pengqianhan/ai-human-research-os

pengqianhan/ai-human-research-os · AGENTS.md

pengqianhan/ai-human-research-os · os-ui/DESIGN.md

pengqianhan/ai-human-research-os · os-ui/client/DESIGN.md

pengqianhan/ai-human-research-os · projects-folder/nanochat_cpu/AGENTS.md

pengqianhan/ai-human-research-os · projects-folder/templates/ai_research_template/AGENTS.md

pengqianhan/ai-human-research-os · research-skills-hub/claude-science-skills/skills/algorithmic-art/SKILL.md · Creating algorithmic art using p5.js with seeded randomness and interactive parameter exploration. Use this when users…

pengqianhan/ai-human-research-os · research-skills-hub/claude-science-skills/skills/alphafold2/SKILL.md · Predict protein structure for monomers and multimers with AlphaFold2 via the ColabFold runner (Mirdita et al. 2022…

pengqianhan/ai-human-research-os · research-skills-hub/claude-science-skills/skills/boltz/SKILL.md · Structure prediction for protein, nucleic-acid, and small-molecule complexes with Boltz-2 (Passaro & Wohlwend et al…

pengqianhan/ai-human-research-os · research-skills-hub/claude-science-skills/skills/borzoi/SKILL.md · Predict genome-wide functional tracks (RNA-seq, CAGE, DNase, ChIP) from DNA sequence with Borzoi. Use this skill when…

pengqianhan/ai-human-research-os · research-skills-hub/claude-science-skills/skills/chai1/SKILL.md · Structure prediction for protein, nucleic-acid, and small-molecule complexes with the Chai-1 foundation model (Chai…

pengqianhan/ai-human-research-os · research-skills-hub/claude-science-skills/skills/compute-env-setup/SKILL.md · Set up a compute environment on a remote provider so Claude Science jobs can run there. Covers direct SSH/conda hosts…

pengqianhan/ai-human-research-os · research-skills-hub/claude-science-skills/skills/customize/SKILL.md · Create, configure, and maintain custom agent profiles and author new skills via the `repl` tool. Use when the user…

pengqianhan/ai-human-research-os · research-skills-hub/claude-science-skills/skills/diffdock/SKILL.md · Predict small-molecule binding poses with DiffDock-L (Corso et al. 2023/2024, github.com/gcorso/DiffDock) — blind…

pengqianhan/ai-human-research-os · research-skills-hub/claude-science-skills/skills/esmfold2/SKILL.md · Biohub ESMFold2 / ESMFold2-Fast all-atom co-folding (Candido et al. 2026, github.com/Biohub/esm). Single-sequence and…

pengqianhan/ai-human-research-os · research-skills-hub/claude-science-skills/skills/evo2/SKILL.md · Score, embed, and generate DNA sequences with Evo 2, a long-context genomic foundation model. Use this skill when: (1)…

pengqianhan/ai-human-research-os · research-skills-hub/claude-science-skills/skills/fair-esm2/SKILL.md · Embed proteins with Meta AI's ESM-2 (`fair-esm` package). Use this skill when: (1) Extracting per-residue or…

pengqianhan/ai-human-research-os · research-skills-hub/claude-science-skills/skills/figure-composer/SKILL.md · Compose one publication-grade multi-panel figure. Entry from a one-line claim + data refs, OR from an existing figure…

pengqianhan/ai-human-research-os · research-skills-hub/claude-science-skills/skills/figure-style/SKILL.md · Publication-grade figure correctness and legibility rules. Load before drawing any plot and call `apply_figure_style()`…

pengqianhan/ai-human-research-os · research-skills-hub/claude-science-skills/skills/indication-dossier/SKILL.md · Generate a therapeutic indication dossier. Covers the patient population, epidemiology, disease biology, standard of…

pengqianhan/ai-human-research-os · research-skills-hub/claude-science-skills/skills/learn/SKILL.md · Use this skill when the user wants intellectual understanding — learning how or why something works, not getting a task…

pengqianhan/ai-human-research-os · research-skills-hub/claude-science-skills/skills/ligandmpnn/SKILL.md · Inverse-fold a backbone with ligand, nucleic-acid, and metal context using LigandMPNN (Dauparas et al. 2023…

pengqianhan/ai-human-research-os · research-skills-hub/claude-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…

pengqianhan/ai-human-research-os · research-skills-hub/claude-science-skills/skills/managed-model-endpoints/SKILL.md · Register a model service in the managed family — a local model server container the daemon starts/stops on demand, or a…

pengqianhan/ai-human-research-os · research-skills-hub/claude-science-skills/skills/openfold3/SKILL.md · Structure prediction using OpenFold3, an open-weights PyTorch reproduction of AlphaFold3 from the AlQuraishi Lab. Use…

pengqianhan/ai-human-research-os · research-skills-hub/claude-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 —…

pengqianhan/ai-human-research-os · research-skills-hub/claude-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…

pengqianhan/ai-human-research-os · research-skills-hub/claude-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…

pengqianhan/ai-human-research-os · research-skills-hub/claude-science-skills/skills/proteinmpnn/SKILL.md · Inverse-fold a protein backbone (PDB structure) into amino-acid sequence with ProteinMPNN (Dauparas et al. 2022…

pengqianhan/ai-human-research-os · research-skills-hub/claude-science-skills/skills/remote-compute-modal/SKILL.md · Run GPU jobs on the user's own Modal account via host.compute.create('byoc:modal', ...). Covers the…

pengqianhan/ai-human-research-os · research-skills-hub/claude-science-skills/skills/remote-compute-ssh/SKILL.md · Submit→wait_for_notification→harvest workflow for the user's SSH/SLURM hosts. Load once you've decided to dispatch…

pengqianhan/ai-human-research-os · research-skills-hub/claude-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…

pengqianhan/ai-human-research-os · research-skills-hub/claude-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…

pengqianhan/ai-human-research-os · research-skills-hub/claude-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…

pengqianhan/ai-human-research-os · research-skills-hub/claude-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…

pengqianhan/ai-human-research-os · research-skills-hub/claude-science-skills/skills/solublempnn/SKILL.md · Inverse-fold a backbone with SolubleMPNN — ProteinMPNN retrained on a soluble-PDB subset (Dauparas et al. 2022) — for…

pengqianhan/ai-human-research-os · research-skills-hub/claude-science-skills/skills/using-model-endpoint/SKILL.md · Call a registered model endpoint over its native HTTP API from the endpoint's scoped inference kernel (BASE_URL…

pengqianhan/ai-human-research-os · research-skills-hub/claude-science-skills/skills/web-artifacts-builder/SKILL.md · Suite of tools for creating elaborate, multi-component claude.ai HTML artifacts using modern frontend web technologies…

pengqianhan/ai-human-research-os · research-skills-hub/collected-skills/ResearchStudio-Idea/evaluation/idea_quality/SKILL.md · Score the QUALITY of a research idea at the idea stage — given a Markdown file with Title / Motivation / Method…

pengqianhan/ai-human-research-os · research-skills-hub/collected-skills/ResearchStudio-Idea/skills/idea_spark/SKILL.md · Generate ONE reviewer-defensible, implementable research idea with a concrete method and falsification plan from a…

pengqianhan/ai-human-research-os · research-skills-hub/collected-skills/ResearchStudio-Idea/skills/paper_search/SKILL.md · Search papers across arXiv, DBLP, OpenAlex, OpenReview, Semantic Scholar, and Crossref for a given query and year…

pengqianhan/ai-human-research-os · research-skills-hub/collected-skills/ResearchStudio-Idea/skills/scoop_check/SKILL.md · Check whether a proposed research novelty (given a problem statement and claimed idea/novelty) overlaps with existing…

pengqianhan/ai-human-research-os · research-skills-hub/collected-skills/academic-rebuttal/SKILL.md · Two-stage academic rebuttal assistant. Given the paper abstract, reviewer comments, scores, confidences, and venue…

pengqianhan/ai-human-research-os · research-skills-hub/collected-skills/alphaxiv-paper-lookup/SKILL.md · Look up any arxiv paper on alphaxiv.org to get a structured AI-generated overview. This is faster and more reliable…

pengqianhan/ai-human-research-os · research-skills-hub/collected-skills/arxiv2md/SKILL.md · Convert arXiv papers to clean Markdown. Use when the user wants to read, fetch, or summarize an arXiv paper.

pengqianhan/ai-human-research-os · research-skills-hub/collected-skills/baseline-selector/SKILL.md · Use when selecting, auditing, or justifying experimental baselines for a research idea, paper draft, task, benchmark…

pengqianhan/ai-human-research-os · research-skills-hub/collected-skills/deepxiv-baseline-table/SKILL.md · Build a markdown baseline table for a research topic using deepxiv search, brief, head, and experiment-section reads…

pengqianhan/ai-human-research-os · research-skills-hub/collected-skills/deepxiv-cli/SKILL.md · Access academic papers (arXiv, PMC, and coming soon bioRxiv, medRxiv) via CLI with hybrid search and intelligent…

pengqianhan/ai-human-research-os · research-skills-hub/collected-skills/deepxiv-trending-digest/SKILL.md · Summarize recent hot academic papers using deepxiv trending, brief, head, and section reads, then produce a markdown…

pengqianhan/ai-human-research-os · research-skills-hub/collected-skills/deli-autoresearch/SKILL.md · A protocol framework for long-horizon autonomous tasks. Targets three empirically-observed failure modes — cognitive…

pengqianhan/ai-human-research-os · research-skills-hub/collected-skills/drawio/SKILL.md · Generate draw.io diagrams as .drawio files, optionally export to PNG/SVG/PDF with embedded XML

pengqianhan/ai-human-research-os · research-skills-hub/collected-skills/explain-diff-html/SKILL.md · Use when the user asks for a rich explanation of a code change, diff, branch, or PR. Produces HTML output.

pengqianhan/ai-human-research-os · research-skills-hub/collected-skills/explain-this/SKILL.md · Explain any digital artifact — a paper, PDF, article, code diff, or codebase — so the person actually understands it…

pengqianhan/ai-human-research-os · research-skills-hub/collected-skills/grill-for-unknowns/SKILL.md · Use when starting or reviewing a complex implementation where the user wants an agent to interrogate the plan against…

pengqianhan/ai-human-research-os · research-skills-hub/collected-skills/hf-cli/SKILL.md · Hugging Face Hub CLI (`hf`) for downloading, uploading, and managing models, datasets, spaces, buckets, repos, papers…

pengqianhan/ai-human-research-os · research-skills-hub/collected-skills/hugging-face-paper-pages/SKILL.md · Look up and read Hugging Face paper pages in markdown, and use the papers API for structured metadata such as authors…

pengqianhan/ai-human-research-os · research-skills-hub/collected-skills/humanizer/AGENTS.md

pengqianhan/ai-human-research-os · research-skills-hub/collected-skills/humanizer/SKILL.md · Rewrite AI-sounding text so it reads naturally without changing what it says. Use when editing or reviewing prose for…

pengqianhan/ai-human-research-os · research-skills-hub/collected-skills/ml-paper-writing/SKILL.md · Write publication-ready ML/AI papers for NeurIPS, ICML, ICLR, ACL, AAAI, COLM. Use when drafting papers from research…

pengqianhan/ai-human-research-os · research-skills-hub/collected-skills/paper-finder/SKILL.md · Finds and organizes ML, CV, NLP, and AI research papers based on textual descriptions and keywords. Searches across…

pengqianhan/ai-human-research-os · research-skills-hub/collected-skills/pyzotero/SKILL.md · Interact with Zotero reference management libraries using the pyzotero Python client. Retrieve, create, update, and…

pengqianhan/ai-human-research-os · research-skills-hub/collected-skills/show-me/SKILL.md · Help the user understand the current topic visually with concise diagrams, code-shape sketches, and focused HTML…

pengqianhan/ai-human-research-os · research-skills-hub/collected-skills/skill-doctor/SKILL.md · Grades agent skills by scoring agent conversations against efficiency and code-quality rubrics, then drafts concrete…

pengqianhan/ai-human-research-os · research-skills-hub/mattpocock-skills/engineering/ask-matt/SKILL.md · Ask which skill or flow fits your situation. A router over the skills in this repo.

pengqianhan/ai-human-research-os · research-skills-hub/mattpocock-skills/engineering/code-review/SKILL.md · Review the changes since a fixed point (commit, branch, tag, or merge-base) along two axes: Standards (does the code…

pengqianhan/ai-human-research-os · research-skills-hub/mattpocock-skills/engineering/codebase-design/SKILL.md · Shared vocabulary for designing deep modules. Use when the user wants to design or improve a module's interface, find…

pengqianhan/ai-human-research-os · research-skills-hub/mattpocock-skills/engineering/diagnosing-bugs/SKILL.md · Diagnosis loop for hard bugs and performance regressions. Use when the user says "diagnose"/"debug this", or reports…

pengqianhan/ai-human-research-os · research-skills-hub/mattpocock-skills/engineering/domain-modeling/SKILL.md · Build and sharpen a project's domain model. Use when discussing codebase terminology, writing or editing a GLOSSARY.md…

pengqianhan/ai-human-research-os · research-skills-hub/mattpocock-skills/engineering/grill-with-docs/SKILL.md · A relentless interview to sharpen a plan or design, which also creates docs (ADR's and glossary) as we go.

pengqianhan/ai-human-research-os · research-skills-hub/mattpocock-skills/engineering/implement-spec/SKILL.md · Implement the result of /to-spec and /to-tickets in code.

pengqianhan/ai-human-research-os · research-skills-hub/mattpocock-skills/engineering/implement/SKILL.md · Implement a piece of work based on a spec or set of tickets.

pengqianhan/ai-human-research-os · research-skills-hub/mattpocock-skills/engineering/improve-codebase-architecture/SKILL.md · Scan a codebase for deepening opportunities, present them as a visual HTML report, then grill through whichever one you…

pengqianhan/ai-human-research-os · research-skills-hub/mattpocock-skills/engineering/pr/SKILL.md · Use when writing a PR body.

pengqianhan/ai-human-research-os · research-skills-hub/mattpocock-skills/engineering/prototype/SKILL.md · Build a throwaway prototype to answer a design question. Use when the user wants to sanity-check whether a state model…

pengqianhan/ai-human-research-os · research-skills-hub/mattpocock-skills/engineering/research/SKILL.md · Investigate a question against high-trust primary sources and capture the findings as a Markdown file in the repo. Use…

pengqianhan/ai-human-research-os · research-skills-hub/mattpocock-skills/engineering/retro/SKILL.md · Conduct a retrospective on a coding session.

pengqianhan/ai-human-research-os · research-skills-hub/mattpocock-skills/engineering/setup-matt-pocock-skills/SKILL.md · Configure this repo for the engineering skills: set up its issue tracker, triage label vocabulary, and domain doc…

pengqianhan/ai-human-research-os · research-skills-hub/mattpocock-skills/engineering/tdd/SKILL.md · Test-driven development. Use when the user wants to build features or fix bugs test-first, mentions…

pengqianhan/ai-human-research-os · research-skills-hub/mattpocock-skills/engineering/to-spec/SKILL.md · Turn the current conversation into a spec and publish it to the project issue tracker: no interview, just synthesis of…

pengqianhan/ai-human-research-os · research-skills-hub/mattpocock-skills/engineering/to-tickets/SKILL.md · Break a plan, spec, or the current conversation into a set of tracer-bullet tickets, each declaring its blocking edges…

pengqianhan/ai-human-research-os · research-skills-hub/mattpocock-skills/engineering/triage/SKILL.md · Move issues and external PRs through a state machine of triage roles, categorise, verify, grill if needed, and write…

pengqianhan/ai-human-research-os · research-skills-hub/mattpocock-skills/engineering/wayfinder/SKILL.md · Plan a huge chunk of work (more than one agent session can hold) as a shared map of decision tickets on your issue…

pengqianhan/ai-human-research-os · research-skills-hub/mattpocock-skills/engineering/wizard/SKILL.md · Generate an interactive bash wizard that walks a human through steps only they can perform. Use when provisioning…

pengqianhan/ai-human-research-os · research-skills-hub/mattpocock-skills/productivity/grill-me/SKILL.md · A relentless interview to sharpen a plan or design.

pengqianhan/ai-human-research-os · research-skills-hub/mattpocock-skills/productivity/grilling/SKILL.md · Grill the user relentlessly about a plan, decision, or idea. Use when the user wants to stress-test their thinking, or…

pengqianhan/ai-human-research-os · research-skills-hub/mattpocock-skills/productivity/handoff/SKILL.md · Compact the current conversation into a handoff document for another agent to pick up.

pengqianhan/ai-human-research-os · research-skills-hub/mattpocock-skills/productivity/teach/SKILL.md · Teach the user a new skill or concept, within this workspace.

pengqianhan/ai-human-research-os · research-skills-hub/mattpocock-skills/productivity/to-questionnaire/SKILL.md · Turn a decision you can't fully answer into a questionnaire for someone else to fill in.

pengqianhan/ai-human-research-os · research-skills-hub/mattpocock-skills/productivity/wait-what/SKILL.md · Stop. That last message did not land: re-pitch it.

pengqianhan/ai-human-research-os · research-skills-hub/mattpocock-skills/productivity/writing-for-agents/SKILL.md · Writing documents for agents. Use when creating or editing skills, or modifying AGENTS.md or CLAUDE.md.

pengqianhan/ai-human-research-os · research-skills-hub/open-paper-skills/codex-paper-figure-skill/SKILL.md · Create editable academic-paper figures from natural-language figure descriptions, manuscript sections, methods/results…

pengqianhan/ai-human-research-os · research-skills-hub/open-paper-skills/discover-academic-skills/SKILL.md · Discover research/academic agent-skills from skills.sh (and user-supplied candidates), filter them through strict hard…

pengqianhan/ai-human-research-os · research-skills-hub/open-paper-skills/drawio-paper/SKILL.md · Generate publication-quality academic paper diagrams (.drawio) and statistical plots (.png via Python/matplotlib) using…

pengqianhan/ai-human-research-os · research-skills-hub/open-paper-skills/explain-anything-html/SKILL.md · Use when the user asks for a rich explanation of a research paper, blog post, article, documentation, or any complex…

pengqianhan/ai-human-research-os · research-skills-hub/open-paper-skills/explain-paper-html/SKILL.md · Lesson builder for academic papers. Use when Codex needs a deep teaching-oriented paper/PDF explanation, a…

pengqianhan/ai-human-research-os · research-skills-hub/open-paper-skills/filetree-simple/SKILL.md · Generate or lint a compact top-level FILETREE.md navigation map. Use when repository structure changes or FILETREE.md…

pengqianhan/ai-human-research-os · research-skills-hub/open-paper-skills/human-cognition-cache/SKILL.md · Scaffold human cognition with a project-local, git-trackable four-quadrant cache. Use when (1) initializing, reading…

pengqianhan/ai-human-research-os · research-skills-hub/open-paper-skills/karpathy-coding-rules/SKILL.md · Andrej Karpathy's field notes (CLAUDE.md, v260626) on getting a language model to write code you will NOT have to…

pengqianhan/ai-human-research-os · research-skills-hub/open-paper-skills/map-then-territory/SKILL.md · Map scattered ideas into a human-approved DAG of verifiable states, then drive fresh agents through it edge by edge…

pengqianhan/ai-human-research-os · research-skills-hub/open-paper-skills/okf-repo-organizer/SKILL.md · Organize a repository, folder, or knowledge corpus into generic Open Knowledge Format (OKF) bundles. Use when you are…

pengqianhan/ai-human-research-os · research-skills-hub/open-paper-skills/paper-search/SKILL.md · Search and read research papers across alphaXiv, OpenAlex, bioRxiv, PubMed, Hugging Face Papers, Papers with Code, and…