biomed-skill

General biomedical workflows. Repository: mianaz/biomed-skills. The suite includes scientific framing, manuscript writing, figures, paper reading, protocols and submission preparation. Version 0.6.1.

Skill	Deliverable
paper-framing	Central contribution, biological significance, conceptual model and overall figure sequence
paper-writing	Manuscript text drafted or restructured from evidence
paper-polishing	Existing prose polished, translated or compressed with its meaning preserved
paper-review	Prioritized scientific review findings with evidence locations, repairs and resolution checks
citation-audit	Claim-to-source verification with source locators, support verdicts and coverage
scientific-plotting	R/cowplot or Prism figures, editable source, direct plotting data and rendered checks
scientific-plotting-tidyplots	tidyplots R figures with 50 mm plot areas and shared scientific, font and delivery standards
figure-plan	Manuscript figure story, evidence/gap inventory, separate main/supplemental PowerPoint decks and inspected PNG/TIFF exports
graphpad-prism	Native Prism workflow, template editing and accurately labeled PZFX exports
scientific-reproducibility	Shared analysis outputs, source data, parameters and Methods records
paper-distill	Paper contribution, experimental logic, reusable methods and project-specific next steps
paper-evidence-map	Editable claim–experiment–result graph, evidence tables and visual preview
scientific-visual-explainer	Interactive HTML lessons for concepts, reviews and papers; visual slides or animated video when requested
paper-to-protocol	Sourced step-by-step protocol, printable HTML/Markdown and Labmate import JSON
protocol-to-methods	Publication-style Methods based on protocol plus actual experiment records
submission-check	Current journal/stage checklist and organized submission files for Cell, Nature or Science journals

Demos and examples

Open the GitHub Pages demo site. It includes detailed guides for all 16 skills, three basic mechanism examples (the default), two detailed mechanism demos, and a curated 38-icon gallery (14 basic symbols and 24 detailed assets) and three current plotting examples, copyable prompts, teaching data and a downloadable skill bundle. Writing and study examples are fictional; literature-based mechanism lessons include their sources and reading scope.

Build the static site with python3 scripts/build_pages.py, then serve _site/ with a local HTTP server. The build uses tracked skill resources and the explicit teaching fixtures in site/; local prototypes and benchmark outputs are excluded. GitHub Actions publishes the same build through .github/workflows/pages.yml. Set repository Settings → Pages → Source → GitHub Actions for first deployment.

Use

For Claude Code:

claude plugin marketplace add mianaz/biomed-skills
claude plugin install biomed-skill@biomed-skill

For Codex or Cursor, copy complete directories under skills/, including biomed-shared/, into the configured skill directory. The shared directory is a support package without an independent task entry point. The suite supplies all its editorial workflows and shared guidance within this package. R, Python, Prism and application connections are needed for tasks using those tools.

Install scientific-plotting-tidyplots together with scientific-plotting; the variation uses its shared standards and export helpers.

• “Use $scientific-plotting-tidyplots to compare these groups and verify text at the final figure size.”
• “Use $figure-plan to assemble main and supplemental figures in editable PowerPoint decks.”
• “Use $scientific-visual-explainer to teach this paper through an interactive HTML lesson.”

For a focused writing installation, run:

python3 scripts/build_writing_bundle.py /tmp/biomed-writing.zip

The bundle includes paper-framing, paper-writing, paper-polishing, paper-review, citation-audit and biomed-shared. Keep all six directories together. Copying one of these skills requires copying the shared directory beside it. Installation instructions are included in the bundle; installation is performed in the user's agent environment.

• “Use $paper-framing to develop the biological story and overall figure sequence.”
• “Use $paper-writing to draft Results from these figures.”
• “Use $paper-polishing to improve the English in this paragraph.”
• “Use $paper-review to assess the scientific argument and prioritize repairs.”
• “Use $citation-audit to verify these claims against their cited sources.”
• “Use $paper-distill and $paper-evidence-map to explain this paper.”
• “Use $protocol-to-methods with my protocol and completed experiment record.”
• “Use $submission-check to prepare the submission files.”

The protocol exporter uses Labmate's existing Guide → Backup & restore → Import workflow. It creates a local custom protocol. A new ID adds an item; the same ID replaces that item. The printable copy and import file come from one JSON source.

This is the beginning of the README. Read the rest at the original. Read the full README ↗