NeuroAIHub/BrainPilot

audit-code-artifact

Audit scientific implementation, exported-model equivalence, dependency completeness, manifests, packaging, and isolated inference. Use when claims depend on code, trained artifacts, evaluators, or deployable entry points.

audit-data-integrity

Audit scientific data semantics, sample and label alignment, leakage, group splits, preprocessing boundaries, and train-to-inference transforms. Use for any result based on datasets, feature matrices, tensors, repeated observations, or learned preprocessing.

audit-evidence

Audit numeric, artifact, log, citation, and cross-report claims against inspectable evidence. Use for reports, syntheses, benchmark claims, external citations, or conflicting Expert outputs.

audit-feedback-loop

Coordinate iterative evidence and reliability reviews between BrainPilot's Principal Investigator and Auditor. Use when PI needs to audit its own draft, an Expert result, or a multi-agent synthesis; when Auditor receives such a review task; or when a previous…

audit-model-validation

Audit whether method discovery, comparison, representative real-data validation, collapse diagnostics, pruning, and selection evidence support claims of suitability or superiority. Use for research-method selection, empirical evaluation, benchmarking,…

create-data-inventory

Create or update the canonical Markdown inventory of task-relevant research data. Engineer must invoke this skill before creating or updating any data inventory, data contract, or dataset-coverage summary that downstream agents will use.

source-grounded-research-report

Research a bounded factual, documentation, API, or literature question from authoritative sources and save a self-contained Markdown report with claim-level citations. Use for reading-heavy evidence gathering, not experiment execution or data analysis.

brainstorming

You MUST use this before any creative work - creating features, building components, adding functionality, or modifying behavior. Explores user intent, requirements and design before implementation.

executing-plans

Use when you have a written implementation plan to execute in a separate session with review checkpoints

finishing-a-development-branch

Use when implementation is complete, all tests pass, and you need to decide how to integrate the work

requesting-code-review

Use when completing tasks, implementing major features, or before merging to verify work meets requirements

subagent-driven-development

Use when executing implementation plans with independent tasks in the current session

systematic-debugging

Use when encountering any bug, test failure, or unexpected behavior, before proposing fixes

test-driven-development

Use when implementing any feature or bugfix, before writing implementation code

using-superpowers

Use when starting any conversation - establishes how to find and use skills, requiring skill invocation before ANY response including clarifying questions

writing-plans

Use when you have a spec or requirements for a multi-step task, before touching code

writing-skills

Use when creating new skills, editing existing skills, or verifying skills work before deployment

curate-research-trace

Curate BrainPilot Trace Events into human-readable research Episodes, appropriately granular nodes, and direct depends_on relationships. Use when a report contains multiple settings, results, analyses, visualizations, findings, or conclusions; when Episode…

spikeinterface-skill

Domain knowledge for building extracellular electrophysiology pipelines with SpikeInterface: loading data with extractors, preprocessing, running spike sorters, post-processing via SortingAnalyzer, quality metrics, curation, comparison, visualization, and…

fmriprep

Preprocess task-based or resting-state fMRI data with fMRIPrep — a robust, BIDS-App preprocessing pipeline built on FSL, ANTs, FreeSurfer, AFNI, and Nilearn. Use this skill whenever the user asks to preprocess fMRI/BOLD data, run fMRIPrep on a BIDS dataset,…

workflow-skill-creator

Distills a completed user workflow or interaction into a reusable agent skill. Use when the user asks to turn their workflow, interaction, or multi-step process into a skill, or when they say "make this a skill", "create a skill from what we just did",…

netneurotools-guide

Domain-validated guidance for network neuroscience analysis using netneurotools: datasets, brain network metrics, connectivity consensus, modularity, spatial statistics, null models, and cortical surface visualization. Use this skill whenever the user works…

alphafold-database-fetch-and-analyze

Retrieve and analyze AlphaFold predicted structures for a protein. Use when the user provides a specific UniProt Accession ID and wants structural confidence metrics (pLDDT), domain boundary analysis, or disorder assessment. Do not use if the user only has a…

gtex-database

Use when you want to retrieve quantitative RNA expression data and variant eQTL information from the GTEx (Genotype-Tissue Expression) Project across 54 non-diseased tissue sites.

human-protein-atlas-database

Use when you want to retrieve semi-quantitative protein expression and spatial localisation data from the Human Protein Atlas (HPA).

pdb-database

Use when you want to search for or download experimentally-determined 3D structures for biomolecules (proteins, nucleic acids, bound ligands). Supports searching by sequence similarity, structure similarity, chemical and other attributes. Also use to get…

pymol

Visualize, analyze, and render protein and molecular structures using PyMOL. Use when the user wants to create images of protein structures, perform structural alignments or superposition, measure distances or contacts, highlight binding sites or active site…

literature-search-arxiv

Search for scientific papers, preprints, and publications on arXiv. Extract metadata, abstracts, and download full-text PDFs or HTML versions of papers. Use when the user asks to find research papers, literature, or specific arXiv IDs.

literature-search-biorxiv

Browse, filter, and download life sciences, biology, and medical preprints from bioRxiv and medRxiv. Supports fetching paper metadata by DOI, and browsing by date range with category and keyword filters. Keyword filtering is local, so date ranges MUST be…

literature-search-europepmc

Search Europe PMC for scientific literature and download open-access full texts and PDFs. Retrieve full-text XML/plain text by PMCID, get citation lists and bibliography.

literature-search-openalex

Query the OpenAlex scholarly database for research papers, authors, institutions, topics, sources, publishers, funders, geo-locations, and keywords. Use when searching academic papers, resolving DOIs, downloading open-access PDFs, finding an author's…

pubmed-database

Search PubMed for scientific literature, including published clinical trials. Fetch abstracts and full text. Link published research to biological databases (gene, protein, nucleotide, PubChem) to discover associations between papers and specific compounds or…

alphagenome-single-variant-analysis

Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API. Use when the user asks about non-coding variant effects, pathogenicity, clinical…

clinvar-database

Use when needing clinical significance, pathogenicity classifications (e.g., Pathogenic, Benign, VUS), clinical evidence rationales, or finding "hard positive" benchmark controls for human genomic variants.

dbsnp-database

Use when you want to look up, map, and search for short genetic variants (SNPs, indels) in NCBI's dbSNP database. Resolves between rsIDs, genomic coordinates in VCF format, and HGVS strings. For an rsID, returns variant type, gene associations, clinical…

gnomad-database

Query the Genome Aggregation Database (gnomAD). Use when determining the rarity or allele frequency of specific genetic variants, retrieving gene constraint metrics (pLI, LOEUF) to assess loss-of-function intolerance, finding variants in a genomic region or…

chembl-database

Query the ChEMBL database for bioactive molecules, drug targets, bioactivity data, approved drugs, and chemical structures. Use when the user asks about compounds, targets, IC50/Ki values, drug mechanisms, or structure searches.

clinical-trials-database

Query ClinicalTrials.gov via APIv2. Use when you want to search for trials by condition, drug, location, status, or phase; retrieve trial details by NCT ID; check eligibility/inclusion criteria; count trials across conditions or time periods; identify a…

openfda-database

Query, search, and download data from the openFDA API for drugs, devices, foods, tobacco, cosmetics, animal and veterinary products, substances, and transparency data. Use for FDA adverse events, recalls, labeling, approvals, shortages, 510(k) clearances, NDC…

opentargets-database

Query Open Targets Platform for target-disease associations, drug target discovery, tractability/safety data, genetics/omics evidence, known drugs, for therapeutic target identification.