All Skills

Query JASPAR for transcription factor binding site (TFBS) profiles (PWMs/PFMs), searching by TF name, species, or class, scanning DNA sequences for binding sites, and comparing matrices. Use when doing motif analysis, regulatory genomics, transcription factor binding prediction, or interpreting regulatory/non-coding GWAS variants. Part of the AlterLab Academic Skills suite.

Bayesian modeling and probabilistic programming with PyMC — hierarchical models, MCMC (NUTS) sampling, variational inference, LOO/WAIC model comparison, and posterior predictive checks. Use when fitting Bayesian or hierarchical models, estimating posteriors and credible intervals, running probabilistic inference, or comparing models with LOO/WAIC. Part of the AlterLab Academic Skills suite.

Search the bioRxiv preprint server and retrieve paper metadata or download PDFs via its API. Use when finding life sciences preprints by keywords, authors, DOI, date ranges, or categories, or when conducting a biology literature review of not-yet-peer-reviewed work. Part of the AlterLab Academic Skills suite.

Query the Monarch Initiative knowledge graph for disease-gene-phenotype associations across species, integrating OMIM, ORPHANET, HPO, ClinVar, and model organism databases. Use when discovering rare disease genes, mapping phenotypes to genes, modeling disease across species, or looking up HPO terms. Part of the AlterLab Academic Skills suite.

Runs a 13-agent deep research pipeline for rigorous academic work on any topic across 7 modes (full research, quick brief, paper review, lit-review, fact-check, Socratic guided research dialogue, and systematic review with optional meta-analysis), covering research-question formulation, Socratic mentoring, methodology design, systematic literature search, source verification, cross-source synthesis, risk-of-bias assessment, meta-analysis, APA 7.0 report compilation, editorial and devil's-advocate review, ethics review, and post-research literature monitoring. Use when the request mentions research, deep research, literature review, systematic review, meta-analysis, PRISMA, evidence synthesis, fact-check, guide my research, help me think through, or 研究, 深度研究, 文獻回顧, 文獻探討, 系統性回顧, 後設分析, 事實查核, 引導我的研究, 幫我釐清, 幫我想想, 我不確定要研究什麼, 研究方向, 研究主題. Part of the AlterLab Academic Skills suite.

Query the EMBL-EBI InterPro REST API for protein family, domain, and functional-site annotations integrated from member databases (Pfam, PANTHER, PRINTS, SMART, SUPERFAMILY, CDD, ProSite, NCBIfam, and others). Use when predicting protein function, analyzing or comparing domain architecture, classifying a protein by family or homologous superfamily, resolving a Pfam/InterPro accession, or mapping a protein's signatures to GO terms. Not for raw UniProt entry/FASTA retrieval or AlphaFold 3D structures. Part of the AlterLab Academic Skills suite.

Simulates a full multi-reviewer journal review PANEL — 5 personas (Editor-in-Chief + 3 peer reviewers + a Devil's Advocate) debate a manuscript and produce a consensus Editorial Decision (accept/minor/major/reject) plus a prioritized Revision Roadmap. Modes: full, re-review (verify revisions addressed prior comments), quick, methodology-focus, Socratic guided. Use for: simulate peer review, mock review panel, editorial review before submission, multiple reviewer perspectives, re-review of a revised manuscript, or 'critique my paper hard'. For a single-reviewer referee report use alterlab-peer-review; for rubric/grade scoring use alterlab-scholar-eval; to write/revise the paper use alterlab-paper-writer. Part of the AlterLab Academic Skills suite.

Co-fold biomolecular complexes with Boltz-2, an open AlphaFold3-style model — predict protein + ligand (SMILES/CCD), protein + nucleic-acid, and multi-chain structures in one pass, with binding-affinity prediction. Use when folding a protein together with a small-molecule ligand, predicting a holo (ligand-bound) complex or its binding affinity, or co-folding protein–DNA/RNA assemblies. For protein-only or protein–protein folding without ligands prefer alterlab-alphafold; for antibody–antigen complexes prefer alterlab-chai; to dock a ligand into a FIXED receptor structure prefer alterlab-diffdock; to look up an existing structure prefer alterlab-pdb. Part of the AlterLab Academic Skills suite.

Query cBioPortal via its keyless REST API for cancer genomics across TCGA, GENIE, MSK-IMPACT and hundreds of studies — somatic mutations, copy-number alterations (GISTIC), mRNA/protein expression, structural variants, and patient-level clinical/survival data. Use when asked how often a gene is mutated/amplified/deleted in a tumor type, to profile oncogenes or tumor suppressors across cancers (pan-cancer alteration frequency), to pull patient-level mutations joined to OS/clinical outcomes, or to validate a cancer target from cohort genomics. For germline variant pathogenicity use alterlab-clinvar; for mutational-signature (SBS) decomposition use alterlab-cosmic; for CRISPR/RNAi gene-dependency use alterlab-depmap; for aggregated target-disease evidence use alterlab-opentargets. Part of the AlterLab Academic Skills suite.

Parse and write FCS (Flow Cytometry Standard) files v2.0-3.1 with FlowIO — extract event data as NumPy arrays, read $-keyword metadata and channel/parameter definitions, and convert events to CSV or pandas DataFrame. Use when loading raw .fcs flow-cytometry files, inspecting channels and metadata, or preprocessing cytometry data for downstream gating and analysis. Part of the AlterLab Academic Skills suite.

Provides the RDKit cheminformatics toolkit for low-level, fine-grained molecular primitives — SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure/SMARTS search, 2D/3D coordinate generation, similarity, and reaction handling. Use when custom sanitization, specialized fingerprint or descriptor algorithms, reaction enumeration, or conformer generation demand direct API control; for a high-level pandas-friendly wrapper over RDKit prefer alterlab-datamol, and for turning molecules into ML feature vectors prefer alterlab-molfeat. Part of the AlterLab Academic Skills suite.

Runs high-performance genomic interval analysis with gtars (databio), a Rust toolkit with Python bindings — the performance-critical backend for the geniml ML library. Use when computing overlaps/jaccard/coverage between BED region sets, indexing intervals with IGD, generating uniwig accumulation/coverage tracks, tokenizing genomic regions for ML, splitting single-cell fragments into pseudobulks, or computing GA4GH refget sequence digests. NOT for training region embeddings (use alterlab-geniml) or non-genomic spatial joins (use alterlab-geopandas). Part of the AlterLab Academic Skills suite.

Build, slice, concatenate, read, and write AnnData annotated data matrices (obs, var, X, layers, obsm, uns) — the scverse data STRUCTURE, not an analysis pipeline. Use when creating or wrangling .h5ad/zarr files, managing cell and gene annotations, concatenating batches, or handling layers/obsm/backed-mode; for the QC, normalization, clustering, UMAP, and differential-expression analysis pipeline prefer alterlab-scanpy instead, and for RNA velocity from spliced/unspliced layers prefer alterlab-scvelo instead. Part of the AlterLab Academic Skills suite.

Supervises theses and dissertations end to end — structure guidance from proposal through defense, chapter-by-chapter writing support (introduction, literature review, methodology, results, discussion), supervision strategies, committee management, defense and viva voce preparation, timeline planning, feedback integration, examiner-expectation guidance, and formatting (APA 7, Chicago, university styles). Use when the request mentions thesis, dissertation, supervision, defense preparation, viva, proposal defense, thesis structure, thesis chapter, literature review chapter, methodology chapter, results chapter, discussion chapter, thesis timeline, committee, thesis formatting, or dissertation proposal. Part of the AlterLab Academic Skills suite.

Queries the FRED (Federal Reserve Economic Data) API for 800,000+ economic time series from 100+ sources, covering GDP, unemployment, inflation, interest rates, exchange rates, housing, and regional data. Use for macroeconomic analysis, financial research, policy studies, economic forecasting, fetching U.S. or international economic indicators by FRED series ID, and academic research requiring historical economic time series. Part of the AlterLab Academic Skills suite.

Build complete mass-spectrometry workflows with pyOpenMS — feature detection, peptide identification, protein quantification, and full LC-MS/MS pipelines across many MS file formats (mzML, mzXML) and algorithms. Use for comprehensive proteomics and MS data processing — for simple spectral comparison and metabolite identification use matchms. Part of the AlterLab Academic Skills suite.

Queries the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biomedical relationships across genes, drugs, diseases, phenotypes, pathways, and biological processes. Use when exploring drug-disease or gene-disease links, building disease-centric knowledge subgraphs, or sourcing relations for drug repurposing and precision-medicine analyses. Part of the AlterLab Academic Skills suite.

Read, create, and convert Microsoft PowerPoint (.pptx) presentations — extract slide text to JSON/markdown, build decks from JSON/markdown outlines, and export to PDF.

Drafts enforceable End-User License Agreements for software licensors across desktop, mobile, SaaS, and cloud models. Covers click-wrap formation, IP ownership, liability limitations, data privacy compliance (GDPR/CCPA/COPPA), and export controls. Use when drafting software license agreements, app store terms, SaaS subscription agreements, or trial/freemium license terms.

Drafts a Written Information Security Program compliant with Massachusetts 201 CMR 17.00 and supplementary frameworks (GDPR, CCPA, HIPAA, GLBA, PCI-DSS). Produces a board-ready regulatory document covering coordinator designation, risk assessment, safeguards, training, incident response with breach notification, and vendor oversight. Use when an organization handles personal information of MA residents and needs a standalone WISP for regulatory examination or executive approval.

Drafts SEC Form 8-K current reports with item-accurate narratives, exhibit indexing, and EDGAR-ready formatting. Use when a public company must disclose a reportable event (material agreement, acquisition, personnel change, Reg FD disclosure) or file a current report within four business days. Trigger on "Form 8-K", "current report", "8-K filing", "EDGAR", "Item 1.01", "Item 2.01", "Item 5.02", "Reg FD".

Drafts SEC- or state-filed Form ADV Parts 1A/1B/2A/2B for investment adviser registration, producing IARD-ready responses, brochures, and supplements. Use when drafting or amending Form ADV, preparing RIA registration, building Part 2A brochures or Part 2B supplements, or compiling IARD filings. Trigger: "Form ADV", "RIA registration", "investment adviser brochure", "Part 1A", "Part 1B", "Part 2A", "Part 2B", "IARD", "SEC filing", "state registration".

Drafts a GDPR- and CCPA-compliant Data Subject Access Request (DSAR) intake form for collecting requester information and processing privacy rights. Use when drafting DSAR forms, privacy rights request templates, or data subject rights workflows for EU/US-regulated organizations.

Drafts a Spill Prevention, Control, and Countermeasure (SPCC) Plan compliant with 40 CFR Part 112 under the Clean Water Act. Covers facility characterization, oil storage inventory, secondary containment, prevention measures, response procedures, training, and PE certification language. Use when drafting SPCC plans, oil spill prevention documents, or EPA compliance submissions.

Drafts U.S. internal legal memoranda using IRAC structure to analyze issues, synthesize authority, assess risks, and recommend strategy. Use when asked to draft a research memo, internal memo, issue analysis, case strategy memo, or any IRAC-based legal analysis.

Drafts FinCEN Suspicious Activity Reports (Form 111) for BSA/AML regulatory filing. Compiles subject identification, transaction timelines, red-flag analysis, and activity classifications. Use when a financial institution detects suspicious transactions requiring mandatory SAR filing, continuing activity reports, or BSA compliance documentation.

Drafts structured client memoranda translating legal analysis and strategic recommendations into plain language for non-lawyer audiences. Covers corporate governance, fiduciary duties, compliance, and transactional advice. Enforces standard memo architecture: heading block, executive summary, background, analysis, options, and recommendations. Use when preparing client-facing memos, opinion letters, or governance briefings.

Drafts a U.S. Lis Pendens (Notice of Pending Action) for recording against real property. Covers intake, statutory authority mapping, legal description, verification, and proof of service. Use when preparing a lis pendens, notice of pending action, or recording notice tied to title or possession claims. Trigger: lis pendens, notice of pending action, quiet title, specific performance, foreclosure, partition, lien enforcement, expungement.

Drafts FDA product recall plans compliant with 21 CFR Part 7, covering Recall Committee governance, health hazard evaluation, recall classification, notification protocols, effectiveness checks, product disposition, and termination procedures. Use when developing recall SOPs, updating recall procedures, drafting recall readiness plans, or preparing FDA-regulated product recall documentation.

Drafts and analyzes U.S. appellate amicus curiae briefs for non-parties with Rule 29/Rule 37 compliance, unique perspective development, and Bluebook-ready citations. Use when asked to draft or review an amicus brief, friend-of-the-court brief, non-party brief, or anything involving FRAP 29, Supreme Court Rule 37, or appellate amicus practice.

Drafts U.S. employee non-disclosure/confidentiality agreements that protect employer trade secrets and proprietary information while preserving employee mobility. Triggers on: employee NDA, confidentiality agreement, non-disclosure agreement, trade secret protection, proprietary information, onboarding confidentiality clause, pre-employment NDA.

Drafts an HOA Addendum to a residential purchase agreement covering mandatory membership, financial obligations, governing documents, use restrictions, and buyer acknowledgments. Use when drafting HOA addenda, HOA disclosure forms, purchase addenda for HOA-governed properties, or CC&R disclosure documents.

Drafts a Master Service Agreement for upstream oilfield services (Operator-Contractor). Covers knock-for-knock indemnification, anti-indemnity statute compliance (TX, LA, WY, NM), work order framework, HSE, insurance minimums, and IP/data ownership. Use when drafting oilfield MSAs, drilling service agreements, well service contracts, or upstream operator-contractor master agreements.

Drafts evaluation-ready U.S. federal RFP responses across all standard proposal volumes (cover letter, technical, cost/price, reps and certs). Enforces FAR compliance, CPARS references, and Section L/M alignment. Use when preparing federal solicitation submissions, responding to government RFPs, or drafting procurement bids.

Guides attorneys through deposition witness preparation using a two-session model with document review, practice examination, and day-of logistics. Covers party witnesses, fact witnesses, 30(b)(6) corporate representatives, and experts. Produces preparation memos, document review lists, topic summaries, and day-of checklists. Enforces ABA Opinion 508 ethical boundaries. Use when preparing any witness for deposition, scheduling prep sessions, or building witness preparation materials.

Drafts combined Deed of Trust and Security Agreement instruments creating real property and UCC Article 9 personal property security interests for commercial financing. Use when drafting trust deeds, security agreements, commercial real estate financing documents, or combined real/personal property security instruments.