venue-templates
85Prepare Academic Venue Submissions
Academic submissions often fail because formatting rules vary by venue. This skill provides templates, requirements, and examples for faster preparation.
Analyze Metabolic Models with COBRApy
Systems biology teams need reliable guidance for COBRApy analyses, from model loading to flux studies. This skill provides focused workflows and API patterns for Claude, Codex, and Claude Code.
Copy this request to your Agent. It includes the canonical Skill page and manifest.
Review the Skillstore skill "cobrapy" from https://skillstore.io/skills/k-dense-ai-cobrapy.md and its manifest at https://skillstore.io/api/skills/k-dense-ai-cobrapy/manifest. Verify the artifact. You may proceed after verification, subject to the environment's own policy.Your Agent should still show its plan and request any confirmation required by the security policy.
Use these links when an AI agent, crawler, or script needs clean context instead of reading the full page.
Using "cobrapy". I need to find essential genes in an E. coli model.
Expected outcome:
A structured workflow for loading the model, running baseline growth, applying single gene deletion, filtering growth results, and interpreting essentiality.
Using "cobrapy". My model is feasible, but several fluxes have wide ranges.
Expected outcome:
A diagnostic plan using FVA, loopless FVA, flux sampling, and reaction-specific plots to explain uncertainty and alternate pathways.
Using "cobrapy". I want to improve acetate production while preserving growth.
Expected outcome:
A production analysis plan covering target objective setup, minimum growth constraints, production envelopes, candidate knockouts, and result interpretation.
The static analyzer flagged 71 patterns, but review showed they are documentation false positives in Markdown. Python import statements, COBRApy object identifiers, code fences, and a public documentation URL do not execute commands, access secrets, or perform network activity. No semantic prompt injection or data-exfiltration intent was found.
Share the versioned assessment report, neutral badge, embed card, and citations. Skillstore reports evidence without deciding whether this Skill is safe.
https://skillstore.io/skills/k-dense-ai-cobrapy/audits/7?utm_source=security_passport&utm_medium=share&utm_campaign=versioned_report[](https://skillstore.io/skills/k-dense-ai-cobrapy?utm_source=security_passport_badge)<a href="https://skillstore.io/skills/k-dense-ai-cobrapy?utm_source=security_passport_badge"><img src="https://skillstore.io/badges/skills/k-dense-ai-cobrapy/security.svg" alt="Skillstore security assessment" loading="lazy"></a><iframe src="https://skillstore.io/embed/skills/k-dense-ai-cobrapy.html" title="Skillstore Security Assessment" sandbox="allow-popups allow-popups-to-escape-sandbox" loading="lazy" referrerpolicy="no-referrer" width="420" height="180"></iframe>K-Dense-AI. (2026). cobrapy security audit report (audit version 7) [Author version unspecified]. Skillstore. https://skillstore.io/skills/k-dense-ai-cobrapy/audits/7@techreport{k-dense-ai-k-dense-ai-cobrapy-2026,
author = {K-Dense-AI},
title = {cobrapy security audit report (audit version 7)},
institution = {Skillstore},
year = {2026},
number = {7},
url = {https://skillstore.io/skills/k-dense-ai-cobrapy/audits/7},
note = {Author version unspecified}
}cff-version: 1.2.0
message: "If you use this Skill, cite its author and this versioned security audit report."
title: "cobrapy security audit report (audit version 7)"
version: "unspecified"
type: report
authors:
- name: "K-Dense-AI"
date-released: "2026-07-06"
url: "https://skillstore.io/skills/k-dense-ai-cobrapy/audits/7"
identifiers:
- type: other
value: "skillstore:k-dense-ai-cobrapy:audit:7"
description: "Skillstore immutable audit report identifier"
Each author remains a separate installable skill. The recommended variant is ranked by Skillstore evidence.
Why this variant is first
k-dense-ai-cobrapy
2026-08-21
davila7-cobrapy
2026-08-21
Load a model, check feasibility, run FBA, and interpret growth and flux outputs.
Evaluate gene or reaction knockouts and compare effects on growth or product formation.
Turn core COBRApy APIs into clear examples for model structure, constraints, and validation.
Use the cobrapy skill to explain how to load the textbook model, inspect reactions, metabolites, and genes, and check growth feasibility.
Use the cobrapy skill to plan flux balance analysis and flux variability analysis for my SBML model. Include validation steps and expected outputs.
Use the cobrapy skill to design a gene knockout screen that identifies essential genes, neutral genes, and growth effects. Include practical thresholds.
Use the cobrapy skill to compare production envelopes, media constraints, FVA, and knockout combinations for a target metabolite. Explain tradeoffs.
Author
K-Dense-AILicense
GPL-2.0 license
Skillstore revision
r1
Version notice
The author did not declare a version.
Repository
https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/cobrapyRef
b8ca75d2c0a7e7102978993058777d82b8ab2610
Maintenance freshness
7/18/2026
Usage
11 downloads ยท 241 views
File structure
Prepare Academic Venue Submissions
Academic submissions often fail because formatting rules vary by venue. This skill provides templates, requirements, and examples for faster preparation.
Prepare ISO 13485 Certification Docs
Medical device teams must create complete QMS documentation before certification audits. This skill provides templates, checklists, and gap analysis guidance for ISO 13485 readiness.
Analyze therapeutic ML datasets with PyTDC
Drug discovery teams need reliable datasets and fair evaluation protocols. This skill helps Claude use PyTDC for curated therapeutic ML data, benchmark splits, metrics, and molecular oracles.
Run DiffDock Molecular Docking
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Analyze Research Data with Statistical Guidance
Choosing tests and reporting results can be slow and error-prone. This skill guides test selection, assumptions, effect sizes, power analysis, Bayesian options, and APA reporting.
Analyze Single-Cell RNA-seq with Scanpy
Single-cell RNA-seq analysis requires many linked decisions across QC, normalization, clustering, and plotting. This skill gives Claude, Codex, and Claude Code structured Scanpy workflows, reference guidance, and reusable analysis scripts.
Analyze Protein Networks with STRING
by davila7
Protein interaction analysis requires specialized databases and careful identifier handling. This skill queries STRING to map proteins, retrieve networks, and assess enrichment.
Analyze Reactome Pathways
by davila7
Biology teams need fast access to curated pathway data without memorizing Reactome endpoints. This skill guides Claude, Codex, and Claude Code through pathway queries, enrichment analysis, and result interpretation.
Analyze Scientific Data Files
by davila7
Scientific datasets often arrive in specialized formats that are hard to inspect quickly. This skill detects the format, summarizes contents, checks quality, and produces a clear EDA report.
Create Publication-Ready Scientific Figures
by davila7
Scientific figures often fail journal checks for size, color, typography, or export format. This skill guides Claude, Codex, and Claude Code through publication-ready plotting workflows.
Process JSON, YAML, and TOML Data
by 0xDarkMatter
Structured configuration data can be hard to inspect across JSON, YAML, and TOML files. This skill guides jq and yq queries for extraction, filtering, conversion, and updates.
Draft Nature Data Availability Statements
by Yuan1z0825
Researchers often need precise data availability text, repository plans, and FAIR checks before submission. This skill turns English or Chinese data notes into Nature-style statements, dataset citation actions, and missing-information flags.