Skills real projects publish on GitHub, most starred first. Each one says what it will make an agent do before you copy it.
Files you open will collect here, so you can find them again.
Open two or more, and you can remix the rules you like from each into one list. Kept in this browser only.
JimLiuSkillJimLiu/science-skills/skills/indication-dossier/SKILL.md
Generate a therapeutic indication dossier. Covers the patient population, epidemiology, disease biology, standard of care, regulatory precedent, and landmark clinical trials.
JimLiuSkillJimLiu/science-skills/skills/ligandmpnn/SKILL.md
Inverse-fold a backbone with ligand, nucleic-acid, and metal context using LigandMPNN (Dauparas et al. 2023, github.com/dauparas/LigandMPNN). Reach for this skill to redesign the residues lining a binding pocket around a bound small molecule or cofactor, to design metal-coordinating sites where the geometry must be respected, or to get threaded designed-sequence PDBs out of any MPNN run.
JimLiuSkillJimLiu/science-skills/skills/literature-review/SKILL.md
Find, verify, and synthesize scientific literature — from "what's the seminal paper for X" through full multi-source reviews. Covers grounding claims in real retrieved sources, avoiding fabricated citations, handling retractions, and calibrating confidence to evidence strength.
JimLiuSkillJimLiu/science-skills/skills/openfold3/SKILL.md
Structure prediction using OpenFold3, an open-weights PyTorch reproduction of AlphaFold3 from the AlQuraishi Lab. Use this skill when predicting protein/nucleic-acid/ligand complex structures with an Apache-2.0-licensed AF3 reimplementation.
JimLiuSkillJimLiu/science-skills/skills/paper-narrative/SKILL.md
Judge and reshape the STORY a paper's figures tell. Input is the work itself — manuscript (or abstract) + figure deck — no hand-written brief. `derive_paper_brief(abstract, captions)` extracts pitch/vision/per-figure-claims; a handling-editor reviewer on the full deck returns hook_verdict (would Fig 1 make me send this for review?), arc (hook→mechanism→evidence→application), figure_moves (panels in the wrong figure), missing_panels (concrete analyses to RUN), kill_list, and boldest_defensible_fig1. Hands per-figure claims to `figure-composer`. Load when writing or revising a paper.
JimLiuSkillJimLiu/science-skills/skills/pdf-explore/SKILL.md
Use this skill when the user has attached a PDF, paper, report, or other document and the answer needs content from more than one place in it: summarize the methods or any other section, compare sections, find where a topic is discussed, read a value or label off a figure or chart, or find/list/extract every instance of something across the whole document (datasets, benchmarks, citations, figures, table rows, accession numbers — including appendices). Skip it only for a single lookup of 1–4 pages quoted in your very next response — `read_file(pages=[...])` attaches pages as images that are dropped from context after one turn, so multi-section answers end up re-reading the same ranges repeatedly. Parses the PDF once in the Python kernel: `pdf_pages` (pages as persistent text), `pdf_outline` (TOC), `pdf_scan` (rank pages by relevance), `pdf_map`/`pdf_extract` (per-page summary / structured fields via parallel haiku calls). For PDF creation/manipulation, use reportlab/pypdf directly.
JimLiuSkillJimLiu/science-skills/skills/product-self-knowledge/SKILL.md
Stop and consult this skill whenever your response would include specific facts about Anthropic's products. Covers: Claude Code (how to install, Node.js requirements, platform/OS support, MCP server integration, configuration), Claude API (function calling/tool use, batch processing, SDK usage, rate limits, pricing, models, streaming), and Claude.ai (Pro vs Team vs Enterprise plans, feature limits). Trigger this even for coding tasks that use the Anthropic SDK, content creation mentioning Claude capabilities or pricing, or LLM provider comparisons. Any time you would otherwise rely on memory for Anthropic product details, verify here instead — your training data may be outdated or wrong.
Often used withfile-readingskill-creatorpdf-reading
JimLiuSkillJimLiu/science-skills/skills/proteinmpnn/SKILL.md
Inverse-fold a protein backbone (PDB structure) into amino-acid sequence with ProteinMPNN (Dauparas et al. 2022, github.com/dauparas/ProteinMPNN). Reach for this skill to run sequence design on RFdiffusion backbones, to redesign one chain of a PDB while holding interface residues fixed, or to generate a temperature-swept set of sequences for downstream folding.
JimLiuSkillJimLiu/science-skills/skills/remote-compute-modal/SKILL.md
Run GPU jobs on the user's own Modal account via host.compute.create('modal', provider_params={...}) — the create→submit→wait_for_notification flow, the compute_provider kernel for env setup, image/volume resolution, and the two approval cards. Load once you've decided to dispatch to Modal.
JimLiuSkillJimLiu/science-skills/skills/scgpt/SKILL.md
Embed and annotate single-cell expression data with scGPT, a foundation model for single-cell biology. Use this skill when: (1) Producing cell embeddings from an AnnData for clustering/integration, (2) Zero-shot or fine-tuned cell-type annotation, (3) Gene-level representation for perturbation/GRN tasks.
JimLiuSkillJimLiu/science-skills/skills/scvi-tools/SKILL.md
Probabilistic single-cell RNA-seq with scvi-tools — scVI for a batch-corrected latent space, scANVI for semi-supervised label transfer, and Bayesian differential expression. Reach for this skill to integrate scRNA-seq batches, embed cells for clustering, transfer annotations from a reference onto a query, or score differentially expressed genes per cluster. For spatial deconvolution / mapping use the cell2location, DestVI, or Tangram methods instead.
JimLiuSkillJimLiu/science-skills/skills/self-awareness/SKILL.md
Claude Science's own session database schema and SDK surface for introspection via host.query(). Load this when you need to query your own conversation history, token usage, cost accounting, execution log, or artifact metadata beyond what host.frames()/host.artifacts() provide — e.g. "how many tokens has this session used", "what was my last tool call", "list every file I've written", "where are messages stored", "what tables can I query", "inspect frames.context_data", or any time you're about to PRAGMA-probe the Claude Science metadata DB to discover its schema.
JimLiuSkillJimLiu/science-skills/skills/skill-creator/SKILL.md
Create new skills, modify and improve existing skills, and measure skill performance. Use when users want to create a skill from scratch, edit, or optimize an existing skill, run evals to test a skill, benchmark skill performance with variance analysis, or optimize a skill's description for better triggering accuracy.
Often used withtaskflow-inbox-triagecommunity-led-growthsession-logs
JimLiuSkillJimLiu/science-skills/skills/solublempnn/SKILL.md
Inverse-fold a backbone with SolubleMPNN — ProteinMPNN retrained on a soluble-PDB subset (Dauparas et al. 2022) — for sequences biased toward cytosolic expression and reduced aggregation. Reach for this skill when designs from vanilla ProteinMPNN are aggregating or going to inclusion bodies, when redesigning a membrane-adjacent fold for soluble expression, or when an E. coli expression screen is the next step.
A folder with a SKILL.md file: a name, a description of when to use it, and instructions. Claude loads a skill only when the task matches its description.
Copy the folder into your project's .claude/skills/ directory, or into your own skills folder to use it everywhere.
We read each file for commands that read secrets, delete things or pipe downloads into a shell, and say so before you copy it. No warning is not a promise that a file is safe.
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