cobrapy
No security findings. Scanned 1 time, most recently 2026-10-21.
Second scanner: NVIDIA SkillSpector
SkillSpector found no issues but could not fully inspect the package, usually because SKILL.md refers to a file that is not present, so it fails closed to CAUTION instead of SAFE. Read it as "not fully checked", not as a finding. How the two scanners compare across the whole corpus: Two scanners, one corpus.
What this skill does
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.
- Package
- 3 files, 43 KB
- SKILL.md
- 1293 words, 12+ sections
- Code
- None. Instructions only.
- Allowed tools
ReadWriteEditBash- License
- GPL-2.0 license
- Compatibility
- Requires Python 3.9+ and cobra; examples tested with Python 3.12 and cobra 0.32.1. GLPK installs via swiglpk; commercial solvers need separate installation/licensing. Remote model downloads need network access; bundled textbook examples run offline.
SKILL.md covers: COBRApy - Constraint-Based Reconstruction and Analysis · When to use · Setup and reproducibility · Optional SciPy support for MATLAB I/O and array operations: · Workflow · 1. Load, inspect, and validate a model · These names are bundled: textbook, iJO1366, salmonella. · error_value=None raises on a failed solve; the default instead returns NaN. · 2. Compare FBA, pFBA, and FVA under stated constraints · parsimonious.objective_value is the minimized total flux, not biomass growth. · 3. Knockouts and media · 4. Sample the same feasible region as the FVA comparison
Findings
No findings. SAFE
What is in the package
| File | Kind | Size |
|---|---|---|
SKILL.md | doc | 11 KB |
references/api_quick_reference.md | doc | 16 KB |
references/workflows.md | doc | 16 KB |
External hosts referenced
cobrapy.readthedocs.io github.com bigg.ucsd.edu arxiv.org www.biomodels.org doi.org export.arxiv.org
Hostnames that appear in the skill's files. Referencing a host is not a finding; compare against the findings above and the skill's stated purpose.
Package contents recorded 2026-10-22 at commit 593377bb0487. The scan above ran against the version current at scan time; the two can differ if the skill has since been updated.
What we checked
- Static analyzer. Pattern rules over SKILL.md and bundled files: known-bad commands, exfiltration URLs, secrets, obfuscation.
- Bytecode analyzer.
- Pipeline analyzer.
- Correlation analyzer.
- Behavioral analyzer. Checks what the skill asks the agent to do against what its description claims it does.
- Trigger analyzer. Looks for instructions that fire on conditions the user did not ask for.
What we did not check
- Runtime behaviour. The skill was not executed; findings come from reading its files.
- Anything fetched at install or run time, including remote scripts, package dependencies, and URLs the skill tells the agent to open.
- Content the analyzers cannot read: images, binaries, and some non-English text.
- Known scanner bypass classes. See the methodology and limitations page.
Sources
- Repository: https://github.com/K-Dense-AI/scientific-agent-skills
- Raw scan result: skills-cobrapy-scan.json
- Badge for your README:
- Request a re-scan