AlterLab-IEU/AlterLab-Academic-Skills.

alterlab-abm-mesa

Builds agent-based models of social systems with Mesa 3 — the current AgentSet API (model.agents.shuffle_do('step'), auto-assigned unique_id, mandatory super().__init__(seed=...)), cell spaces (mesa.discrete_space OrthogonalMooreGrid / classic mesa.space grids), the DataCollector, batch_run parameter sweeps, and SolaraViz — for emergence, segregation, diffusion, opinion dynamics, and cooperation models. It uses the Mesa 3.x API (the old mesa.time schedulers like RandomActivation are removed) and treats the model as a generative theory to be validated, not just run. Use when the request mentions an agent-based model, Mesa, simulating interacting agents, or emergent macro behavior from micro rules. For discrete-event (queueing/process) simulation prefer alterlab-simpy; for reinforcement learning prefer alterlab-stable-baselines3. Part of the AlterLab Academic Skills suite.

alterlab-academic-career

Prepares academic career documents and professional-development materials for faculty and researchers. Use when drafting academic CVs, research statements, teaching philosophies, diversity statements, faculty-position cover letters, tenure dossiers, promotion narratives, academic portfolios, or mentorship statements, and when planning conference-networking strategy, building academic web presence, setting up ORCID profiles, or understanding impact metrics. Part of the AlterLab Academic Skills suite.

alterlab-accreditation-aol

Scaffolds program-level Assurance-of-Learning (AoL) documentation for AACSB (2020 Standard 5) and ABET (Criterion 3 Student Outcomes, Criterion 4 Continuous Improvement) accreditation — program learning outcomes / competency goals, curriculum-to-outcome mapping matrices, direct- and indirect-assessment plans, rubric design, and closing-the-loop continuous-improvement narratives — and validates the structure of an outcome-mapping matrix with scripts/aol_matrix.py. Use when the user needs AACSB or ABET assurance-of-learning material, a program-learning-outcomes set, a curriculum/outcome map or coverage matrix, a direct/indirect assessment plan, a closing-the-loop report, or accreditation self-study text. For single-course design or course rubrics prefer alterlab-teaching-design; for post-award grant reports prefer alterlab-grant-reporting. Part of the AlterLab Academic Skills suite.

alterlab-adaptyv

Submits and tracks protein-testing experiments on the Adaptyv Bio Foundry cloud lab (wet-lab validation), and optimizes protein sequences before submission with computational tools (NetSolP, SoluProt, SolubleMPNN, ESM). Use when designing proteins that need wet-lab validation - binding/affinity screening, expression testing, thermostability, or fluorescence assays - or when submitting experiments to the Foundry API, browsing the target catalog, tracking experiment status, retrieving results, or pre-screening sequences for solubility/expression. Triggers on "Adaptyv", "Foundry API", "cloud lab", "biolayer interferometry / BLI", "wet-lab validation". Part of the AlterLab Academic Skills suite.

alterlab-aeon

Runs time series machine learning with the aeon library — classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search via scikit-learn compatible APIs. Use when working with temporal data, sequential patterns, or time-indexed observations (univariate or multivariate) that need specialized algorithms beyond standard ML approaches. Part of the AlterLab Academic Skills suite.

alterlab-akademik-tesvik

Computes the annual Turkish academic-incentive (akademik teşvik) score for Devlet (state) university öğretim elemanı (academic staff) from a classified activity list, applying the verified Akademik Teşvik Ödeneği Yönetmeliği (2018/11834) Faaliyet Hesaplama Tablosu headline puanları (Proje 20, Araştırma 15, Yayın 30, Patent 30, Atıf 30, Tebliğ 20, Ödül 20) with the k (author-count), p (Q1 1/Q2 0.8/Q3 0.5/Q4 0.25), and r (project-role) coefficients via türü puanı = Σ(faaliyet oranları) × headline (MADDE 8/2), then enforcing the per-type headline ceilings, the 100 cap (MADDE 8/3), and the net-30 payment gate (MADDE 10/3) in a deterministic scripts/tesvik_score.py. Use when the user wants to calculate akademik teşvik puanı, check the en az 30 (net-30) threshold, apply TABLO 4 ceilings, or estimate teşvik eligibility; keeps its coefficients separate from doçentlik scoring. For doçentlik point eligibility prefer alterlab-docentlik-eligibility. Part of the AlterLab Academic Skills suite.

alterlab-alpha-vantage

Accesses real-time and historical stock market data, forex rates, cryptocurrency prices, commodities, economic indicators, and 50+ technical indicators via the Alpha Vantage API (requires a free API key from alphavantage.co). Use when fetching stock prices (OHLCV), company fundamentals (income statement, balance sheet, cash flow), earnings, options data, market news/sentiment, insider transactions, GDP, CPI, treasury yields, gold/silver/oil prices, Bitcoin/crypto prices, forex exchange rates, or calculating technical indicators (SMA, EMA, MACD, RSI, Bollinger Bands). Part of the AlterLab Academic Skills suite.

alterlab-alphafold

Predict protein 3D structures with AlphaFold2 via ColabFold — MMseqs2-accelerated MSAs, monomer and AlphaFold2-Multimer complex folding, and confidence-based validation (pLDDT, pTM/ipTM, PAE). Use when folding a protein sequence or complex from FASTA, generating a predicted structure with confidence metrics, ranking models, or checking self-consistency of a design. For co-folding a protein WITH a small-molecule ligand or predicting binding affinity prefer alterlab-boltz; for antibody–antigen or one-FASTA multi-entity complexes prefer alterlab-chai; to LOOK UP an already-computed structure prefer alterlab-alphafold-db; for ESM embeddings or inverse folding prefer alterlab-esm. Part of the AlterLab Academic Skills suite.

alterlab-alphafold-db

Access the AlphaFold DB of 200M+ AI-PREDICTED protein structures — retrieve models by UniProt accession, download PDB/mmCIF files, and analyze prediction confidence metrics (pLDDT, PAE). Use when a UniProt ID needs a computationally predicted 3D structure or when no experimental structure exists, for homology modeling, protein engineering, or structure-based drug discovery; for EXPERIMENTALLY determined structures (X-ray, cryo-EM, NMR) prefer alterlab-pdb, and for protein sequences, annotations, or accession ID mapping prefer alterlab-uniprot instead. Part of the AlterLab Academic Skills suite.

alterlab-anndata

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.

alterlab-aperta

Drives TÜBİTAK Açık Bilim Politikası (Open Science Policy) compliance and deposition into Aperta — TÜBİTAK ULAKBİM's national open archive at aperta.ulakbim.gov.tr — encoding the binding mandates (green-road deposit of the accepted manuscript on acceptance; open access within 6 months for fen/mühendislik (STEM) and 12 months for sosyal/beşeri (SSH); İlke-6 documentation when data must stay closed for KVKK/privacy reasons) and scaffolding a TÜBİTAK Veri Yönetim Planı / VYP (data management plan) at grant-application time. Use when depositing to Aperta, complying with the TÜBİTAK açık bilim policy, preparing a TÜBİTAK data management plan (VYP), reporting open-access compliance in a final report, or documenting a justified data embargo. For Zenodo/Dryad/OSF and international DMPs prefer alterlab-open-science; for the KVKK lawful-basis/anonymisation plan prefer alterlab-kvkk-dmp. Part of the AlterLab Academic Skills suite.

alterlab-arboreto

Infer gene regulatory networks (GRNs) from expression matrices using arboreto's scalable GRNBoost2 and GENIE3 tree-ensemble algorithms with Dask-distributed computation. Use when analyzing bulk or single-cell RNA-seq transcriptomics to map transcription-factor-to-target-gene regulatory interactions, build adjacency networks, or run the GRN-inference step of a SCENIC pipeline on large datasets. Part of the AlterLab Academic Skills suite.

alterlab-arxiv

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.

alterlab-astropy

Processes astronomy and astrophysics data with the Astropy Python library — celestial coordinates, physical units, FITS files, cosmological calculations, time systems, tables, and world coordinate systems (WCS). Use when tasks involve coordinate transformations, unit conversions, FITS file manipulation, cosmological distance calculations, time scale conversions, or general astronomical data analysis. Part of the AlterLab Academic Skills suite.

alterlab-benchling

Integrates the Benchling R&D platform via its REST API and SDK — access the registry (DNA, proteins), inventory, ELN entries and workflows, build Benchling Apps, and query the Benchling Data Warehouse. Use when automating Benchling lab data management, syncing sample registry or inventory records, scripting ELN entries/workflows, or running SQL against the Benchling Data Warehouse. Part of the AlterLab Academic Skills suite.

alterlab-bgpt-search

Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server, returning 25+ fields per paper (methods, results, sample sizes, quality scores, conclusions). Use when running a literature review or evidence synthesis, or when needing experimental details (sample sizes, effect sizes, methods, quality scores) that abstracts alone do not provide. Part of the AlterLab Academic Skills suite.

alterlab-bindingdb

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.

alterlab-biopython

Manipulate biological sequences, parse FASTA/GenBank/PDB files, run phylogenetics, and access NCBI/PubMed programmatically via Biopython (Bio.SeqIO, Bio.Entrez, Bio.PDB, Bio.Blast). Use when scripting custom bioinformatics pipelines, batch-processing sequence files, automating BLAST, or fetching records from Entrez — for quick one-off database lookups use gget, for unified multi-service integration use bioservices. Part of the AlterLab Academic Skills suite.

alterlab-biorxiv

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.

alterlab-bioservices

Query 40+ bioinformatics web services through one consistent Python API with bioservices (UniProt, KEGG, ChEMBL, Reactome, Ensembl, NCBI and more). Use when a workflow must hit multiple databases together, map identifiers across services, or run cross-database analyses — for quick single-database lookups use gget, for sequence and file manipulation use biopython. Part of the AlterLab Academic Skills suite.

alterlab-blast

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.

alterlab-boltz

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.

alterlab-borzoi

Predict genome-wide functional genomics tracks from DNA sequence with Borzoi (Linder 2025) — a sequence-to-function model outputting RNA-seq, CAGE, ATAC, and ChIP coverage across long context, used to score non-coding and regulatory variant effects. Use when predicting functional tracks from a DNA sequence, scoring a non-coding/regulatory variant's effect on expression or chromatin, or doing in-silico mutagenesis of a locus. To LOOK UP a variant's population frequency prefer alterlab-gnomad; for its clinical significance prefer alterlab-clinvar; for protein-structure effects prefer alterlab-alphafold; for single-cell foundation models prefer alterlab-scgpt. Part of the AlterLab Academic Skills suite.

alterlab-brenda

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.

alterlab-causal-inference

Estimates causal effects from observational and quasi-experimental data — difference-in-differences, instrumental variables, regression discontinuity, panel fixed effects, propensity-score / doubly-robust methods, and heterogeneous treatment effects (CATE) — using the verified Python stack: statsmodels and linearmodels (PanelOLS, IV2SLS), pyfixest (feols, event studies, Sun-Abraham, did2s), DoWhy (identify -> estimate -> refute), EconML (LinearDML, CausalForestDML, DRLearner), and rdrobust for RD. It names the identifying assumption before estimating and runs a refutation/robustness check after. Use when the request mentions difference-in-differences, instrumental variables, regression discontinuity, fixed effects / panel causal estimation, propensity scores, or treatment-effect estimation from non-randomized data. For choosing the design first prefer alterlab-ssci-design-gate; for plain regression or descriptive stats prefer alterlab-statistical-analysis. Part of the AlterLab Academic Skills suite.

alterlab-cbioportal

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.

alterlab-cellxgene

Query the CZ CELLxGENE Census (61M+ cells) programmatically via cellxgene-census and TileDB-SOMA, slicing expression by tissue, disease, or cell type and returning AnnData. Use when pulling reference single-cell RNA-seq data from the largest curated public atlas, running population-scale queries, or benchmarking your data against a reference — for analyzing your own dataset use scanpy or scvi-tools. Part of the AlterLab Academic Skills suite.

alterlab-chai

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.

alterlab-chembl

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.

alterlab-cirq

Builds, simulates, and runs quantum circuits with Cirq, Google Quantum AI's framework for NISQ hardware, noise-aware low-level circuit design, and noise characterization. Use when targeting Google Quantum AI processors (Sycamore/Weber), designing noise-aware NISQ circuits, or running characterization experiments (randomized benchmarking, XEB). For IBM Quantum hardware and Qiskit Runtime prefer alterlab-qiskit; for gradient-trained quantum ML and hybrid quantum-classical models prefer alterlab-pennylane; for open-system Lindblad/master-equation dynamics prefer alterlab-qutip. Part of the AlterLab Academic Skills suite.

alterlab-citation-graph

Free, key-less ResearchRabbit analog — builds a citation and co-citation graph around one or more seed papers using the OpenAlex API. Walks both directions of the citation network (works the seed cites and works that cite the seed), ranks the discovered neighbourhood by co-citation strength and bibliographic coupling to surface the papers most central to a topic's literature, and exports the network as GraphML (Gephi / Cytoscape / yEd) and JSON. Use when mapping a literature landscape, finding seminal or highly co-cited papers from a seed DOI, snowballing a reference network, building a citation map / co-citation analysis, or visualizing how a research area's papers connect — no API key required (polite mailto only). Part of the AlterLab Academic Skills suite.

alterlab-citation-mgmt

Manages citations for academic research — searches Google Scholar and PubMed for papers, extracts accurate metadata, validates citations, and generates properly formatted BibTeX entries. Use when finding papers, verifying citation information, converting DOIs to BibTeX, checking reference accuracy in scientific writing, or building a bibliography. Part of the AlterLab Academic Skills suite.

alterlab-citation-verifier

Verifies that every entry in a bibliography ACTUALLY EXISTS by cross-checking it against four keyless public scholarly APIs (Crossref, OpenAlex, Semantic Scholar, arXiv) with a polite mailto identifier, resolving DOI/arXiv IDs, fuzzy-matching title and authors (difflib SequenceMatcher ratio >=0.70), flagging retractions marked in Crossref (update-to) or OpenAlex (is_retracted), and emitting per-entry JSON verdicts mapped to the AlterLab citation-hallucination taxonomy (TF/PAC/IH/PH/SH). Accepts BibTeX, a DOI/arXiv ID list, or free-form references; degrades gracefully offline by emitting 'unverified' verdicts and never silently passing. Use when the request mentions verify citations, check references, fabricated or hallucinated references, fake DOI, retraction check, bibliography audit, or reference existence check. Does NOT write or draft papers — for authoring a manuscript (whose citation-check mode inserts citations) prefer alterlab-paper-writer instead. Part of the AlterLab Academic Skills suite.

alterlab-clinical-decision

Generates professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings — biomarker-stratified patient cohort analyses with outcomes and evidence-based treatment recommendation reports with decision algorithms, supporting GRADE evidence grading, statistical analysis (hazard ratios, survival curves, waterfall plots), biomarker integration, and regulatory compliance, output as publication-ready LaTeX/PDF. Use when building a CDS document, cohort analysis, or treatment recommendation report for drug development, clinical research, or evidence synthesis, or when GRADE grading, hazard ratios, survival/waterfall plots, or biomarker stratification are requested. Part of the AlterLab Academic Skills suite.

alterlab-clinical-reports

Writes comprehensive clinical reports — case reports (CARE guidelines), diagnostic reports (radiology, pathology, lab), clinical trial reports (ICH-E3, SAE, CSR), and patient documentation (SOAP notes, H&P, discharge summaries) — with templates, regulatory compliance (HIPAA, FDA, ICH-GCP), and validation tools. Use when drafting a case report for journal publication, a radiology/pathology/lab diagnostic report, an ICH-E3 clinical study report (CSR) or SAE narrative, or SOAP/H&P/discharge patient records needing regulatory-compliant formatting. Part of the AlterLab Academic Skills suite.

alterlab-clinicaltrials

Query ClinicalTrials.gov via its API v2 to search trials by condition, drug, location, recruitment status, or phase and retrieve trial details by NCT ID. Use when finding interventional or observational studies, checking trial status and eligibility for patient matching, or exporting clinical trial records for research. Part of the AlterLab Academic Skills suite.

alterlab-clinpgx

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.

alterlab-clinvar

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.

alterlab-cobrapy

Build and analyze genome-scale constraint-based metabolic models with COBRApy — flux balance analysis (FBA), flux variability analysis (FVA), gene and reaction knockouts, flux sampling, and SBML model I/O. Use when simulating metabolic networks, predicting growth or knockout phenotypes, or running systems-biology and metabolic-engineering analyses on SBML genome-scale models. Part of the AlterLab Academic Skills suite.

alterlab-cosmic

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.

alterlab-dask

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.

alterlab-datacommons

Query Google Data Commons for public statistical data aggregated from global sources, resolving geographic entities and pulling time-series statistics. Use when working with demographic data, economic indicators, health statistics, or environmental data — population counts, GDP figures, unemployment rates, disease prevalence — or when resolving places to DCIDs and exploring relationships between statistical entities. Part of the AlterLab Academic Skills suite.

alterlab-datamol

Wraps RDKit in a high-level, pandas-friendly datamol interface with sensible defaults for everyday drug discovery — SMILES/SDF loading into DataFrames, molecule standardization, descriptors, fingerprints, Butina clustering, 3D conformer generation, scaffold analysis, and parallel batch processing, returning native rdkit.Chem.Mol objects. Use when running standard cheminformatics pipelines on molecule tables with minimal boilerplate; for low-level control, custom sanitization, or specialized algorithms prefer alterlab-rdkit. Part of the AlterLab Academic Skills suite.

alterlab-deep-research

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.

alterlab-deepchem

Runs molecular machine learning with DeepChem — diverse featurizers, pre-built MoleculeNet benchmark datasets, and pre-trained models (ChemBERTa, GROVER) for property prediction (ADMET, toxicity, solubility) via traditional ML or graph neural networks. Use when running end-to-end molecular ML experiments that need MoleculeNet benchmarks, scaffold splitting, or ready-made models with minimal setup; for building custom PyTorch graph architectures prefer alterlab-torchdrug, and for standalone molecule-to-feature-vector generation prefer alterlab-molfeat. Part of the AlterLab Academic Skills suite.

alterlab-deeptools

Process and visualize deep-sequencing coverage with the deepTools CLI — convert BAM to bigWig (bamCoverage), build log2 ratio tracks (bamCompare), run QC (multiBamSummary correlation, PCA, plotFingerprint), apply the ATAC-seq Tn5 shift (alignmentSieve --ATACshift), and make TSS/peak heatmaps and profiles (computeMatrix, plotHeatmap, plotProfile). Use for coverage tracks, signal heatmaps/profiles, normalization (RPGC/CPM/RPKM), and effective-genome-size lookups for ChIP-seq, ATAC-seq, MNase-seq, or RNA-seq. NOT for per-read/CIGAR/MAPQ BAM record access — that is pysam. Part of the AlterLab Academic Skills suite.

alterlab-denario

Runs Denario (AstroPilot-AI), a multiagent AI system for scientific research assistance that automates end-to-end research workflows from a described dataset through idea, methodology, computational results, and a publication-ready LaTeX paper. Built on AG2 + LangGraph with a cmbagent analysis backend. Use when driving the Denario pipeline (Denario.get_idea/get_method/get_results/get_paper), generating research ideas from a dataset description, auto-developing methodology, executing analysis agents, or emitting a journal-formatted (APS/AAS/JHEP/ICML/NeurIPS/PASJ) LaTeX manuscript. Part of the AlterLab Academic Skills suite.

alterlab-depmap

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.

alterlab-dergipark

Harvests article metadata, abstracts, and full-text PDFs from DergiPark (TÜBİTAK ULAKBİM's national journal-hosting platform, ~2,537 journals) via its verified platform-wide OAI-PMH endpoint (https://dergipark.org.tr/api/public/oai/; verbs Identify/ListSets/ListRecords/GetRecord; prefixes oai_dc/oai_mods/oai_marc/oai_etdms; setSpec=journal-slug), parses Highwire citation_* and DC.* meta tags on /pub/{slug}/article/{id} pages, pulls PDFs from the citation_pdf_url path, and emits BibTeX/RIS locally. Use when the user wants to harvest a Turkish journal, fetch DergiPark articles, list a journal archive, get BibTeX/RIS for a DergiPark paper, or read a journal aim-and-scope (öz/kapsam). For TR Dizin indexing status use alterlab-trdizin; for YÖK theses use alterlab-yok-tez; for academic profiles use alterlab-yok-akademik. Part of the AlterLab Academic Skills suite.

alterlab-diffdock

Predicts protein-ligand binding poses with DiffDock diffusion-based molecular docking from PDB structures and SMILES, producing pose confidence scores for virtual screening and structure-based drug design. Use when docking ligands into a protein, generating binding poses, or screening compounds against a target; not for binding affinity prediction. Part of the AlterLab Academic Skills suite.

alterlab-digital-humanities

Applies computational methods to humanities research — text mining and NLP (LDA/BERTopic topic modeling, sentiment, named entity recognition with spaCy/NLTK), corpus linguistics (concordance, collocation, keyness), digital archives (Dublin Core, TEI XML), GIS for history, network analysis, stylometry and authorship attribution, OCR (Tesseract, Kraken, Transkribus), and data visualization (Gephi, Palladio). Use when distant-reading a literary corpus, mapping historical events or trade networks, attributing disputed authorship, digitizing historical documents, or building digital scholarly editions. Part of the AlterLab Academic Skills suite.

alterlab-dnanexus

Develops and runs genomics pipelines on the DNAnexus cloud platform using the dxpy Python SDK and dx CLI — build apps/applets, write dxapp.json, upload/download data, and execute jobs/workflows over FASTQ/BAM/VCF files. Use when building or running a DNAnexus app, applet, or workflow, writing dxapp.json, using dx-app-wizard or dx build, calling dxpy (find_data_objects, DXApplet.run, upload_local_file), or uploading/downloading sequencing data on DNAnexus. For LatchBio (Latch SDK @workflow/@task, LatchFile) use alterlab-latchbio instead; for Benchling LIMS use alterlab-benchling. Part of the AlterLab Academic Skills suite.

alterlab-docentlik-eligibility

Runs a PARTIAL pre-screen of a Turkish associate-professorship (doçentlik) publication list against the ÜAK (Üniversitelerarası Kurul) Sağlık Bilimleri TABLO 10 criteria, applying the author-share rule (full; 0.8 + 0.5; lead-author half-the-rest split) and pass-fail checking the four computable minimums (≥100 total, ≥90 post-doctorate, ≥40 SCIE/SSCI article points, ≥3 lead-author Q1–Q4 articles). It deliberately does NOT emit an ELIGIBLE verdict — it lists the unmodelled mandatory minimums (TR Dizin/national article, citation, congress, teaching, per-category caps) for the user to verify. Use when the user wants to estimate doçentlik eligibility, calculate ÜAK points, or audit lead-author (başlıca yazar) requirements; resolve a journal's live TR Dizin status with alterlab-trdizin first, and compute the akademik teşvik (academic-incentive) score with alterlab-akademik-tesvik. Always verify the full live TABLO 10 — criteria change each term and differ per field. Part of the AlterLab Academic Skills suite.

alterlab-drugbank

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.

alterlab-eda

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.

alterlab-edgartools

Accesses, analyzes, and extracts data from SEC EDGAR filings using the edgartools Python library. Use when working with SEC filings, financial statements (income statement, balance sheet, cash flow), XBRL financial data, insider trading (Form 4), institutional holdings (13F), company financials, annual/quarterly reports (10-K, 10-Q), proxy statements (DEF 14A), 8-K current events, company screening by ticker/CIK/industry, multi-period financial analysis, or any SEC regulatory filings. Part of the AlterLab Academic Skills suite.

alterlab-ena

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.

alterlab-ensembl

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.

alterlab-esm

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.

alterlab-etetoolkit

Manipulate, annotate, and render phylogenetic trees programmatically with the ETE Toolkit (ete3) — parse and edit Newick/NHX, detect duplication/speciation events, infer orthology and paralogy, query NCBI taxonomy, and export PDF/SVG figures. Use when traversing or reformatting tree files, doing phylogenomic comparative analysis, or producing publication tree graphics in Python. Part of the AlterLab Academic Skills suite.

alterlab-fda

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.

alterlab-figure-qa

Verify publication figures with a render-then-check QA pass — data-fidelity against every underlying row, axis/label floor-and-ceiling legibility, bounding-box collision detection for overlapping text/markers, and 300-dpi print-readiness. Use when proofing or auditing a finished figure for correctness and print quality, catching mislabeled or overlapping elements, or confirming a plot faithfully represents its data before submission. For CREATING the plot prefer alterlab-matplotlib (or alterlab-seaborn / alterlab-plotly); for multi-panel publication layout prefer alterlab-scientific-viz; for schematic diagrams prefer alterlab-scientific-schematics. Part of the AlterLab Academic Skills suite.

alterlab-flowio

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.

alterlab-fluidsim

Runs computational fluid dynamics simulations with the FluidSim Python framework using pseudospectral FFT methods, with HPC support and output analysis. Use when simulating Navier-Stokes equations (2D/3D), shallow water equations, or stratified flows, or when analyzing turbulence, vortex dynamics, or geophysical flows. Part of the AlterLab Academic Skills suite.

alterlab-fred

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.

alterlab-gene-db

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.

alterlab-generate-image

Generates or edits raster images via AI models (FLUX.2, Gemini 3.1 Flash Image / "Nano Banana 2") through an OpenRouter API key. Use when the request is to generate or edit a photo, illustration, artwork, concept art, poster hero image, or presentation/slide visual asset — anything that is not a technical diagram or a data chart. For flowcharts, circuits, pathways, neural-net architectures, and technical/methodology diagrams use alterlab-scientific-schematics; for plotting numeric data (scatter, bar, line) use alterlab-matplotlib instead. Part of the AlterLab Academic Skills suite.

alterlab-geniml

Machine learning on genomic interval data (BED files) with the geniml Python package — region embeddings (Region2Vec), joint region+metadata embeddings (BEDspace/StarSpace), single-cell ATAC-seq embeddings (scEmbed), consensus peak sets / universes (build-universe), tokenization, BEDshift randomization, and BBClient/BEDbase caching. Use when training or using region/cell embeddings, clustering scATAC-seq, building a tokenization universe from BED collections, or any ML/feature-learning task over genomic regions. NOT for plain interval arithmetic (overlap/intersect/merge counts) — that is gtars, not geniml. Part of the AlterLab Academic Skills suite.

alterlab-geo

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.

alterlab-geomaster

Covers geospatial science across remote sensing, GIS, spatial analysis, and machine learning for earth observation — satellite imagery processing (Sentinel, Landsat, MODIS, SAR, hyperspectral), raster and DEM operations, spectral indices (NDVI/EVI/NDWI), spatial statistics, point cloud processing, network analysis, and cloud-native workflows (STAC, COG, Planetary Computer), with examples across Python, R, Julia, JavaScript, C++, Java, Go, and Rust. Use for remote sensing workflows, satellite/raster image classification, terrain/slope/hillshade analysis, spatial ML on earth-observation data, hydrological modeling, marine spatial analysis, or atmospheric science. For pure tabular vector work with no raster/EO aspect (plain GeoPandas sjoin, buffer, overlay, dissolve, choropleths) prefer the geopandas skill; for celestial-sphere astronomy coordinates (ICRS/galactic, FITS, WCS) prefer the astropy skill. Part of the AlterLab Academic Skills suite.

alterlab-geopandas

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.

alterlab-gget

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.

alterlab-ginkgo-cloud

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.

alterlab-glycoengineering

Analyze and engineer protein glycosylation — scan sequences for N-glycosylation sequons (N-X-S/T), predict O-glycosylation hotspots, and reach curated glycoengineering tools (NetOGlyc, GlycoShield, GlycoWorkbench). Use when identifying or designing glycosylation sites, optimizing therapeutic-antibody or biologic glycoforms, or doing glycoprotein engineering and vaccine-design work. Part of the AlterLab Academic Skills suite.

alterlab-gnomad

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.

alterlab-grant-reporting

Drafts post-award grant deliverables across funder formats — NIH RPPR (Annual/Interim/Final via eRA Commons), NSF annual/final project reports and the public Project Outcomes Report (Research.gov), and Horizon Europe / ERC periodic and final reports (technical Part A/B + financial statements on the EU Funding & Tenders Portal) — plus milestone and deliverable tracking, budget-vs-actual variance narratives, no-cost-extension and rebudgeting justifications, and effort/closeout reporting. Computes report due dates from the award period with scripts/report_deadlines.py. Use when the user needs a grant progress or final report, post-award reporting, an RPPR, a periodic report, a no-cost-extension request, milestone tracking, or a budget-variance narrative. For writing new proposals prefer alterlab-research-grants; for TÜBİTAK proposals prefer alterlab-tubitak-proposal. Part of the AlterLab Academic Skills suite.

alterlab-gtars

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.

alterlab-gtex

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.

alterlab-gwas

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.

alterlab-hedgefund-monitor

Queries the OFR (Office of Financial Research) Hedge Fund Monitor API for time series on hedge fund size, leverage, counterparties, liquidity, complexity, and risk management, including SEC Form PF aggregated statistics, CFTC Traders in Financial Futures, FICC Sponsored Repo volumes, and FRB SCOOS dealer financing terms (no API key or registration required). Use when working with hedge fund data, systemic risk monitoring, financial stability research, hedge fund leverage or leverage ratios, counterparty concentration, Form PF statistics, repo market data, or OFR financial research data. Part of the AlterLab Academic Skills suite.

alterlab-histolab

Extract and preprocess tiles from whole-slide images (WSI) with histolab — OpenSlide-backed slide loading, tissue detection and masks, Random/Grid/Score tile extraction, and image/morphological filters for H&E preprocessing. Use when the user needs lightweight WSI slide preprocessing — building tile datasets for ML training, tissue segmentation, or quick tile-based inspection of histopathology slides. For end-to-end computational-pathology, deep-learning model training, nucleus segmentation, or multiplexed/spatial-proteomics (CODEX, Vectra) pipelines prefer alterlab-pathml instead. Part of the AlterLab Academic Skills suite.

alterlab-hmdb

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.

alterlab-hypogenic

Runs automated LLM-driven hypothesis generation and testing on tabular datasets with HypoGeniC, combining literature insights with data-driven testing. Use when systematically exploring hypotheses about patterns in empirical data (for example deception detection or content analysis). For manual hypothesis formulation use alterlab-hypothesis-gen; for open-ended creative ideation use alterlab-scientific-brainstorm. Part of the AlterLab Academic Skills suite.

alterlab-hypothesis-gen

Formulates structured, testable hypotheses from experimental observations using a scientific-method framework — derives predictions, proposes mechanisms, and designs experiments to test them, then renders a LaTeX report. Use when turning observations or data into falsifiable, mechanistic hypotheses, competing-explanation sets, testable predictions, or experimental designs. For a standalone systematic literature review or evidence synthesis (not a means to hypotheses) use alterlab-literature-review; to evaluate an existing manuscript use alterlab-peer-review. Part of the AlterLab Academic Skills suite.

alterlab-imaging-data-commons

Query and download public cancer imaging data from the NCI Imaging Data Commons (IDC) using the idc-index Python package, filtering by metadata, visualizing in-browser, and checking licenses, with no authentication required. Use when obtaining large-scale radiology (CT, MR, PET) or digital pathology DICOM datasets for AI/ML training or cancer imaging research. Part of the AlterLab Academic Skills suite.

alterlab-infographics

Creates professional infographics with Nano Banana Pro AI and smart iterative refinement, using Gemini 3 Pro for automated quality review and an optional Perplexity Sonar research phase for accurate, sourced data — supports 10 infographic types, 8 industry styles, and colorblind-safe palettes. Use when the request is for an infographic, data-story graphic, statistical poster, comparison chart, timeline, process/how-to visual, or list/social graphic that pairs a designed layout with figures. Use alterlab-scientific-schematics instead for technical flowcharts, CONSORT/PRISMA, pathways, or architecture diagrams; alterlab-generate-image for non-infographic illustrations. Part of the AlterLab Academic Skills suite.

alterlab-interpro

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.

alterlab-iso13485

Prepares ISO 13485 certification documentation for medical device Quality Management Systems (QMS) — gap analysis of existing documentation, Quality Manuals, required procedures and work instructions, and Medical Device Files. Use for ISO 13485 QMS documentation, conducting a documentation gap analysis, drafting a Quality Manual or SOP/work instruction, assembling a Medical Device File, identifying missing documentation for medical device certification, or when medical device regulations, QMS certification, FDA QMSR, or EU MDR are mentioned. Part of the AlterLab Academic Skills suite.

alterlab-jaspar

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.

alterlab-kegg

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.

alterlab-kvkk-dmp

Produces KVKK-compliant (Law 6698, as amended by Law 7499 — published in the Official Gazette 12 Mar 2024, KVKK provisions effective 1 Jun 2024) data management plans for Turkish research, encoding the açık rıza (explicit consent) default basis, the Art. 28(1)(b) anonymization exemption as the primary compliance lever, the Art. 6 special-category regime for health/genetic/biometric data, Art. 7 deletion/destruction/anonymization at purpose-end, the Art. 13 thirty-day data-subject response window, Art. 9 cross-border adequacy-decision rules for cloud/overseas data, and Art. 16 VERBIS pre-processing registration, with a KVKK-vs-GDPR crosswalk. Use when the user needs a KVKK data management plan, to anonymize a research dataset under Turkish law, a VERBIS check, or to fix EU DMP boilerplate for Turkey; for pure GDPR/HIPAA use alterlab-research-ethics. Part of the AlterLab Academic Skills suite.

alterlab-labarchive

Integrates the LabArchives electronic lab notebook (ELN) via its REST API — access notebooks, manage entries and attachments, back up notebooks, and bridge to Protocols.io, Jupyter, and REDCap. Use when automating LabArchives ELN workflows, programmatically reading/writing notebook entries or attachments, backing up a LabArchives notebook, or syncing it with Protocols.io, Jupyter, or REDCap. Part of the AlterLab Academic Skills suite.

alterlab-lamindb

Manage, annotate, and trace biological data with LaminDB, an open-source FAIR data framework that makes datasets queryable, versioned, and reproducible. Use when registering or querying biological datasets (scRNA-seq, spatial, flow cytometry), validating and curating data against ontologies (genes, cell types, diseases, tissues), tracking data lineage and computational workflows, building data lakehouses, or wiring integrations with Nextflow, Snakemake, W&B, or MLflow. Part of the AlterLab Academic Skills suite.

alterlab-latchbio

Builds and deploys bioinformatics pipelines on the LatchBio platform using the Latch SDK — author workflows with @workflow/@task decorators, handle LatchFile/LatchDir I/O, register serverless workflows, configure CPU/GPU task resources, organize data in the Latch Registry, and wrap Nextflow/Snakemake pipelines. Use when developing or deploying a Latch SDK workflow, sizing task resources, working with the Registry, or porting a Nextflow/Snakemake bioinformatics pipeline onto LatchBio. Not for DNAnexus (dxpy/dx CLI) or generic Flyte. Part of the AlterLab Academic Skills suite.

alterlab-latex-posters

Creates professional research posters in LaTeX using beamerposter, tikzposter, or baposter — handles layout design, color schemes, multi-column formats, figure integration, and poster-specific visual-communication best practices. Use when building a conference or academic poster in LaTeX. For PowerPoint/PPTX poster output prefer pptx-posters instead. Part of the AlterLab Academic Skills suite.

alterlab-ligandmpnn

Design protein sequences around bound ligands, metals, and nucleic acids with LigandMPNN (Dauparas 2023) — inverse folding that conditions on non-protein context, so binding-pocket and metal-site residues are chosen to fit the actual ligand. Use when designing a small-molecule or metal binding pocket, redesigning residues that contact a ligand/ion/nucleic acid, or doing enzyme active-site design where the substrate matters. For backbone sequence design with NO ligand/metal context prefer alterlab-proteinmpnn; to GENERATE a backbone or scaffold a functional site prefer alterlab-rfdiffusion; to validate a design by refolding prefer alterlab-alphafold; to co-fold or dock the ligand prefer alterlab-boltz or alterlab-diffdock. Part of the AlterLab Academic Skills suite.

alterlab-link-health

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.

alterlab-literature-review

Conducts comprehensive, systematic literature reviews across multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar), with PRISMA flow tracking, study screening (title/abstract and full-text), evidence-table extraction, and risk-of-bias assessment, producing professionally formatted markdown documents and PDFs with verified citations in multiple styles (APA, Nature, Vancouver). Use when running a systematic literature review, meta-analysis, research synthesis, or broad literature search, building a PRISMA flow diagram, screening studies, extracting an evidence table, or assessing risk-of-bias across biomedical, scientific, and technical domains. Part of the AlterLab Academic Skills suite.

alterlab-market-research

Generates comprehensive market research reports (50+ pages) in the style of top consulting firms (McKinsey, BCG, Gartner), with professional LaTeX formatting, extensive visuals via scientific-schematics and generate-image, data gathering through research-lookup, and multi-framework strategic analysis (Porter Five Forces, PESTLE, SWOT, TAM/SAM/SOM, BCG Matrix). Use when producing a market analysis, competitive landscape, industry report, market-sizing study, or consulting-style strategic deliverable. NOT for a single focused, source-cited research question with no report/frameworks (use alterlab-deep-research) or for pulling raw financial data points from an API (use alterlab-alpha-vantage). Part of the AlterLab Academic Skills suite.

alterlab-markitdown

Convert files and Office documents to clean, LLM-friendly Markdown with Microsoft MarkItDown (markitdown CLI/Python), supporting PDF, DOCX, PPTX, XLSX, images (EXIF + OCR), audio (transcription), HTML, CSV, JSON, XML, ZIP archives, EPUB e-books, and YouTube transcript URLs, with optional AI image descriptions. Use when converting a document, PDF, slide deck, spreadsheet, scanned image, audio file, web page, or e-book into Markdown text for ingestion or LLM processing, extracting text via OCR, transcribing audio, or batch-converting mixed file formats to token-efficient Markdown. Part of the AlterLab Academic Skills suite.

alterlab-matchms

Computes mass-spectral similarity and identifies compounds for metabolomics with matchms — comparing mass spectra, scoring similarity (cosine, modified cosine), and searching spectral libraries to annotate unknowns. Use when matching MS/MS spectra, identifying metabolites, or library searching; for full LC-MS/MS proteomics pipelines use pyopenms. Part of the AlterLab Academic Skills suite.

alterlab-matplotlib

Builds plots with the matplotlib Python library (pyplot and the object-oriented Figure/Axes API) for full low-level customization, exporting to PNG/PDF/SVG. Use when fine-grained control over individual plot elements is needed — custom line/scatter/bar/histogram/heatmap/contour/box/violin/3D plots, rcParams and style-sheet tuning, or GridSpec subplot layouts inside a scientific Python workflow. Does NOT cover opinionated journal-ready multi-panel figure workflows (Nature/Science/Cell formatting, colorblind-safe palettes, significance annotations); for those prefer alterlab-scientific-viz instead. Part of the AlterLab Academic Skills suite.

alterlab-medchem

Applies medicinal-chemistry filters with the medchem library — drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, and molecular complexity metrics for compound prioritization and library cleanup. Use when filtering or triaging a compound library, flagging PAINS or reactive groups, or assessing drug-likeness of candidate molecules. Part of the AlterLab Academic Skills suite.

alterlab-mermaid

Writes Markdown documents and text-based Mermaid diagrams (flowcharts, sequence, class, ER, gantt, state, and more) with full style guides, 24 diagram-type references, and 9 document templates. Use when authoring a scientific document, report, analysis, or README, or when a diagram should be expressed as version-controllable Mermaid/Markdown text rather than a rendered image. For AI-rendered publication schematics use scientific-schematics instead. Part of the AlterLab Academic Skills suite.

alterlab-meta-analysis

Runs quantitative meta-analysis — computes effect sizes (Hedges' g / standardized mean difference, log odds/risk ratios) with their variances, pools them under fixed-effect and random-effects models, quantifies heterogeneity (I-squared, tau-squared, Cochran's Q), draws forest and funnel plots, and tests publication bias (Egger's regression, trim-and-fill) — using statsmodels.stats.meta_analysis in Python or the field-standard R metafor via Rscript. It enforces PRISMA reporting and the random- vs fixed-effect decision. Use when pooling effect sizes across studies, running a systematic review's quantitative synthesis, or assessing heterogeneity and publication bias. For finding and screening the literature prefer alterlab-deep-research; for a single study's statistics prefer alterlab-statistical-analysis. Part of the AlterLab Academic Skills suite.

alterlab-metabolomics-wb

Access the NIH Metabolomics Workbench via its REST API (4,200+ studies), querying metabolites, RefMet standardized nomenclature, MS/NMR data, m/z mass searches, and study metadata. Use when retrieving public metabolomics study data, standardizing metabolite names with RefMet, running m/z lookups, or doing biomarker discovery. Part of the AlterLab Academic Skills suite.

alterlab-missing-data

Handles missing data with principled methods — forces an explicit MCAR / MAR / MNAR mechanism statement, then applies multiple imputation by chained equations (MICE) with Rubin's-rules pooling of estimates and standard errors, or full-information maximum likelihood (FIML) where a likelihood/SEM model applies. Uses statsmodels MICE / MICEData in Python or the field-standard R mice via Rscript, and warns that single (mean/regression) imputation and scikit-learn's IterativeImputer return one completed dataset without Rubin's-rules pooling, so they understate standard errors if used as multiple imputation. Use when a dataset has missing values, when choosing an imputation strategy, or when reporting how missingness was handled. For general modeling on complete data prefer alterlab-statistical-analysis; for latent-variable models with FIML prefer alterlab-sem-psychometrics. Part of the AlterLab Academic Skills suite.

alterlab-mixed-methods

Mixed methods research design and integration strategies for combining qualitative and quantitative approaches. Use when planning convergent, explanatory sequential, exploratory sequential, embedded, transformative, or multiphase designs; when integrating diverse data sources through merging, connecting, or embedding; when constructing joint displays or meta-inferences; or when evaluating quality criteria specific to mixed methods research. Covers Creswell & Plano Clark frameworks, notation systems, and software tools for integration. For single-strand qualitative coding (thematic analysis, grounded theory, saturation, inter-coder reliability) use alterlab-qualitative-methods; for questionnaire/Likert/instrument-validation mechanics use alterlab-survey-design. Part of the AlterLab Academic Skills suite.

alterlab-modal

Runs Python code in the cloud with Modal — serverless containers, on-demand GPUs, and autoscaling. Use when deploying ML models, running batch processing jobs, scheduling compute-intensive tasks, or serving APIs that need GPU acceleration or dynamic scaling. Part of the AlterLab Academic Skills suite.

alterlab-molecular-dynamics

Runs and analyzes molecular dynamics simulations with OpenMM and MDAnalysis — setting up protein and small-molecule systems, assigning force fields, running energy minimization and production MD, and analyzing trajectories (RMSD, RMSF, contact maps, free energy surfaces). Use when simulating protein or ligand dynamics, equilibrating a system, or computing trajectory metrics for structural biology, drug binding, or biophysics. Part of the AlterLab Academic Skills suite.

alterlab-molfeat

Featurizes molecules for machine learning with molfeat (100+ featurizers) — ECFP/MACCS/MAP4 fingerprints, RDKit and Mordred physicochemical descriptors, and pretrained embeddings (ChemBERTa, ChemGPT, GIN) exposed as scikit-learn transformers that convert SMILES into feature vectors. Use when turning molecules into ML-ready feature matrices for QSAR/QSPR or virtual screening, or benchmarking fingerprint against descriptor and embedding representations; for training models and MoleculeNet benchmarks on those features prefer alterlab-deepchem, and for low-level fingerprint or descriptor primitives prefer alterlab-rdkit. Part of the AlterLab Academic Skills suite.

alterlab-monarch

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.

alterlab-multilevel-models

Fits and reports mixed-effects / multilevel / hierarchical models for clustered, nested, longitudinal, and repeated-measures data — random intercepts and slopes, variance components and the ICC, cross-level interactions, and GLMMs (logistic/Poisson) — using statsmodels MixedLM and bambi (Bayesian on PyMC) in Python, or the field-standard R lme4 / glmmTMB / brms via Rscript. It enforces the reporting items reviews find under-reported: full fixed + random specification, centering, variance components + ICC, estimation method, assumption checks, model comparisons, and effect sizes. Use when data are grouped/nested (students in schools, repeated measures, panel/longitudinal) and the question concerns within- vs between-cluster variation. For general single-level regression prefer alterlab-statsmodels; for panel fixed effects used for causal identification prefer alterlab-causal-inference. Part of the AlterLab Academic Skills suite.

alterlab-networkx

Creates, analyzes, and visualizes complex networks and graphs in Python with NetworkX. Use when working with network/graph data structures, analyzing relationships between entities, computing graph algorithms (shortest paths, centrality, clustering), detecting communities, generating synthetic networks, or visualizing topologies — applicable to social, biological, transportation, citation, and any pairwise-relationship networks. This is classical graph analytics, not deep learning — for training graph neural networks (GCN/message passing, node/edge/graph classification on Cora-style data) use alterlab-torch-geometric instead. Part of the AlterLab Academic Skills suite.

alterlab-neurokit2

Processes and analyzes physiological biosignals with the NeuroKit2 Python toolkit — ECG, EEG, EDA, RSP, PPG, EMG, and EOG signals. Use when processing cardiovascular signals, brain activity, electrodermal responses, respiratory patterns, muscle activity, or eye movements, or when computing heart rate variability (HRV), event-related potentials, complexity measures, autonomic nervous system assessment, or multi-modal physiological signal integration for psychophysiology research. Part of the AlterLab Academic Skills suite.

alterlab-neuropixels

Analyze Neuropixels 1.0/2.0 extracellular electrophysiology with SpikeInterface — load SpikeGLX/Open Ephys recordings, preprocess and motion-correct, run Kilosort4 spike sorting, compute quality metrics, apply Allen/IBL curation, and do AI-assisted visual inspection. Use when working with neural recordings, spike sorting, or extracellular electrophysiology, or when the user mentions Neuropixels, SpikeGLX, Open Ephys, Kilosort, quality metrics, or unit curation. Part of the AlterLab Academic Skills suite.

alterlab-nf-core-sarek

Runs FASTQ-to-VCF germline and somatic variant calling via the Nextflow nf-core/sarek pipeline pinned to -r 3.8.1 — builds the samplesheet.csv (patient, sex, status, sample, lane, fastq_1, fastq_2), runs bwa-mem/bwa-mem2/dragmap alignment plus GATK4 MarkDuplicates and BQSR against the GATK GRCh38 resource bundle (dbSNP, Mills/1000G indels), and selects callers — explicitly correcting that sarek defaults to Strelka when --tools is unset (pass haplotypecaller for GATK best practice or deepvariant for CNN accuracy), with a non-Nextflow manual GATK4 fallback. Use when the user wants a variant-calling pipeline, FASTQ to VCF, germline or somatic SNV/indel calling, nf-core/sarek, GATK best-practices alignment-to-VCF, or BQSR/HaplotypeCaller/Mutect2/DeepVariant; annotate hits with alterlab-clinvar/alterlab-gnomad/alterlab-cosmic, parse VCFs with alterlab-pysam, store at scale with alterlab-tiledbvcf. Part of the AlterLab Academic Skills suite.

alterlab-omero

Manages microscopy image data on an OMERO server via the OMERO Python API (BlitzGateway) — access images, retrieve datasets, read pixel data, manage ROIs and annotations, and batch-process. Use when connecting to an OMERO server, pulling microscopy images or datasets, analyzing pixels, managing ROIs/annotations, or running high-content screening and microscopy workflows. Part of the AlterLab Academic Skills suite.

alterlab-open-notebook

Run Open Notebook, a self-hosted open-source alternative to Google NotebookLM with a full REST API, for AI-powered research and document analysis. Use when organizing research materials into notebooks, ingesting diverse content sources (PDFs, videos, audio, web pages, Office documents), generating AI-powered notes and summaries, creating multi-speaker podcasts from research, chatting with documents using context-aware AI, searching across materials with full-text and vector search, or running custom content transformations. Supports 18+ AI providers including OpenAI, Anthropic, Google, Ollama, LM Studio, Groq, and Mistral with complete data privacy through self-hosting. For a one-shot file-to-Markdown conversion (no notebook, chat, or search), use alterlab-markitdown instead. Part of the AlterLab Academic Skills suite.

alterlab-open-science

Guidance for open science practices — preregistration (OSF Registries, AsPredicted, PROSPERO, ClinicalTrials.gov), open data and FAIR principles, repository choice (Zenodo, Dryad, Figshare), open access routes (Green/Gold/Diamond), Creative Commons licensing, reproducible computational workflows (Docker, Binder, Code Ocean), registered reports, open peer review, and TOP Guidelines. Use when preregistering a study, writing the FAIR data-sharing and repository section of a grant data management plan (NSF, NIH, ERC, UKRI), choosing a data repository, navigating open access, or building reproducible analyses. For human-subjects ethics, IRB applications, informed consent, or GDPR/HIPAA compliance, defer to alterlab-research-ethics. Part of the AlterLab Academic Skills suite.

alterlab-openalex

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.

alterlab-opentargets

Query the Open Targets Platform GraphQL API for target-disease associations, tractability and safety data, genetics/omics evidence, and known drugs. Use when identifying or prioritizing therapeutic drug targets, assessing target druggability/safety, or gathering target-disease evidence for drug discovery. Part of the AlterLab Academic Skills suite.

alterlab-opentrons

Writes liquid-handling protocols for Opentrons OT-2 and Flex robots using the official Opentrons Protocol API v2, with full access to v2 features for production-grade, officially compatible protocols. Use when authoring or running protocols specifically for Opentrons hardware. For multi-vendor automation or broader equipment control use pylabrobot instead. Part of the AlterLab Academic Skills suite.

alterlab-paper-2-web

Converts academic papers into promotional and presentation formats — interactive websites (Paper2Web), presentation videos (Paper2Video), and conference posters (Paper2Poster) from LaTeX or PDF sources. Use when disseminating a paper, preparing for a conference, building an explorable academic homepage, generating a video abstract, or producing a print-ready poster from a paper. Part of the AlterLab Academic Skills suite.

alterlab-paper-reviewer

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.

alterlab-paper-writer

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.

alterlab-parallel-web

Search the web, run deep research, and extract content from known URLs via the Parallel Web Systems Chat API (OpenAI-compatible) and Extract API, returning synthesized summaries with inline citations. Use when running general web searches, current-events/market/technical lookups, broad information gathering, comprehensive research reports, or verifying a specific URL's content (requires PARALLEL_API_KEY). For scholarly paper retrieval or dual-backend academic lookup that auto-routes to Perplexity prefer alterlab-research-lookup instead. Part of the AlterLab Academic Skills suite.

alterlab-pathml

Run full computational-pathology workflows with PathML — whole-slide-image (WSI) analysis across 160+ slide formats, multiplexed immunofluorescence (CODEX, Vectra, MERFISH), nucleus segmentation/classification (HoVer-Net, HACTNet), tissue- and cell-graph construction, HDF5 dataset management, and deep-learning model training on pathology data. Use when the user builds end-to-end deep-learning pathology pipelines, analyzes multiplexed or spatial-proteomics slides, or segments nuclei. For lightweight H&E slide preprocessing, tissue masking, or plain Random/Grid/Score tile extraction prefer alterlab-histolab instead. Part of the AlterLab Academic Skills suite.

alterlab-pdb

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.

alterlab-pdf-explore

Explore a single PDF in depth — parse it once, then answer questions across its sections, figures, tables, and appendices — comparing methods across sections, extracting every instance of a pattern within the document, and reading values off its charts and tables. Use when interrogating one paper or report end-to-end, pulling every occurrence of something inside a document, or reading data from a figure/table in a PDF, serving the literature-review and paper-review pipeline. To build a comparison table across MANY papers prefer alterlab-pdf-extract; to simply convert a PDF to Markdown prefer alterlab-markitdown; for reference/citation management prefer alterlab-pyzotero. Part of the AlterLab Academic Skills suite.

alterlab-pdf-extract

Free Elicit-columns analog — ingest N PDFs (or any MarkItDown-supported document) and build a per-paper evidence table with user-defined columns, one row per paper and one column per attribute/question you want pulled from every source. Use when extracting structured data across many papers into a comparison table or data-extraction sheet (sample size, methods, main finding, effect, population/intervention/outcome, limitations), screening a corpus into a spreadsheet, or pulling the same fields from a stack of PDFs into CSV/Markdown. Routes conversion through MarkItDown; offline heuristic backend by default, optional LLM backend for precise answers. Part of the AlterLab Academic Skills suite.

alterlab-peer-review

Writes structured, checklist-based manuscript and grant peer reviews — assesses methodology, statistical validity, reporting-standards compliance (CONSORT/STROBE/PRISMA), and gives constructive feedback. Use when writing a formal reviewer report, responding to a journal/grant review invitation, or revising a manuscript against reviewer criteria. For evaluating claims/evidence quality prefer alterlab-scientific-thinking; for a multi-reviewer mock-panel verdict use alterlab-paper-reviewer; for quantitative rubric scoring use alterlab-scholar-eval. Part of the AlterLab Academic Skills suite.

alterlab-pennylane

Trains and differentiates quantum circuits with PennyLane, a hardware-agnostic quantum machine-learning framework with automatic differentiation and PyTorch/JAX/TensorFlow integration. Use when training quantum circuits via gradients (parameter-shift, backprop, adjoint), building hybrid quantum-classical models or quantum neural networks, or running differentiable variational algorithms (VQE, QAOA). For IBM Quantum hardware and Qiskit Runtime prefer alterlab-qiskit; for Google Quantum AI or NISQ circuits prefer alterlab-cirq; for open-system Lindblad/master-equation dynamics prefer alterlab-qutip. Part of the AlterLab Academic Skills suite.

alterlab-perplexity

Run AI web searches with real-time, citation-grounded answers using Perplexity Sonar models (sonar, sonar-pro, sonar-pro-search agentic search, sonar-reasoning, sonar-reasoning-pro) via LiteLLM and a single OpenRouter API key. Use when searching for current information or recent scientific literature, getting answers grounded in cited web sources, verifying a claim against current evidence, or reaching information beyond the model's training cutoff. Requires an OpenRouter API key. This is the direct single-backend Perplexity tool: for automatic routing between Perplexity and other backends use alterlab-research-lookup, and for structured per-paper experimental-data extraction (sample sizes, effect sizes, quality scores) use alterlab-bgpt-search. Part of the AlterLab Academic Skills suite.

alterlab-phylogenetics

Build phylogenetic trees end-to-end from raw sequences — MAFFT multiple sequence alignment, optional TrimAl trimming, IQ-TREE 2 maximum-likelihood inference with model selection and bootstraps, FastTree for large datasets, then visualize with ETE3 or FigTree. Use when reconstructing trees from sequences (FASTA) for evolutionary analysis, microbial genomics, viral phylodynamics, protein-family studies, or molecular-clock dating. For manipulating/comparing an EXISTING Newick tree (prune, root, Robinson-Foulds, duplication/speciation events) use alterlab-etetoolkit; for plain sequence parsing/translation use alterlab-biopython. Part of the AlterLab Academic Skills suite.

alterlab-plotly

Builds INTERACTIVE charts with the Plotly Python library (plotly.express / graph_objects) — hover tooltips, zoom/pan, animations, rangesliders, 3D rotation, and standalone HTML/web-embeddable output. Use when a chart must be interactive or web-embedded, for dashboards (incl. Dash), exploratory data analysis, or rotatable 3D plots. For static publication figures defer to alterlab-matplotlib; for static statistical charts (heatmaps, distributions) defer to alterlab-seaborn; for diagrams/schematics defer to alterlab-scientific-viz. Part of the AlterLab Academic Skills suite.

alterlab-polars

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.

alterlab-pptx-posters

Creates research posters in HTML/CSS with responsive layouts and easy visual integration, exportable to PDF or PPTX. Use ONLY when the user explicitly requests a PowerPoint/PPTX/PPT poster, an HTML/web-based poster, or a poster they will edit in PowerPoint, or when LaTeX is unavailable. For a standard/conference research poster with no format named, use alterlab-latex-posters instead; for a slide deck/oral-talk presentation, use alterlab-scientific-slides. Part of the AlterLab Academic Skills suite.

alterlab-preprint-deposition

Drives preprint deposition across servers (arXiv, bioRxiv, medRxiv, SSRN, OSF Preprints): picks the right server by field, prepares submission metadata, sets the license (arXiv offers CC BY/BY-SA/BY-NC-SA/BY-NC-ND 4.0, the arXiv non-exclusive license, or CC0; bioRxiv/medRxiv offer CC BY/BY-NC/BY-ND/BY-NC-ND/CC0 or No-reuse), maps arXiv category taxonomy, handles immutable versioning and preprint DOIs, checks a journal's preprint/self-archiving policy via the Sherpa Romeo v2 API, and links the posted preprint to the published article. Reuses alterlab-arxiv and alterlab-biorxiv for metadata and alterlab-open-science for data-repository choice. Use when depositing a preprint, choosing a preprint server, preparing an arXiv or bioRxiv submission, setting a preprint license, or checking journal preprint policy; for Zenodo/Dryad/Figshare data deposition prefer alterlab-open-science, for TÜBİTAK Aperta prefer alterlab-aperta. Part of the AlterLab Academic Skills suite.

alterlab-preregistration-discipline

Enforces pre-registration discipline with the Iron Law NO DATA ANALYSIS WITHOUT A PRE-REGISTERED ANALYSIS PLAN FIRST, a spirit-vs-letter line, an Excuse-vs-Reality rationalization table, and a Red-Flags-STOP list (HARKing, optional stopping, post-hoc covariates, outlier-dropping, test-shopping). Runs a PLAN/COLLECT/CONFIRM/EXPLORE workflow that freezes hypotheses, tests, exclusions, and stopping rules before data, then forces unplanned findings to be labeled exploratory (their p-values lose confirmatory status, per COS confirmatory/exploratory model). Orchestrates, not replaces, alterlab-open-science (OSF/AsPredicted registration), alterlab-statistical-analysis (test selection, assumptions), and alterlab-scientific-thinking (bias grading). Use when analyzing data without a frozen plan, switching the primary outcome or adding covariates after seeing results, weighing early stopping, dropping outliers post-hoc, pre-registering a study, or rationalizing deviation. Part of the AlterLab Academic Skills suite.

alterlab-primekg

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.

alterlab-proteinmpnn

Design protein sequences for a fixed backbone with ProteinMPNN (Dauparas 2022) — message-passing inverse folding that outputs sequences predicted to fold to a given structure, with fixed positions, tied/symmetric chains, amino-acid bias, and a soluble-model variant. Use when inverse-folding a backbone PDB into sequences, redesigning selected positions, imposing symmetry across chains, or generating the sequence step of a design→fold→score loop. For pocket/interface design WITH a bound ligand, metal, or nucleic acid prefer alterlab-ligandmpnn; to GENERATE a new backbone prefer alterlab-rfdiffusion; to refold and validate a design prefer alterlab-alphafold; for generative multimodal design prefer alterlab-esm. Part of the AlterLab Academic Skills suite.

alterlab-protocolsio

Manages scientific protocols through the protocols.io API v3 — search, create, update, and publish protocols (with DOI), manage steps and materials, handle protocol/step discussions and comments, organize team workspaces, and upload/manage workspace files. Use when discovering, developing, publishing, or citing protocols.io protocols, collaborating on protocol steps/materials, recording experiment runs, or integrating protocols.io into lab documentation. Not for general ELN entries/notebooks (use alterlab-benchling or alterlab-labarchive) or lab-instrument/liquid-handler control. Part of the AlterLab Academic Skills suite.

alterlab-pubchem

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.

alterlab-pubmed

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.

alterlab-pufferlib

Scales reinforcement learning with PufferLib — high-throughput parallel training (PuffeRL), vectorized environments, and native multi-agent systems achieving 2-10x speedups over standard implementations. Use when scaling RL to millions of steps per second, running vectorized or multi-agent setups, building custom PufferEnv tasks, or integrating game environments (Atari, Procgen, NetHack, PettingZoo). For standard single-agent algorithm implementations (PPO/SAC/DQN) or quick prototyping prefer alterlab-stable-baselines3. Part of the AlterLab Academic Skills suite.

alterlab-pydeseq2

Run differential gene expression analysis on bulk RNA-seq count matrices with PyDESeq2, the Python port of DESeq2 — size-factor normalization, dispersion estimation, Wald tests, FDR (Benjamini-Hochberg) correction, and volcano/MA plots. Use when identifying differentially expressed genes between conditions from raw bulk RNA-seq counts. Part of the AlterLab Academic Skills suite.

alterlab-pydicom

Reads, writes, and manipulates DICOM (Digital Imaging and Communications in Medicine) medical imaging files with the pydicom Python library. Use when reading/writing/modifying DICOM data, extracting pixel data from CT, MRI, X-ray, or ultrasound images, anonymizing DICOM files, working with DICOM metadata and tags, converting DICOM to other formats, handling compressed DICOM, or processing medical imaging datasets for PACS systems, radiology workflows, and healthcare imaging applications. Part of the AlterLab Academic Skills suite.

alterlab-pyhealth

Develops, tests, and deploys clinical machine learning models with the PyHealth healthcare AI toolkit. Use when working with electronic health records (EHR), clinical prediction tasks (mortality, readmission, drug recommendation), medical coding systems (ICD, NDC, ATC), physiological signals (EEG, ECG), healthcare datasets (MIMIC-III/IV, eICU, OMOP), or implementing deep learning models for healthcare (RETAIN, SafeDrug, Transformer, GNN). Part of the AlterLab Academic Skills suite.

alterlab-pylabrobot

Programs lab automation with PyLabRobot, a vendor-agnostic Python framework that unifies control across Hamilton, Tecan, Opentrons, plate readers, and pumps, with simulation support. Use when controlling multiple equipment types or needing unified cross-vendor programming for complex, multi-vendor liquid-handling workflows. For Opentrons-only protocols with the official API, alterlab-opentrons may be simpler. Part of the AlterLab Academic Skills suite.

alterlab-pymatgen

Analyzes and manipulates materials with the pymatgen toolkit — crystal structures and molecules, phase diagrams and thermodynamic stability, electronic structure (band structures, DOS), surfaces and interfaces, and Materials Project database access. Use when working with crystal structures in materials science, converting between structure formats (CIF, POSCAR, XYZ), analyzing symmetry or space groups, computing phase diagrams, querying the Materials Project API, or handling VASP, Gaussian, or Quantum ESPRESSO output. Part of the AlterLab Academic Skills suite.

alterlab-pymc

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.

alterlab-pymoo

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.

alterlab-pyopenms

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.

alterlab-pysam

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.

alterlab-pytdc

Loads Therapeutics Data Commons (TDC, PyTDC) AI-ready drug-discovery datasets and benchmarks — ADME, toxicity, drug-target interaction (DTI), scaffold splits, and molecular oracles for therapeutic ML and pharmacological prediction. Use when fetching a standardized benchmark dataset, applying scaffold or cold-split evaluation, or sourcing labeled molecules for ADMET, toxicity, or DTI modeling. Sources data, splits, and oracles only — defer molecular featurization (ECFP/fingerprints), model training, and transformers to a molecular-ML skill (e.g. deepchem). Part of the AlterLab Academic Skills suite.

alterlab-pytorch-lightning

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.

alterlab-pyzotero

Interact with Zotero reference management libraries using the pyzotero Python client — retrieve, create, update, and delete items, collections, tags, and attachments via the Zotero Web API v3. Use when working with Zotero libraries programmatically, managing bibliographic references, exporting citations, searching library contents, uploading PDF attachments, or building research automation workflows that integrate with Zotero. Part of the AlterLab Academic Skills suite.

alterlab-qca

Runs Qualitative Comparative Analysis — crisp-set (csQCA), multi-value (mvQCA), and fuzzy-set (fsQCA) — for small-to-medium-N configurational research: calibrating raw data into set membership, building and refining a truth table, and Boolean minimization into conservative / parsimonious / intermediate solutions with consistency and coverage. Because there is no maintained Python QCA library, it shells out to R's QCA package (calibrate, truthTable, minimize) via Rscript and documents that dependency honestly rather than faking a Python API. Use when the request mentions QCA, fsQCA, csQCA, configurational or set-theoretic analysis, necessary/sufficient conditions, truth tables, or calibration of conditions. For net-effect estimation of a single treatment prefer alterlab-causal-inference; for interpretive analysis prefer alterlab-qualitative-methods. Part of the AlterLab Academic Skills suite.

alterlab-qiime2-amplicon

Runs 16S/ITS amplicon (microbiome) analysis with the QIIME 2 amplicon distribution (2026.1; renamed to "qiime2" in 2026.4) in the correct order: manifest import, cutadapt trim-paired primer removal BEFORE dada2 denoise-paired (trunc-len chosen from the demux quality .qzv), feature-classifier classify-sklearn against a version-matched SILVA 138 or Greengenes2 classifier, and diversity core-metrics-phylogenetic — teaching the .qza/.qzv artifact-and-provenance model and the 2026.1 feature-table summarize change (the former summarize_plus). Use when the request mentions QIIME2, QIIME 2, qiime, 16S, 18S, ITS, amplicon, microbiome, ASV, DADA2 denoising, feature table, taxonomic classification, or core-metrics diversity. For downstream alpha/beta diversity, PCoA, and PERMANOVA on the exported feature table prefer alterlab-scikit-bio; this is conda-only (no pip install). Part of the AlterLab Academic Skills suite.

alterlab-qiskit

Builds, transpiles, and runs quantum circuits with Qiskit, IBM's quantum computing framework, including Qiskit Runtime primitives (Sampler/Estimator), circuit transpilation, and error mitigation on IBM Quantum hardware. Use when targeting IBM Quantum backends, transpiling circuits, running Runtime sessions or batches, or applying resilience/error mitigation. For Google Quantum AI hardware and NISQ circuits prefer alterlab-cirq; for gradient-trained quantum ML and hybrid quantum-classical models prefer alterlab-pennylane; for open-system Lindblad/master-equation dynamics prefer alterlab-qutip. Part of the AlterLab Academic Skills suite.

alterlab-qualitative-analysis

Analyzes qualitative data as a dispatched pipeline module — codebook development, thematic / framework / content analysis, and inter-coder reliability computed correctly (Krippendorff's alpha as primary via the krippendorff package or a bundled stdlib nominal calculator with bootstrap CIs; Cohen's / Fleiss' kappa via statsmodels) with 95% CIs and thresholds (alpha >= .80 reliable, .667-.80 tentative). It BRANCHES by design: coefficient-based ICR for codebook / content-analytic coding, versus consensus-and-reflexivity for reflexive thematic analysis where a statistic is not the right criterion. Supports human-vs-LLM double-coding with an alpha check against a human gold standard. Use when coding interviews or open-ended text, building a codebook, or reporting intercoder reliability. For topic modeling / embeddings / supervised text classification prefer alterlab-text-as-data; for the reflexivity gate prefer alterlab-ssci-reflexivity-gate. Part of the AlterLab Academic Skills suite.

alterlab-qualitative-methods

Comprehensive qualitative research methods assistant supporting thematic analysis (Braun & Clarke), grounded theory (Strauss & Corbin; Charmaz), interpretative phenomenological analysis (IPA), content analysis, narrative inquiry, ethnography, case study methodology (Yin), coding techniques (open/axial/selective), NVivo-style workflows with Python alternatives, trustworthiness criteria (Lincoln & Guba), reflexivity, and member checking. Use when designing or analyzing qualitative research — thematic analysis, grounded theory, coding data, phenomenology, IPA, ethnography, case study, narrative inquiry, content analysis, qualitative coding, NVivo, trustworthiness, member checking, reflexivity, interview analysis, or focus group analysis. Part of the AlterLab Academic Skills suite.

alterlab-qutip

Simulates open quantum systems with QuTiP, the Quantum Toolbox in Python, solving Lindblad master equations (mesolve), Monte Carlo trajectories (mcsolve), and unitary dynamics (sesolve). Use when studying master-equation or Lindblad dynamics, decoherence, dissipation, quantum optics, cavity QED, or open-system time evolution. NOT for circuit-based quantum computing or hardware execution — for IBM Quantum circuits prefer alterlab-qiskit, for Google Quantum AI or NISQ circuits prefer alterlab-cirq, and for gradient-trained quantum ML prefer alterlab-pennylane. Part of the AlterLab Academic Skills suite.

alterlab-rdkit

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.

alterlab-reactome

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.

alterlab-recommendation-letters

Drafts evidence-anchored academic reference and recommendation letters across types — graduate admission, faculty hiring, tenure/promotion external review, fellowship, and award nomination — from a structured prompt of candidate accomplishments, role context, evaluator relationship, and audience, calibrating specificity and register to the letter type and running a no-fabrication guard that flags unsupported superlatives, unanchored rankings, and claims with no evidence in the supplied dossier. Ships scripts/letter_scaffold.py to emit a typed section skeleton and scripts/claim_guard.py to lint a draft for evidence-free assertions. Use when the request is to write a recommendation or reference letter for a student or colleague, a tenure or promotion external-review letter, a fellowship or award nomination, or to check a letter draft for unsupported claims. For a candidate writing their own CV, research statement, or career narrative prefer alterlab-academic-career. Part of the AlterLab Academic Skills suite.

alterlab-redcap-cdisc

Designs validated research data-capture instruments and aligns them to CDISC submission standards. Builds REDCap projects from a requirements spec: instrument and field design, the 18-column data dictionary (Variable/Field Name, Form Name, Field Type, Choices, Branching Logic, Text Validation, Identifier?), field validation (date_ymd, integer, number, email, phone), branching/show-field logic, longitudinal events and survey settings, and lints a data dictionary for common errors. Maps a study to CDISC: CDASH collection fields, SDTM domain mapping (DM, AE, VS, LB, EX, CM, MH across Interventions/Events/Findings classes), and NCI-EVS controlled terminology. Use when the user wants to build a REDCap project, write or lint a data dictionary, set up branching logic or validation, or map a study to CDISC SDTM/CDASH/CDISC CT. For LabArchives ELN bridging use alterlab-labarchive; for Likert/sampling/reliability use alterlab-survey-design. Part of the AlterLab Academic Skills suite.

alterlab-remote-compute

Dispatch long-running GPU/CPU jobs to remote compute with a provider-agnostic submit → poll → harvest pattern across SLURM/HPC (sbatch, squeue, sacct) and managed APIs (Modal, RunPod, GCP Batch / Vertex AI). Use when submitting a batch job to a cluster, polling job status, retrieving result artifacts from a scheduler or cloud GPU provider, or writing a portable job-submission wrapper; the foundation-model skills (alterlab-alphafold, alterlab-boltz, alterlab-rfdiffusion, and siblings) dispatch their GPU work through this pattern. For Modal-specific serverless container deployment and autoscaling prefer alterlab-modal instead. Part of the AlterLab Academic Skills suite.

alterlab-research-ethics

International research ethics and compliance assistant supporting IRB/ethics board applications, informed consent drafting, data management plans, Belmont Report principles, Declaration of Helsinki (2024), GDPR compliance for research, HIPAA considerations, vulnerable populations protocols, deception research, confidentiality and anonymity, research integrity (fabrication/falsification/plagiarism), conflict of interest disclosure, and dual-use research oversight. Use when preparing an IRB or ethics board application, drafting informed consent, writing a data management plan, addressing GDPR/HIPAA in research, protecting human subjects or vulnerable populations, handling animal ethics, or disclosing conflicts of interest. For Turkey-specific etik kurul use alterlab-tr-research-ethics; for KVKK data plans alterlab-kvkk-dmp; for survey wording alterlab-survey-design; for qualitative methodology alterlab-qualitative-methods. Part of the AlterLab Academic Skills suite.

alterlab-research-grants

Writes competitive research grant proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC — applies agency-specific formatting and review criteria, prepares budgets, and drafts broader-impacts, significance statements, and innovation narratives that comply with submission requirements. Use when drafting or revising a grant proposal, aligning a proposal to a funding agency's review criteria, or preparing grant budgets and compliance sections. For Turkey's TÜBİTAK 1001/1002-A national proposals use alterlab-tubitak-proposal; to write a reviewer's critique of someone else's proposal use alterlab-peer-review; for a journal manuscript use alterlab-scientific-writing. Part of the AlterLab Academic Skills suite.

alterlab-research-lookup

Look up current research and scholarly papers by auto-routing each query to the best backend — the Parallel Web Systems Chat API (general research) or Perplexity sonar-pro-search (academic paper searches) — and save every result with citations to sources/. Use when finding papers, gathering research data, verifying scientific claims, or assembling citation lists and unsure which search backend fits. For plain general web search or extracting content from a known URL prefer alterlab-parallel-web instead (requires PARALLEL_API_KEY and OPENROUTER_API_KEY). Part of the AlterLab Academic Skills suite.

alterlab-research-pipeline

Orchestrates the full academic research pipeline (research, write, integrity check, review, revise, re-review, re-revise, final integrity check, finalize), coordinating alterlab-deep-research, alterlab-paper-writer, and alterlab-paper-reviewer into a seamless 10-stage workflow with mandatory integrity verification, two-stage peer review, and reproducible quality gates. Use when the request mentions academic pipeline, research to paper, full paper workflow, paper pipeline, end-to-end paper, research-to-publication, or complete paper workflow. Part of the AlterLab Academic Skills suite.

alterlab-results-transparency

Enforces results-reporting transparency as a discipline gate built on the Iron Law "NO RESULTS CLAIM WITHOUT REPORTING EVERY ANALYSIS RUN" — a numbered Gate Function (IDENTIFY the claim, LIST every test actually run including the ones that did not "work", CHECK assumptions were reported, CHECK effect size with 95% CI is present, CHECK pre-registration deviations are disclosed, ONLY THEN write the sentence), plus an Excuse-vs-Reality table and Red-Flags-STOP list for selective reporting, cherry-picking, and bare p-values. Use when writing up Results, claiming a finding from a subset of analyses, reporting a p-value without an effect size or confidence interval, dropping outliers post hoc, or omitting analyses that did not pan out. Orchestrates alterlab-statistical-analysis (tests, effect sizes), alterlab-preregistration-discipline (the frozen plan), and alterlab-open-science (TOP, disclosure); it does not run the tests itself. Part of the AlterLab Academic Skills suite.

alterlab-rfdiffusion

Generate de-novo protein backbones with RFdiffusion (Watson 2023) — a diffusion model for unconditional monomer generation, motif scaffolding, binder design against a target, and symmetric oligomers. Use when generating a new protein backbone from scratch, scaffolding a functional motif into a fold, designing a binder backbone to a target surface, or building symmetric assemblies; RFdiffusion produces the STRUCTURE, then alterlab-proteinmpnn designs its sequence and alterlab-alphafold validates it. For sequence design of an existing backbone prefer alterlab-proteinmpnn (or alterlab-ligandmpnn with a ligand); to fold a known sequence prefer alterlab-alphafold; for generative multimodal design prefer alterlab-esm. Part of the AlterLab Academic Skills suite.

alterlab-rnaseq-quant

Quantifies bulk RNA-seq transcript abundance with salmon (v1.11.4 selective alignment) and kallisto (v0.52.0, kb-python workflow), builds a decoy-aware gentrome index, runs quant with --validateMappings --gcBias -l A, then imports estimates via tximport/tximeta with a tx2gene map and hands differential expression to alterlab-pydeseq2. Warns that salmon's index format changed to SSHash (rebuild pre-v1.11.2 indices) and that 'salmon alevin' was REMOVED (single-cell now uses piscem + alevin-fry). Use when quantifying RNA-seq transcript abundance, running salmon or kallisto, building a decoy-aware index, or wiring tximport to DESeq2; for differential expression use alterlab-pydeseq2, for FASTQ-to-VCF variant calling use alterlab-nf-core-sarek. Part of the AlterLab Academic Skills suite.

alterlab-rowan

Drives the Rowan cloud quantum-chemistry platform via its Python API for computational chemistry — pKa prediction, geometry optimization, conformer searching, molecular property calculations, protein-ligand docking (AutoDock Vina), and AI protein cofolding (Chai-1, Boltz-1/2), with cloud compute and no local setup. Use when running DFT or semiempirical methods, neural network potentials (AIMNet2), molecular property or protein-ligand binding predictions, or automated computational chemistry pipelines. Part of the AlterLab Academic Skills suite.

alterlab-scanpy

Run the standard single-cell RNA-seq analysis pipeline with Scanpy on AnnData — QC filtering, normalization, dimensionality reduction (PCA, UMAP, t-SNE), Leiden/Louvain clustering, marker/differential expression, PAGA trajectories, and plotting. Use when analyzing scRNA-seq data through clustering, cell-type annotation, DE, or pseudotime workflows; for building or reading the .h5ad data structure itself (layers, obs/var, concatenation, backed mode) prefer alterlab-anndata instead, and for RNA velocity from spliced/unspliced counts prefer alterlab-scvelo instead. Part of the AlterLab Academic Skills suite.

alterlab-scgpt

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.

alterlab-scholar-eval

Evaluates scholarly work with the ScholarEval framework, producing structured assessment across research-quality dimensions (problem formulation, methodology, analysis, and writing) with quantitative rubric scores and actionable feedback. Use when scoring or grading a paper, thesis, or research output against rubric-style criteria, or benchmarking publication readiness across revisions. For checklist-based narrative reviewer reports prefer alterlab-peer-review; for evidence/claim quality and argument soundness use alterlab-scientific-thinking. Part of the AlterLab Academic Skills suite.

alterlab-scientific-brainstorm

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.

alterlab-scientific-schematics

Creates publication-quality scientific diagrams with Nano Banana 2 AI and smart iterative refinement, using Gemini 3.1 Pro Preview for quality review and regenerating only when quality falls below the document-type threshold. Use when the request is for a technical or scientific diagram — neural-network architectures, system/block diagrams, flowcharts, biological pathways, circuits, or other complex scientific visuals. For general photos, illustrations, or artwork use generate-image, for text-based Mermaid diagrams use mermaid. Part of the AlterLab Academic Skills suite.

alterlab-scientific-slides

Builds slide decks for research talks in PowerPoint and LaTeX Beamer, providing slide structure, design templates, timing guidance, and visual validation. Use when making conference presentations, seminar talks, research presentations, thesis-defense slides, or any scientific talk deck. Part of the AlterLab Academic Skills suite.

alterlab-scientific-thinking

Evaluate scientific claims and evidence quality using evidence grading frameworks (GRADE, Cochrane Risk of Bias), assessing experimental design validity and identifying biases, confounders, statistical pitfalls, and logical fallacies. Use when judging evidence quality, grading certainty of evidence, spotting design or causal-inference flaws, identifying biases or confounders, naming statistical fallacies, or teaching critical analysis. For writing a formal submittable peer review use alterlab-peer-review; for a multi-reviewer mock panel verdict use alterlab-paper-reviewer; for IRB/consent/conflict-of-interest ethics use alterlab-research-ethics. Part of the AlterLab Academic Skills suite.

alterlab-scientific-viz

Orchestrates matplotlib, seaborn, and plotly with opinionated publication styles to produce journal-ready figures. Use when preparing journal-submission figures that need multi-panel layouts with bold panel labels, statistical significance annotations, error bars, colorblind-safe palettes (Okabe-Ito), or specific journal formatting (Nature, Science, Cell). Does NOT cover raw low-level plotting or fine-grained control of individual plot elements; for building custom plots from scratch or tuning every artist and rcParam prefer alterlab-matplotlib instead. Part of the AlterLab Academic Skills suite.

alterlab-scientific-writing

Writes scientific manuscripts in full flowing paragraphs (never bullet points) via a two-stage process — section outlines with key points using research-lookup, then conversion to prose — applying IMRAD structure, citations (APA/AMA/Vancouver), figures/tables, and reporting guidelines (CONSORT/STROBE/PRISMA). Use when drafting or revising research papers, journal submissions, or any manuscript section (abstract, introduction, methods, results, discussion), or professional/technical reports. For a specific venue's LaTeX template and house style use alterlab-venue-templates; to build a BibTeX bibliography or verify reference metadata use alterlab-citation-mgmt. Part of the AlterLab Academic Skills suite.

alterlab-scikit-bio

Analyze biological data with scikit-bio — sequence analysis and alignments, phylogenetic trees, alpha/beta diversity metrics (including UniFrac), ordination (PCoA), PERMANOVA statistics, and FASTA/Newick I/O. Use for microbiome and community-ecology analysis — computing diversity, distance matrices, and ordination from feature tables. Part of the AlterLab Academic Skills suite.

alterlab-scikit-learn

Classical machine learning in Python with scikit-learn — algorithms, preprocessing, pipelines, and best-practice reference documentation. Use when working with supervised learning (classification, regression), unsupervised learning (clustering, dimensionality reduction), model evaluation, hyperparameter tuning, feature preprocessing, or building ML pipelines. Part of the AlterLab Academic Skills suite.

alterlab-scikit-survival

Survival analysis and time-to-event modeling in Python with scikit-survival. Use when working with censored survival data, fitting Cox models, Random Survival Forests, Gradient Boosting models, or Survival SVMs, evaluating predictions with concordance index or Brier score, handling competing risks, or implementing any time-to-event workflow. Part of the AlterLab Academic Skills suite.

alterlab-scvelo

Run RNA velocity analysis with scVelo on single-cell RNA-seq data — estimate cell-state transitions from spliced/unspliced mRNA dynamics, infer trajectory direction, compute latent time, and identify driver genes. Use when adding directionality to trajectories or studying differentiation dynamics from spliced/unspliced layers (velocyto/STARsolo output); for the general QC, clustering, UMAP, and differential-expression analysis pipeline prefer alterlab-scanpy instead, and for .h5ad data-structure I/O and layer wrangling prefer alterlab-anndata instead. Part of the AlterLab Academic Skills suite.

alterlab-scvi-tools

Train deep generative models for single-cell omics with scvi-tools — probabilistic batch correction and integration (scVI), reference-mapping transfer learning (scArches), differential expression with uncertainty, and multimodal models (totalVI for CITE-seq, MultiVI for multiome). Use when correcting batch effects, integrating multimodal data, or doing advanced probabilistic single-cell modeling — for standard analysis pipelines use scanpy. Part of the AlterLab Academic Skills suite.

alterlab-seaborn

Builds statistical plots with the seaborn Python library and pandas DataFrame integration, on attractive matplotlib-based defaults. Use for quick exploration of distributions, relationships, and categorical comparisons — box plots, violin plots, swarm/strip plots, KDE/histograms, pair plots, joint plots, regression plots, correlation heatmaps, and faceted small multiples (relplot/displot/catplot/lmplot). For interactive/hover/zoom charts defer to alterlab-plotly; for exact journal/manuscript styling (column widths, point fonts, CMYK, vector export) defer to alterlab-scientific-viz; for low-level custom matplotlib figures defer to alterlab-matplotlib (seaborn integrates with it for fine-tuning). Part of the AlterLab Academic Skills suite.

alterlab-sem-psychometrics

Fits and evaluates measurement models — confirmatory factor analysis, full structural equation models, exploratory factor analysis, item response theory, and multi-group measurement invariance — using the verified Python stack: semopy (model syntax =~ / ~ / ~~, Model.fit, inspect(std_est=True), calc_stats for CFI/TLI/RMSEA), factor_analyzer (EFA, KMO, Bartlett, ConfirmatoryFactorAnalyzer), and pingouin/girth, computing McDonald's omega from standardized loadings and judging fit against Hu & Bentler cutoffs. Use when the request mentions confirmatory factor analysis, structural equation modeling, a latent variable or construct model, factor loadings, IRT, or measurement invariance across groups. For deciding whether a scale is trustworthy at all prefer alterlab-ssci-measurement-gate; for plain regression prefer alterlab-statistical-analysis. Part of the AlterLab Academic Skills suite.

alterlab-shap

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.

alterlab-simpy

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.

alterlab-skill-finder

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.

alterlab-sna

Applies social-network-analysis method discipline to relational data — degree/betweenness/closeness/eigenvector centrality and PageRank, community detection (Louvain and greedy-modularity native in networkx, Leiden via igraph), and inferential network models (ERGM) — choosing the measure that matches the substantive question and the right dependence assumptions, then routing computation to the existing networkx (and igraph/R) tooling. Use when the request mentions social network analysis, centrality, key players/brokerage, community or cluster detection in a network, ERGM, or modeling ties between nodes. For general graph algorithms and plotting prefer alterlab-networkx; for graph neural networks prefer alterlab-torch-geometric. Part of the AlterLab Academic Skills suite.

alterlab-social-science-methods

Guides advanced social science research methods — discourse analysis (Fairclough CDA, Gee), conversation analysis, quantitative content analysis, Qualitative Comparative Analysis (QCA), process tracing, archival research, participatory/community-based research (PAR, CBPR), Delphi and Q methodology, social network analysis (SNA), bibliometrics and scientometrics, systematic mapping reviews, and program/policy evaluation. Use when designing or conducting any of these studies — choosing a specialized method, building a coding scheme, establishing causal mechanisms in case studies, mapping relational or subjective data, or applying an evaluation framework. For interpretive/qualitative coding (thematic analysis, grounded theory, IPA, ethnography, qualitative content analysis) use alterlab-qualitative-methods; for combining qual+quant strands use alterlab-mixed-methods. Part of the AlterLab Academic Skills suite.

alterlab-squidpy-spatial

Analyzes spatial transcriptomics with squidpy (1.8.x) on AnnData and SpatialData objects, routing platforms correctly: Visium spots use spatial_neighbors(coord_type='grid') and pair with deconvolution, while Xenium/MERFISH single-cell data use coord_type='generic'/Delaunay neighbors and spatialdata-io readers (xenium, visium_hd, merscope). Runs sq.gr.spatial_neighbors, nhood_enrichment, co_occurrence, spatial_autocorr (Moran's I for spatially variable genes), ripley, and ligrec. Use when the user wants spatial transcriptomics, squidpy, Visium/Xenium/MERFISH analysis, neighborhood enrichment, co-occurrence, or spatially variable genes; QC/clustering uses alterlab-scanpy and spot deconvolution (destVI/Tangram) uses alterlab-scvi-tools. Part of the AlterLab Academic Skills suite.

alterlab-ssci-design-gate

Routes a social-science study to its research design — true experiment, quasi-experiment (difference-in-differences, instrumental variables, regression discontinuity, interrupted time series, fixed effects), observational/correlational, qualitative, or mixed — by walking the random-selection and random-assignment decisions, then PINS the identifying assumption the causal claim will rest on (parallel trends, exclusion restriction, continuity at the cutoff, selection-on-observables, or qualitative saturation logic) before any analysis begins. Use when choosing a study design, asking what design to use, framing a causal question from observational data, or deciding experiment vs quasi-experiment vs observational. For executing the analysis prefer alterlab-statistical-analysis; for qualitative design depth prefer alterlab-qualitative-methods; for choosing the statistical test downstream prefer alterlab-test-selection-guard. Part of the AlterLab Academic Skills suite.