mianaz/biomed-skills

General biomedical workflows. Repository: mianaz/biomed-skills.
The suite includes scientific framing, manuscript writing, figures, paper reading,
protocols and submission preparation. Version 0.5.5.
| 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 |
| 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 14 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/buildpages.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:
bash
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 writing guidance; external editorial projects are recorded as design sources.
R, Python, Prism and application connections are needed for tasks using those tools.