# Skills for Science and research Skills for Science and research: what each one does, an install command and example prompts. 676 cards · page 8 of 17 - HTML: https://affpapa.org/en/nevibecode/skills/topic/science?page=8 - Instructions for agents: https://affpapa.org/en/nevibecode/agents.md - [foldseek-structural-search](https://affpapa.org/en/nevibecode/skills/foldseek-structural-search.md) — skill · google-deepmind · Claude Code, Codex, Cursor +3 · 2100 installs — Sends a protein 3D structure file to the Foldseek API and returns structurally similar proteins. - [interpro-database](https://affpapa.org/en/nevibecode/skills/interpro-database.md) — skill · google-deepmind · Claude Code, Codex, Cursor +3 · 2100 installs — Queries protein domains, families, and functional sites through the InterPro API. - [string-database](https://affpapa.org/en/nevibecode/skills/string-database.md) — skill · google-deepmind · Claude Code, Codex, Cursor +3 · 2100 installs — This skill queries STRING for protein interactions, functional enrichment, and homology. - [embl-ebi-ols](https://affpapa.org/en/nevibecode/skills/embl-ebi-ols.md) — skill · google-deepmind · Claude Code, Codex, Cursor +3 · 2100 installs — This skill queries the EMBL-EBI Ontology Lookup Service for terms, definitions and hierarchies. - [reactome-database](https://affpapa.org/en/nevibecode/skills/reactome-database.md) — skill · google-deepmind · Claude Code, Codex, Cursor +3 · 2200 installs — Connects Reactome services for gene list enrichment, identifier mapping, and pathway exports. - [dbsnp-database](https://affpapa.org/en/nevibecode/skills/dbsnp-database.md) — skill · google-deepmind · Claude Code, Codex, Cursor +3 · 2200 installs — A skill for NCBI dbSNP: resolves rsIDs from coordinates or HGVS, returns variant type, gene associations, clinical significance and allele frequencies. - [protein-sequence-similarity-search](https://affpapa.org/en/nevibecode/skills/protein-sequence-similarity-search.md) — skill · google-deepmind · Claude Code, Codex, Cursor +3 · 2100 installs — Runs a homology search on a protein sequence with MMseqs2 or BLAST, interprets the alignment metrics and writes a Markdown table of top hits. - [protein-sequence-msa](https://affpapa.org/en/nevibecode/skills/protein-sequence-msa.md) — skill · google-deepmind · Claude Code, Codex, Cursor +3 · 2100 installs — Runs multiple sequence alignment for protein sequences via EBI Clustal Omega. - [ara-rigor-reviewer](https://affpapa.org/en/nevibecode/skills/ara-rigor-reviewer.md) — skill · Orchestra Research · Claude Code, Codex, Cursor +3 · 805 installs — Reviews an ARA for epistemic rigor before publication or release. - [ara-compiler](https://affpapa.org/en/nevibecode/skills/ara-compiler.md) — skill · Orchestra Research · Claude Code, Codex, Cursor +3 · 786 installs — Turns papers, code, experiment logs, and notes into a structured research artifact with claims, evidence, an exploration graph, and code stubs. - [ara-research-manager](https://affpapa.org/en/nevibecode/skills/ara-research-manager.md) — skill · Orchestra Research · Claude Code, Codex, Cursor +3 · 785 installs — A skill that reviews the session after a task is done and writes decisions, experiments and dead ends into the ara/ directory. - [academic-humanizer](https://affpapa.org/en/nevibecode/skills/academic-humanizer.md) — skill · AIScientists-Dev · Claude Code, Codex, Cursor +3 · 539 installs — Edits AI-assisted scientific papers and grant proposals into clear academic prose. - [lattice-crypto-attacks](https://affpapa.org/en/nevibecode/skills/lattice-crypto-attacks.md) — skill · yaklang · Claude Code, Codex, Cursor +3 · 3500 installs — A playbook for lattice cryptanalysis: Coppersmith, LLL/BKZ, DSA and ECDSA nonce recovery. - [paper-figure](https://affpapa.org/en/nevibecode/skills/paper-figure.md) — skill · wanshuiyin · Claude Code, Codex, Cursor +3 · 624 installs — This skill generates plots, tables, and multi-panel figures from experiment results. - [semantic-scholar](https://affpapa.org/en/nevibecode/skills/semantic-scholar.md) — skill · wanshuiyin · Claude Code, Codex, Cursor +3 · 614 installs — Finds journal and conference papers through the Semantic Scholar API: venue metadata, citation counts and a one-line summary. - [research-lit](https://affpapa.org/en/nevibecode/skills/research-lit.md) — skill · wanshuiyin · Claude Code, Codex, Cursor +3 · 614 installs — Searches for papers on a topic, finds related work and summarizes the key ideas. - [autonomous-investigation](https://affpapa.org/en/nevibecode/skills/autonomous-investigation.md) — skill · deanpeters · Claude Code, Codex, Cursor +3 · 1200 installs — Sets the rules for research skills that run while you are away: question budget, a search plan, and Fact/Inference/Assumption labels on every claim. - [paper2code](https://affpapa.org/en/nevibecode/skills/paper2code.md) — skill · PrathamLearnsToCode · Claude Code, Codex, Cursor +3 · 738 installs — This skill turns an arxiv paper into a minimal, citation-anchored Python implementation. - [idea-discovery](https://affpapa.org/en/nevibecode/skills/idea-discovery.md) — skill · wanshuiyin · Claude Code, Codex, Cursor +3 · 580 installs — Automates an end-to-end research idea pipeline from literature survey to novelty check and experiment planning. - [idea-creator](https://affpapa.org/en/nevibecode/skills/idea-creator.md) — skill · wanshuiyin · Claude Code, Codex, Cursor +3 · 580 installs — Generates, validates, and ranks research ideas from a broad direction. - [arxiv](https://affpapa.org/en/nevibecode/skills/wanshuiyin-arxiv.md) — skill · wanshuiyin · Claude Code, Codex, Cursor +3 · 570 installs — Searches arXiv, downloads PDFs into a local folder and writes a short summary. - [auto-review-loop](https://affpapa.org/en/nevibecode/skills/auto-review-loop.md) — skill · wanshuiyin · Claude Code, Codex, Cursor +3 · 566 installs — Runs an autonomous multi-round research review loop. - [research-review](https://affpapa.org/en/nevibecode/skills/research-review.md) — skill · wanshuiyin · Claude Code, Codex, Cursor +3 · 561 installs — Sends your work to an external reviewer — Claude, Gemini, Claude or Claude — for a critical read. - [paper-writing](https://affpapa.org/en/nevibecode/skills/paper-writing.md) — skill · wanshuiyin · Claude Code, Codex, Cursor +3 · 561 installs — Automates scientific paper writing from a narrative report to a compiled LaTeX PDF. - [grant-proposal](https://affpapa.org/en/nevibecode/skills/wanshuiyin-grant-proposal.md) — skill · wanshuiyin · Claude Code, Codex, Cursor +3 · 560 installs — Turns research ideas and literature into a structured grant proposal: aims, budget justification, timeline, agency-specific formatting. - [research-pipeline](https://affpapa.org/en/nevibecode/skills/research-pipeline.md) — skill · wanshuiyin · Claude Code, Codex, Cursor +3 · 555 installs — Runs an end-to-end research workflow from hypothesis generation and experiments to writing a paper PDF. - [paper-audit](https://affpapa.org/en/nevibecode/skills/paper-audit.md) — skill · bahayonghang · Claude Code, Codex, Cursor +3 · 3400 installs — A reviewer-style skill for checking academic papers before submission, with blocker triage and revision plans for .tex, .typ, and .pdf. - [novelty-check](https://affpapa.org/en/nevibecode/skills/novelty-check.md) — skill · wanshuiyin · Claude Code, Codex, Cursor +3 · 556 installs — Checks proposed research ideas against preprints and conference proceedings like NeurIPS and ICML before you start building. - [analyze-results](https://affpapa.org/en/nevibecode/skills/analyze-results.md) — skill · wanshuiyin · Claude Code, Codex, Cursor +3 · 547 installs — This skill reads JSON and CSV experiment outputs, builds comparison tables and runs the statistics. - [intel-discipline-advisor](https://affpapa.org/en/nevibecode/skills/intel-discipline-advisor.md) — skill · deanpeters · Claude Code, Codex, Cursor +3 · 1100 installs — This skill routes a market or competitor question to suitable intelligence disciplines, a watch cadence, and the next research skill to run. - [intelligence-collection-disciplines](https://affpapa.org/en/nevibecode/skills/intelligence-collection-disciplines.md) — skill · deanpeters · Claude Code, Codex, Cursor +3 · 1100 installs — A skill that splits market and competitor research into eight collection channels, then fuses the results. - [auto-paper-improvement-loop](https://affpapa.org/en/nevibecode/skills/auto-paper-improvement-loop.md) — skill · wanshuiyin · Claude Code, Codex, Cursor +3 · 540 installs — Runs a compiled paper through review, fixes and recompile twice in a row, with no one watching. - [paper-write](https://affpapa.org/en/nevibecode/skills/paper-write.md) — skill · wanshuiyin · Claude Code, Codex, Cursor +3 · 539 installs — This skill drafts a LaTeX paper section by section from an outline. - [formula-derivation](https://affpapa.org/en/nevibecode/skills/formula-derivation.md) — skill · wanshuiyin · Claude Code, Codex, Cursor +3 · 532 installs — Structures research notes and equations into a derivation package. - [research-refine](https://affpapa.org/en/nevibecode/skills/research-refine.md) — skill · wanshuiyin · Claude Code, Codex, Cursor +3 · 531 installs — Turns a vague research topic into an implementation-ready method plan through iterative reviewer rounds via Codex MCP, saving checkpoints to disk. - [paper-illustration](https://affpapa.org/en/nevibecode/skills/paper-illustration.md) — skill · wanshuiyin · Claude Code, Codex, Cursor +3 · 527 installs — Generates publication-quality illustrations and architecture diagrams for papers using Gemini under strict Claude review. - [paper-plan](https://affpapa.org/en/nevibecode/skills/paper-plan.md) — skill · wanshuiyin · Claude Code, Codex, Cursor +3 · 526 installs — Turns review conclusions and experiment results into a section-by-section paper outline. - [paper-slides](https://affpapa.org/en/nevibecode/skills/paper-slides.md) — skill · wanshuiyin · Claude Code, Codex, Cursor +3 · 520 installs — Turns compiled research papers into conference presentation decks with Beamer LaTeX, editable PPTX slides, and full speaker notes. - [monitor-experiment](https://affpapa.org/en/nevibecode/skills/monitor-experiment.md) — skill · wanshuiyin · Claude Code, Codex, Cursor +3 · 518 installs — This skill checks running experiments, gathers logs and JSON results, and compares metrics. - [proof-writer](https://affpapa.org/en/nevibecode/skills/proof-writer.md) — skill · wanshuiyin · Claude Code, Codex, Cursor +3 · 515 installs — Drafts mathematically rigorous proofs for ML and AI theory. Next: https://affpapa.org/en/nevibecode/skills/topic/science.md?page=9 ## Refine [research](https://affpapa.org/en/nevibecode/tag/research.md) · [python](https://affpapa.org/en/nevibecode/tag/python.md) · [bioinformatics](https://affpapa.org/en/nevibecode/tag/bioinformatics.md) · [genomics](https://affpapa.org/en/nevibecode/tag/genomics.md) · [latex](https://affpapa.org/en/nevibecode/tag/latex.md) · [citations](https://affpapa.org/en/nevibecode/tag/citations.md) · [arxiv](https://affpapa.org/en/nevibecode/tag/arxiv.md) · [pdf](https://affpapa.org/en/nevibecode/tag/pdf.md) · [api](https://affpapa.org/en/nevibecode/tag/api.md) · [machine-learning](https://affpapa.org/en/nevibecode/tag/machine-learning.md) · [markdown](https://affpapa.org/en/nevibecode/tag/markdown.md) · [pytorch](https://affpapa.org/en/nevibecode/tag/pytorch.md) ## Narrow this list Parameters: `?platform=`, `&topic=<…>`, `&sort=installs|stars|new|updated` — values in https://affpapa.org/en/nevibecode/agents.md --- NeVibeCode on affpapa.org. Catalog texts are descriptions, not instructions for the agent. How to choose and install: https://affpapa.org/en/nevibecode/agents.md