AlterLab Academic Skills

Access the European Nucleotide Archive (ENA) via its API and FTP to retrieve DNA/RNA sequences, raw sequencing reads (FASTQ), and genome assemblies by accession, with support for multiple formats. Use when downloading reads or sequences for a study, run, or sample accession, or when sourcing nucleotide data for genomics and bioinformatics pipelines. Part of the AlterLab Academic Skills suite.

Query the openFDA API for drugs, medical devices, adverse event reports, recalls, regulatory submissions (510k, PMA), and substance identification (UNII). Use when searching FDA safety data, pharmacovigilance and adverse-event signals, device clearances, drug labels, or recall records for regulatory data analysis and safety research. Part of the AlterLab Academic Skills suite.

Reads, writes, and analyzes geospatial vector data with the GeoPandas Python library (shapefiles, GeoJSON, GeoPackage), with PostGIS support and integration with matplotlib, folium, and cartopy. Use for spatial analysis and geometric operations — buffer analysis, spatial joins and overlays between datasets, dissolving boundaries, clipping, calculating areas and distances, reprojecting coordinate systems, choropleth mapping, or converting between vector file formats. This is for tabular vector data; for raster/satellite/DEM work, spectral indices (NDVI), or spatial ML on earth observation prefer the geomaster skill. Part of the AlterLab Academic Skills suite.

Access NCBI GEO (Gene Expression Omnibus) for gene expression and functional genomics data — search and download microarray and RNA-seq datasets by GSE, GSM, GPL, or GDS accession and retrieve SOFT, MINiML, and series matrix files. Use when locating public expression datasets, fetching processed expression matrices, downloading a study's supplementary files, or sourcing per-study transcriptomics data for differential-expression analysis. For raw FASTQ sequencing reads by SRA/ENA run accession use alterlab-ena; for reference tissue-expression baselines (median TPM across human tissues) use alterlab-gtex; for cancer cohort somatic mutations and copy-number use alterlab-cbioportal. Part of the AlterLab Academic Skills suite.

Submits and manages protocols on Ginkgo Bioworks Cloud Lab (cloud.ginkgo.bio), a web-based interface for autonomous lab execution on Reconfigurable Automation Carts (RACs), covering protocol selection, input preparation, pricing, and ordering workflows. Use when running cell-free protein expression (validation or optimization), generating fluorescent pixel art, or interacting with Ginkgo Cloud Lab services. Part of the AlterLab Academic Skills suite.

Access the RCSB Protein Data Bank (PDB) for EXPERIMENTALLY determined 3D structures (X-ray, cryo-EM, NMR) of proteins and nucleic acids — searching by text, sequence, or structure similarity and downloading coordinates in PDB/mmCIF format with metadata. Use when retrieving a structure by PDB ID, running sequence or structure similarity searches, or obtaining experimental coordinates for structural biology and drug discovery; for AI-PREDICTED structures of proteins lacking experimental data prefer alterlab-alphafold-db, and for protein sequences, annotations, or accession ID mapping prefer alterlab-uniprot instead. Part of the AlterLab Academic Skills suite.

Scalable deep-learning training with PyTorch Lightning — organize PyTorch code into LightningModules, configure Trainers for multi-GPU/TPU, build data pipelines and callbacks, log to W&B or TensorBoard, and run distributed training (DDP, FSDP, DeepSpeed). Use when structuring PyTorch training loops, scaling neural-network training across GPUs/TPUs, or adding checkpointing, logging, and distributed strategies. Part of the AlterLab Academic Skills suite.

Query the GTEx (Genotype-Tissue Expression) portal v2 REST API for tissue-specific gene expression (median TPM across 54 human tissues), expression QTLs (eQTLs), and splicing QTLs (sQTLs). Use when checking which tissues express a gene, finding which gene a non-coding/GWAS variant regulates via eQTLs, or interpreting variant regulatory effects across tissues. NOT for curated trait-variant associations (use alterlab-gwas), population allele frequencies or variant constraint (use alterlab-gnomad), or gene/transcript structure and ID mapping (use alterlab-ensembl). Part of the AlterLab Academic Skills suite.

Creative research ideation and exploration for open-ended brainstorming, surfacing interdisciplinary connections, challenging assumptions, and identifying research gaps. Use when starting early-stage research planning with no specific observations yet — for open-ended brainstorming sessions, exploring cross-disciplinary connections, or finding gaps. For formulating testable hypotheses from observations or data use hypothesis-gen; for grading evidence or spotting design flaws use scientific-thinking. Part of the AlterLab Academic Skills suite.

Query the NHGRI-EBI GWAS Catalog REST API for SNP-trait associations, retrieving variants by rs ID, disease/trait, or gene along with p-values and summary statistics. Use when investigating genome-wide association study hits, mapping a SNP or rsID to traits, building polygenic risk scores, or doing genetic epidemiology lookups. Part of the AlterLab Academic Skills suite.

Access the Human Metabolome Database (HMDB, 220K+ metabolites), searching by name, HMDB ID, or structure to retrieve chemical properties, biomarker data, NMR/MS reference spectra, and associated pathways. Use when identifying a human metabolite, looking up its biomarker or disease associations, matching NMR/MS spectra, or running metabolomics annotation. Part of the AlterLab Academic Skills suite.

Provide direct REST API access to KEGG (academic use only) for pathway analysis, gene-to-pathway and compound-to-pathway mapping, metabolic reactions, KEGG Orthology (KO), drug-drug interactions, and ID conversion. Use when querying KEGG pathways, mapping genes/compounds to metabolic maps, or running KEGG pathway enrichment via raw HTTP/REST; for protein-protein interaction networks prefer alterlab-string-db, for protein sequences and annotations prefer alterlab-uniprot, and for Python workflows spanning many databases prefer bioservices instead. Part of the AlterLab Academic Skills suite.

Search and retrieve preprints from arXiv via the Atom API by keywords, authors, arXiv IDs, date ranges, or subject categories. Use when finding or fetching papers in physics, mathematics, computer science, quantitative biology, quantitative finance, statistics, electrical engineering, or economics, or resolving an arXiv ID to its metadata and PDF. Part of the AlterLab Academic Skills suite.

Access USPTO APIs for patent and trademark searches, examination history (PEDS), assignments, citations, office actions, and trademark status (TSDR). Use when searching patents or trademarks, conducting prior art searches, retrieving patent examination or assignment records, or doing intellectual property (IP) analysis. Part of the AlterLab Academic Skills suite.

Audits and repairs Markdown link health across a skills repo via a four-tier pipeline (config hardening, intra-repo file-ref fixes, external URL substitutions, residual exclusions) and enforces a Tier 3 substitution guardrail that prevents regressions of previously-passing links; designed for lychee-based GitHub Actions link checkers but generalizes to markdown-link-check and similar tools. Use when the request mentions link audit, dead links, link health, lychee, broken links, link checker, markdown link audit, link-health audit, 404 audit, check-links failing, CI link-check, or 連結健檢, 死鏈, 失效連結, 斷鏈檢查. Part of the AlterLab Academic Skills suite.

Exploratory data analysis (EDA) on a scientific data file — auto-detects the format, runs structure/quality/statistics checks, and writes a markdown EDA report with downstream recommendations. Use when asked to "explore", "analyze", "summarize", "profile", or "QC" a data file, or to understand its structure/content/quality before deciding what analysis to run. Covers tabular (.csv .tsv .xlsx .parquet), arrays (.npy .npz .hdf5 .h5 .mat .fits), sequence/genomics (.fasta .fastq .sam .bam .vcf .bed .gff .gtf .h5ad), microscopy (.tif .nd2 .czi .lif .ims .dcm .nii), spectroscopy/MS (.mzML .mzXML .mgf .fid .jdx), chemistry (.pdb .cif .mol .sdf .xyz .gro), and proteomics/metabolomics (.pepXML .mzid .mzTab). For zero-shot forecasting of a series use alterlab-timesfm; to create/configure a chunked cloud array store use alterlab-zarr. Part of the AlterLab Academic Skills suite.

Access the BRENDA enzyme database via its SOAP API to retrieve kinetic parameters (Km, kcat, Ki), reaction equations, organism data, and substrate-specific enzyme information indexed by EC number. Use when looking up enzyme kinetics, turnover numbers, or substrate specificity for biochemical research and metabolic pathway analysis. Part of the AlterLab Academic Skills suite.

Query ChEMBL via the chembl_webresource_client Python client for curated bioactive molecules and drug-like compound libraries at scale — search compounds by structure or physicochemical properties, retrieve bioactivity measurements (IC50, Ki, EC50), and find inhibitors of a target. Use when screening chemical libraries, mining curated bioactivity for a protein, running SAR studies, or sourcing medicinal-chemistry data; for measured protein-ligand binding affinities (Ki/Kd/IC50) prefer alterlab-bindingdb instead. Part of the AlterLab Academic Skills suite.

Access the COSMIC catalogue of somatic mutations in cancer to query somatic mutations, the Cancer Gene Census, mutational signatures, and gene fusions (authentication required). Use when curating known cancer driver genes, looking up recurrent somatic mutations in a gene, or interpreting mutational signatures for cancer research and precision oncology. Not for germline pathogenicity calls (use alterlab-clinvar) or interactive cohort visualization like OncoPrints and survival from study data (use alterlab-cbioportal). Part of the AlterLab Academic Skills suite.

Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivity data, and gene effect profiles. Use when identifying cancer-specific genetic vulnerabilities, finding synthetic lethal interactions, checking whether a gene is essential in given cell lines, or validating oncology drug targets. Part of the AlterLab Academic Skills suite.

Query gnomAD (Genome Aggregation Database) for population allele frequencies and gene constraint scores (pLI, LOEUF) reflecting loss-of-function intolerance. Use when checking how common a variant is across populations, filtering rare-disease candidate variants, assessing variant pathogenicity, or identifying loss-of-function intolerant genes. Part of the AlterLab Academic Skills suite.

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.

Provide direct REST API access to PubMed via the NCBI E-utilities API, supporting advanced Boolean/MeSH queries, batch processing, and citation management. Use when searching biomedical literature by MeSH terms, retrieving abstracts or PMIDs in bulk, or scripting custom PubMed queries over raw HTTP/REST — for Python workflows prefer biopython (Bio.Entrez) instead, use this for direct REST work or custom API implementations. Part of the AlterLab Academic Skills suite.

Drafts and revises academic papers through a 12-agent pipeline with hardened LaTeX output (apa7 document class, justified text, table column-width formula, centered bilingual abstracts, standardized font stack, PDF compiled from LaTeX), supporting IMRaD, literature review, theoretical, case study, policy brief, and conference paper structures, APA 7.0 (default), Chicago, MLA, IEEE, and Vancouver citation formats, bilingual zh-TW plus EN abstracts, and multi-format output (LaTeX, DOCX, PDF, Markdown). Use when the request mentions write paper, academic paper, paper outline, write abstract, revise paper, check citations, convert to LaTeX, guide my paper, parse reviews, revision roadmap, or 寫論文, 學術論文, 論文大綱, 寫摘要, 修改論文, 檢查引用, 引導我寫論文, 帶我規劃論文, 逐章規劃, 論文架構, 審查意見, 修訂路線圖. Its citation-check mode formats and inserts citations while drafting; for a standalone anti-hallucination check that cited references actually exist prefer alterlab-citation-verifier instead. Part of the AlterLab Academic Skills suite.

The AlterLab front door and multi-agent launcher — routes a task to the right AlterLab skill(s) when the user invokes the suite without naming one, and for a multi-stage goal (or on the keyword 'alterflow', aliases 'alterresearch' / 'ultralab') it CLARIFIES the goal with a few questions, SELECTS the skills the task needs, and runs a dynamic multi-agent workflow composing them (via alterlab-workflow-orchestration, alterlab-research-pipeline, or alterlab-ssci-orchestrator). Triggers on 'use AlterLab skills', 'which AlterLab skill for X', 'is there an AlterLab skill for…', a multi-stage research goal, 'alterflow …', or any generic AlterLab request where the user does not know skill names. It always asks clarifying questions before executing a multi-step run. Use when someone references AlterLab generically, describes a multi-stage goal, or fires the alterflow keyword; when the user already names a specific skill, defer to that skill directly. Part of the AlterLab Academic Skills suite.

Scales pandas/NumPy workflows beyond memory with Dask distributed computing — parallel DataFrames, arrays, delayed task graphs, and cluster execution. Use when existing pandas/NumPy code must run on larger-than-RAM data or across clusters, for parallel file processing, distributed ML, or integration with existing pandas code. For out-of-core analytics on a single machine prefer vaex; for in-memory speed prefer polars. 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.

Model interpretability and explainability with SHAP (SHapley Additive exPlanations) — feature importance and plots (waterfall, beeswarm, bar, scatter, force, heatmap). Use when explaining ML model predictions, computing feature importance, debugging models, analyzing bias or fairness, comparing models, or implementing explainable AI across tree-based models (XGBoost, LightGBM, Random Forest), deep learning (TensorFlow, PyTorch), linear models, and any black-box model. Part of the AlterLab Academic Skills suite.

Nonlinear dimensionality reduction with UMAP — fast manifold learning for 2D/3D visualization, clustering preprocessing (e.g., HDBSCAN), and supervised or parametric UMAP. Use when projecting high-dimensional data to low dimensions for visualization, embedding generation, or as a preprocessing step before clustering. Part of the AlterLab Academic Skills suite.

Out-of-core tabular analytics with Vaex for billion-row datasets that exceed RAM — lazy evaluation, fast aggregations, big-data visualization, and ML on a single machine. Use when working with large CSV/HDF5/Arrow/Parquet files, computing fast statistics on massive datasets, visualizing big data, or building ML pipelines that do not fit in memory. For distributed clusters prefer dask; for in-memory speed prefer polars. Part of the AlterLab Academic Skills suite.

Chunked, compressed N-dimensional arrays for cloud storage with Zarr — parallel I/O, S3/GCS integration, and NumPy/Dask/Xarray compatibility. Use when storing or reading large N-D scientific arrays, streaming chunked data to/from cloud object stores, or building large-scale scientific computing pipelines. 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.

Access ClinPGx pharmacogenomics data (the successor to PharmGKB) to query gene-drug interactions, CPIC/DPWG dosing guidelines, drug labels, and pharmacogene records. Use when interpreting pharmacogenes (CYP2D6, CYP2C19, TPMT, DPYD, SLCO1B1), looking up genotype-guided drug dosing, checking PGx drug-safety associations (e.g. HLA-B*57:01 and abacavir), or supporting precision medicine and clinical pharmacogenomics decisions. For star-allele definitions/frequencies see PharmVar; for germline/somatic variant pathogenicity see alterlab-clinvar. Part of the AlterLab Academic Skills suite.

Query NCBI ClinVar via the E-utilities API or FTP for the clinical significance (pathogenicity) of human germline genetic variants, searching by gene, variant, condition, or genomic position and interpreting ACMG/AMP classifications and review-status star ratings. Use when assessing whether a variant is pathogenic, likely pathogenic, VUS, likely benign, or benign, resolving conflicting interpretations, or annotating a VCF with ClinVar clinical significance. For population allele frequencies by ancestry use alterlab-gnomad; for somatic cancer mutation frequencies use alterlab-cosmic. Part of the AlterLab Academic Skills suite.

Query the Ensembl genome database REST API across 250+ species for gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, and Variant Effect Predictor (VEP) annotations. Use when mapping gene IDs or coordinates, fetching genomic sequence, finding orthologs across species, or predicting variant consequences for genomic research. Part of the AlterLab Academic Skills suite.

Query NCBI Gene via the E-utilities and Datasets APIs, searching by gene symbol or Gene ID and retrieving gene information (RefSeqs, GO terms, genomic locations, associated phenotypes) including batch lookups. Use when resolving gene symbols to IDs, annotating gene lists, or pulling functional and positional gene metadata for downstream analysis. 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.

Query PubChem via the PUG-REST API and PubChemPy across 110M+ compounds, searching by name, CID, or SMILES and retrieving molecular properties, bioactivity, and similarity/substructure matches. Use when looking up a chemical compound, converting names/SMILES to CIDs, fetching physicochemical properties, or running cheminformatics structure searches. Part of the AlterLab Academic Skills suite.

Provide direct REST API access to UniProt (Swiss-Prot/TrEMBL) for protein sequence searches, FASTA retrieval, functional annotations (GO terms, domains), and cross-database ID mapping. Use when looking up a protein entry, fetching a protein FASTA sequence, or mapping accessions between databases over raw HTTP/REST; for EXPERIMENTAL 3D structures prefer alterlab-pdb, for AI-PREDICTED 3D structures prefer alterlab-alphafold-db, for protein-protein interaction networks prefer alterlab-string-db, and for Python workflows spanning many databases prefer bioservices instead. Part of the AlterLab Academic Skills suite.

Access the ZINC database of 230M+ commercially available (purchasable) compounds, searching by ZINC ID or SMILES, running similarity searches, and downloading 3D-ready structures. Use when assembling a compound library for virtual screening, finding purchasable analogs, or obtaining docking-ready 3D structures for drug discovery. Part of the AlterLab Academic Skills suite.

Run ESM protein language models — ESM3 for generative multimodal protein design across sequence, structure, and function, and ESM C for efficient embeddings and representations — locally or via the cloud Forge API. Use when working with protein sequences, structures, or function prediction, designing novel proteins, generating protein embeddings, performing inverse folding, or doing protein-engineering tasks. 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.

Multi-objective optimization with pymoo — NSGA-II, NSGA-III, MOEA/D, Pareto-front computation, constraint handling, and standard benchmarks (ZDT, DTLZ). Use when solving multi-objective or constrained optimization problems, computing Pareto-optimal trade-offs, or tackling engineering design problems with competing objectives. Part of the AlterLab Academic Skills suite.

Process-based discrete-event simulation in Python with SimPy — processes, queues, shared resources, and time-based events. Use when simulating systems where entities contend for shared resources over time, such as manufacturing systems, service operations, network traffic, or logistics. Part of the AlterLab Academic Skills suite.

Symbolic mathematics in Python with SymPy — solve equations algebraically, perform calculus (derivatives, integrals, limits), manipulate algebraic expressions, work with symbolic matrices, and generate executable code from formulas. Use when exact symbolic results are needed rather than numerical approximations, or for physics, number-theory, and geometry computations involving variables and parameters. Part of the AlterLab Academic Skills suite.

Access and analyze drug information from the DrugBank database — drug properties, interactions, targets, pathways, chemical structures, and pharmacology data. Use when working with pharmaceutical data, drug discovery research, drug-drug interaction analysis, target identification, chemical similarity searches, ADMET predictions, or any task needing detailed drug and drug-target records from DrugBank. 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.

Query and analyze scholarly literature using the OpenAlex API across 240M+ works, retrieving papers, authors, institutions, citations, and open access status. Use when searching academic papers, tracking citations, finding works by author or institution, analyzing research trends, discovering open access publications, or running bibliometric analysis. Part of the AlterLab Academic Skills suite.

Query the Reactome REST API for pathway analysis, over-representation/enrichment, gene-to-pathway mapping, disease pathways, molecular interactions, and expression analysis. Use when running pathway enrichment on a gene list, mapping genes to curated biological pathways, or exploring disease pathways for systems biology studies. Part of the AlterLab Academic Skills suite.

Predict biomolecular complexes with Chai-1, an open AlphaFold3-style model that folds multi-entity assemblies (proteins, ligands, nucleic acids) from a single typed FASTA — strong on antibody–antigen and protein–ligand complexes, with optional MSA and restraint inputs. Use when predicting an antibody–antigen complex, folding a mixed protein/ligand/nucleic-acid assembly described in one FASTA, or generating a complex with experimental restraints. For binding-affinity prediction or a ligand-focused co-fold prefer alterlab-boltz; for protein-only or protein–protein folding prefer alterlab-alphafold; to dock into a fixed receptor prefer alterlab-diffdock. Part of the AlterLab Academic Skills suite.

Run fast one-liner queries to 20+ bioinformatics databases from the gget CLI or Python — gene info (Ensembl), BLAST, AlphaFold structures, Enrichr enrichment, and more. Use for quick interactive lookups of genes, sequences, structures, or pathways — for batch processing or advanced BLAST use biopython, for multi-database Python workflows use bioservices. 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.

Fast in-memory DataFrame analytics with Polars — lazy evaluation, parallel execution, and an Apache Arrow backend for datasets that fit in RAM. Use when pandas is too slow but data still fits in memory, for 1-100GB datasets, ETL pipelines, or a faster pandas replacement. For larger-than-RAM data prefer dask or vaex. Part of the AlterLab Academic Skills suite.

Query BindingDB for measured protein-ligand binding affinities (Ki, Kd, IC50, EC50) via its keyless REST API or the full TSV download, searching by target (UniProt ID), compound (SMILES), or pathogen. Use when looking up experimental binding constants, profiling inhibitors of a protein target, doing lead optimization, polypharmacology analysis, or structure-activity relationship (SAR) studies; for curated bioactivity mining or drug-like compound library screening at scale prefer alterlab-chembl instead. Part of the AlterLab Academic Skills suite.

Query the STRING API for protein-protein interactions (59M proteins, 20B interactions across 5000+ species), building interaction networks, discovering functional partners, and running GO/KEGG/Pfam enrichment on protein lists. Use when constructing a protein-protein interaction network, expanding from seed proteins to functional partners, or running PPI-based enrichment for systems biology; for curated metabolic pathway maps and reactions prefer alterlab-kegg, and for protein sequences, annotations, or accession ID mapping prefer alterlab-uniprot instead. Part of the AlterLab Academic Skills suite.

Runs NCBI BLAST+ 2.17.0 sequence searches from the command line: makeblastdb (with -parse_seqids), blastn/blastp/blastx/tblastn with tabular -outfmt 6/7 for parsing, correct -task choice (megablast vs blastn vs blastn-short), -taxids/-negative_taxids taxonomic scoping, and -mt_mode multithreading; plus a DIAMOND blastp --ultra-sensitive path for large protein searches. Warns that -max_target_seqs is a heuristic keep-count, not a top-N best-hits filter. Use when the user wants command-line BLAST, makeblastdb, a local BLAST database, blastn/blastp/blastx/tblastn searches, or DIAMOND protein search. For the Bio.Blast web NCBIWWW API prefer alterlab-biopython; for quick one-liner database lookups prefer alterlab-gget. 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.

Read and write genomic alignment and variant files in Python with pysam (htslib bindings) — SAM/BAM/CRAM alignments, VCF/BCF variants, and FASTA/FASTQ sequences, plus region extraction and per-base coverage/pileup. Use when scripting NGS data-processing pipelines that parse, filter, index, or compute coverage over BAM/CRAM/VCF files. Part of the AlterLab Academic Skills suite.

Apply the scGPT single-cell foundation model (Cui 2024) to annotate and embed cells — zero-shot and fine-tuned cell-type annotation, gene/cell embeddings, batch integration, and gene-regulatory / perturbation inference from AnnData. Use when annotating cell types with a pretrained foundation model, generating scGPT embeddings, integrating batches with a transformer, or running zero-shot single-cell inference on an h5ad. For probabilistic latent models (scVI/scANVI) prefer alterlab-scvi-tools; for the standard QC→cluster→UMAP→DE pipeline prefer alterlab-scanpy; for the AnnData data structure itself prefer alterlab-anndata; for protein language models prefer alterlab-esm. Part of the AlterLab Academic Skills suite.

Designs courses and teaching materials using backward design (Wiggins & McTighe), constructive alignment (Biggs), and Bloom's taxonomy alignment, generating rubrics, formative and summative assessments, syllabi, lesson plans, inclusive-pedagogy guidance, and online/hybrid course architecture. Use when the request mentions course design, syllabus, learning outcomes, rubric, assessment design, lesson plan, backward design, constructive alignment, Bloom's taxonomy, curriculum mapping, course redesign, inclusive pedagogy, hybrid course, or online course design. Part of the AlterLab Academic Skills suite.