scientific-agent-skills/cobrapy GET https://markdownregistry.com/api/v1/blob/b11365507e183d8e153dd415df3a85a00f34b068bcf8edbad28c0580253564db
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.
More from k-dense-ai/scientific-agent-skills
Every file in k-dense-ai/scientific-agent-skills