Agent Skills

---

name: geniml

description: This skill should be used when working with genomic interval data (BED files) for machine learning tasks. Use for training region embeddings (Region2Vec, BEDspace), single-cell ATAC-seq analysis (scEmbed), building consensus peaks (universes), or any ML-based analysis of genomic regions. Applies to BED file collections, scATAC-seq data, chromatin accessibility datasets, and region-based genomic feature learning.

---

name: geo-database

description: Access NCBI GEO for gene expression/genomics data. Search/download microarray and RNA-seq datasets (GSE, GSM, GPL), retrieve SOFT/Matrix files, for transcriptomics and expression analysis.

---

name: gget

description: Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST searches, AlphaFold structures, enrichment analysis. Best for interactive exploration, simple queries. For batch processing or advanced BLAST use biopython; for multi-database Python workflows use bioservices.

---

name: goal-test

description: Turn a vague task into a testable definition of done and generate an executable goal-test script for it, optionally with a bounded retry loop around a headless agent. Use when the user wants to run an agent in a loop, asks how to know when an agent task is finished, or says a goal like "improve X" needs to become checkable. Do NOT use for building eval suites over many cases — that is evals-bootstrap.

---

name: gtars

description: High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment analysis in computational genomics and machine learning applications.

---

name: gwas-database

description: Query NHGRI-EBI GWAS Catalog for SNP-trait associations. Search variants by rs ID, disease/trait, gene, retrieve p-values and summary statistics, for genetic epidemiology and polygenic risk scores.

---

name: harness-audit

description: Audit an agent's harness against the four rings: containment, guides, sensors, permissions. Use when the user asks whether their agent setup is safe, wants a review of sandboxing / permissions / hooks / AGENTS.md guardrails, or asks what a bad session could break. Read-only: reports the blast radius and a hardening list, changes nothing. Do NOT use for context layout (context-audit) or cost routing (gate-check).

---

name: histolab

description: Lightweight WSI tile extraction and preprocessing. Use for basic slide processing tissue detection, tile extraction, stain normalization for H&E images. Best for simple pipelines, dataset preparation, quick tile-based analysis. For advanced spatial proteomics, multiplexed imaging, or deep learning pipelines use pathml.

---

name: second-brain-backfill

description: Import a large archive into the vault in controlled batches: triage what is worth ingesting, process oldest first, checkpoint after every batch, and keep cost visible. Use this skill whenever the user wants to import years of bookmarks, an export from another notes app, a downloads folder, a chat history dump, or says "backfill", "bulk import", "process my archive". Do NOT use for ingesting one or a few new sources, which is second-brain-ingest.

---

name: second-brain-changed-my-mind

description: Trace where the user's recorded position on something has shifted: superseded claims, contradictions between sources of different dates, and what evidence moved them. Use this skill when the user asks what they have changed their mind about, how their thinking on a topic developed, what they used to believe, or wants a quarterly look back at their own positions. Do NOT use for finding contradictions between sources with no time dimension, or for a current-state answer.

---

name: second-brain-chat-import

description: Triage an exported chat history into what to ingest, what to archive and what to delete, with a privacy pass first. Use this skill when the user has exported their Claude or ChatGPT history, asks to import old conversations, or asks what in their chat archive is worth keeping. Do NOT use for ingesting a single pasted conversation, or for any material the user has not explicitly asked to bring into the vault.

---

name: second-brain-graph

description: Analyse the vault's link graph and report on its shape: orphan rate, average degree, components, hubs, bridges and clusters, with what each number means for retrieval. Use this skill when the user asks about the health or structure of their graph, wants metrics, asks which pages are most connected or most isolated, or asks whether the vault is fragmented. Do NOT use for fixing what it finds, which is second-brain-lint, or for answering a content question.

---

name: second-brain-ingest

description: Turn raw source material in a second-brain vault into linked wiki pages: read the source, split it into concepts and entities, write or update pages, connect them to existing pages, and record the run in the log. Use this skill whenever the user drops a file into raw/, pastes an article, transcript or PDF and asks to add it to the vault, says "ingest this", "add this to my second brain", "process raw", or asks to catch up on unprocessed sources, even if they do not name the ingest command. Do NOT use for answering questions from an existing vault, for linting or repairing pages, or for editing notes the user wrote by hand.

---

name: second-brain-lint

description: Audit a second-brain vault for structural problems and repair them: broken wikilinks, orphan pages, empty stubs, frontmatter that violates the schema, near-duplicate pages, and stale index entries. Use this skill whenever the user asks to lint, clean, audit or check the health of their vault, says pages feel messy or links are broken, after a large bulk import, or when a scheduled maintenance run fires. Do NOT use for ingesting new sources, for answering questions from the vault, or for rewriting page content that is structurally fine but reads badly.

---

name: second-brain-merge

description: Merge two pages that describe the same thing, preserving every distinct claim, redirecting inbound links, and recording the merge. Use this skill when the user approves a duplicate merge, says "these are the same page", "merge X into Y", or asks to clean up near-duplicates that a lint run proposed. Do NOT use to merge pages on your own judgement, to delete a page outright, or to split one page into several.

---

name: second-brain-metrics

description: Record a dated snapshot of the vault's health numbers and compare against previous snapshots so trends are visible. Use this skill for a monthly or quarterly check, when the user asks whether the vault is improving, or asks to track its numbers over time. Do NOT use for a one-off graph analysis, which is second-brain-graph, or for structural repairs.

---

name: second-brain-privacy

description: Audit the vault for material that should not be in it: credentials, other people's private information, confidential work, and anything the user would not want synced or backed up. Use this skill when the user asks about privacy, is about to share or sync the vault, has just imported chat history or meeting notes, or asks what is sensitive in their notes. Do NOT use to delete anything on your own, or as a substitute for the publishing check.

---

name: second-brain-project

description: Set up or update a project in the vault: the four-stage folder pipeline, a project-scoped CLAUDE.md with one goal, and links to the concept pages it depends on. Use this skill when the user starts something new they will work on over time, says "create a project", "set up a folder for X", or asks to define the goal and structure of ongoing work. Do NOT use for one-off tasks, for wiki pages about a topic, or for scoping an existing project down to work in it.

---

name: second-brain-publish

description: Prepare a subset of the vault for publishing: check opt-in flags, find private material, and report what would leak through links before anything is exported. Use this skill when the user wants to publish notes as a site or digital garden, asks what is safe to make public, or is setting up an export. Do NOT use for exporting a single document, or for running the publishing tool itself.

---

name: second-brain-query

description: Answer a question from a second-brain vault by reading its own pages, citing the pages used, and saying plainly when the vault does not contain the answer. Use this skill whenever the user asks what they know about a topic, what they have read on something, what connects two ideas, what they have changed their mind about, or asks any question that should be answered from their own notes rather than general knowledge. Do NOT use for ingesting new material, for general questions the vault has nothing to do with, or when the user explicitly wants an answer from the open web.

---

name: second-brain-quiz

description: Generate questions from the user's own concept pages so they can find out what they saved but never learned, and compare their answers against what the pages say. Use this skill when the user wants to test themselves, revise, make flashcards from their notes, or asks what they have forgotten. Do NOT use for generic quizzing on a topic the vault does not cover, or for answering a question from the vault.

---

name: second-brain-rename

description: Rename a page safely: update the file, fix every inbound wikilink, add the old name as an alias, and log it. Use this skill whenever a page needs a different canonical title, the user says "rename X to Y", asks to fix an inconsistent title, or after a lint run flags naming problems. Do NOT use for merging two pages, for moving a page between folders without a name change, or for renaming files outside the wiki.

---

name: second-brain-report

description: Produce a research report from the vault: scope the question against existing pages, name the gaps, and write findings with citations, disagreements and limits. Use this skill when the user asks for a research report, a deep write-up on a topic, or wants to understand a subject thoroughly using what they have collected. Do NOT use for a quick answer from the vault, for drafting an article in the user's voice, or for summarising a single source.

---

name: second-brain-review

description: Produce a periodic review of a second-brain vault: what was added, which topics are growing, what contradicts what, which questions are still open, and what is worth reading next. Use this skill whenever the user asks for a weekly or monthly review, asks what changed in their vault, what they have been learning about lately, or what they should look at next, and when a scheduled review task fires. Do NOT use for structural linting, for ingesting sources, or for answering a specific factual question.