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Claude Skills by AlterLab-IEU
github.com/AlterLab-IEU346 skills4 installs520 views
- Alterlab Metabolomics WbAccess the NIH Metabolomics Workbench via its REST API (4,500+ public 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.Votes: 0GitHub stars: 68
- Alterlab MonarchQuery 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.Votes: 0GitHub stars: 68
- Alterlab OpenalexQuery and analyze scholarly literature using the OpenAlex API across 300M+ 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.Votes: 0GitHub stars: 68
- Alterlab OpentargetsQuery 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.Votes: 0GitHub stars: 68
- Alterlab PdbAccess 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 pr...Votes: 0GitHub stars: 68
- Alterlab PubchemQuery PubChem via the PUG-REST API and PubChemPy across 119M+ 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.Votes: 0GitHub stars: 68
- Alterlab PubmedProvide 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.Votes: 0GitHub stars: 68
- Alterlab ReactomeQuery 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.Votes: 0GitHub stars: 68
- Alterlab String DbQuery the STRING API for protein-protein interactions (59M proteins, 20B+ interactions across 12,500+ organisms), building interaction networks, discovering functional partners, and running GO/KEGG/Pfam enrichment on protein lists. Use when constructing a protein-protein interaction network, expanding from seed proteins to functional partners, or running PPI-based enrichment for systems biology; for curated metabolic pathway maps and reactions prefer alterlab-kegg, and for protein sequences, ...Votes: 0GitHub stars: 68
- Alterlab UniprotProvide direct REST API access to UniProt (Swiss-Prot/TrEMBL) for protein sequence searches, FASTA retrieval, functional annotations (GO terms, domains), and cross-database ID mapping. Use when looking up a protein entry, fetching a protein FASTA sequence, or mapping accessions between databases over raw HTTP/REST; for EXPERIMENTAL 3D structures prefer alterlab-pdb, for AI-PREDICTED 3D structures prefer alterlab-alphafold-db, for protein-protein interaction networks prefer alterlab-string-db,...Votes: 0GitHub stars: 68
- Alterlab UsptoAccess USPTO patent and trademark data through the Open Data Portal (ODP) APIs — Patent File Wrapper search, examination history (the PEDS successor), continuity, assignments, office actions, PTAB decisions — and trademark status via TSDR. Use when searching patents or trademarks, conducting prior art searches, retrieving patent examination or assignment records, or doing intellectual property (IP) analysis. Part of the AlterLab Academic Skills suite.Votes: 0GitHub stars: 68
- Alterlab Zinc DbAccess the ZINC database of 230M+ commercially available (purchasable) compounds, searching by ZINC ID or SMILES, running similarity searches, and downloading 3D-ready structures. Use when assembling a compound library for virtual screening, finding purchasable analogs, or obtaining docking-ready 3D structures for drug discovery. Part of the AlterLab Academic Skills suite.Votes: 0GitHub stars: 68
- Alterlab MarkitdownConverts files and Office documents to clean, LLM-friendly Markdown with Microsoft MarkItDown (markitdown CLI, Python API, and markitdown-mcp server), supporting PDF, DOCX, PPTX, XLSX/XLS, images (EXIF metadata, LLM descriptions), audio (transcription), HTML, CSV, JSON, XML, ZIP archives, EPUB e-books, Outlook MSG, Jupyter notebooks, and YouTube transcript URLs, with OCR through the markitdown-ocr plugin or Azure Document Intelligence. Use when converting a document, PDF, slide deck, spreadsh...Votes: 0GitHub stars: 68
- Alterlab Open NotebookRuns and scripts 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 searc...Votes: 0GitHub stars: 68
- Alterlab AdaptyvSubmits 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, ...Votes: 0GitHub stars: 68
- Alterlab AeonRuns 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.Votes: 0GitHub stars: 68
- Alterlab AstropyProcesses 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.Votes: 0GitHub stars: 68
- Alterlab CirqBuilds, 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 or their Quantum Virtual Machine models (Willow, Sycamore-class Rainbow/Weber), IonQ/AQT/Pasqal via Cirq plugins, designing noise-aware NISQ circuits, or running characterization experiments (randomized benchmarking, XEB). For IBM Quantum hardware and Qiskit Runtime prefer alte...Votes: 0GitHub stars: 68
- Alterlab Digital HumanitiesApplies 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...Votes: 0GitHub stars: 68
- Alterlab FluidsimRuns 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.Votes: 0GitHub stars: 68
- Alterlab GenimlMachine 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 o...Votes: 0GitHub stars: 68
- Alterlab GeomasterCovers 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/...Votes: 0GitHub stars: 68
- Alterlab GeopandasReads, 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...Votes: 0GitHub stars: 68
- Alterlab GtarsRuns 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-geni...Votes: 0GitHub stars: 68
- Alterlab HypogenicRuns 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.Votes: 0GitHub stars: 68
- Alterlab ModalRuns 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.Votes: 0GitHub stars: 68
- Alterlab PennylaneTrains and differentiates quantum circuits with PennyLane, a hardware-agnostic quantum machine-learning framework with automatic differentiation and PyTorch/JAX 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 circuit...Votes: 0GitHub stars: 68
- Alterlab PymatgenAnalyzes 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, o...Votes: 0GitHub stars: 68
- Alterlab QiskitBuilds, 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 mode...Votes: 0GitHub stars: 68
- Alterlab QutipSimulates 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-c...Votes: 0GitHub stars: 68
- Alterlab Social Science MethodsGuides 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 specia...Votes: 0GitHub stars: 68
- Alterlab Alpha VantageAccesses stock market data, forex rates, cryptocurrency prices, commodities, economic indicators, company fundamentals, news sentiment, and 50+ technical indicators via the Alpha Vantage REST API (free API key from alphavantage.co; realtime/intraday data and full daily history need a premium key). 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 yie...Votes: 0GitHub stars: 68
- Alterlab DenarioRuns 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 ...Votes: 0GitHub stars: 68
- Alterlab EdgartoolsAccesses, 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...Votes: 0GitHub stars: 68
- Alterlab FredQueries 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.Votes: 0GitHub stars: 68
- Alterlab Hedgefund MonitorQueries 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, c...Votes: 0GitHub stars: 68
- Alterlab Market ResearchGenerates 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 deliv...Votes: 0GitHub stars: 68
- Alterlab UsfiscaldataQueries the U.S. Treasury Fiscal Data API across 50+ datasets and roughly 180 data tables (no API key required) for federal financial data on national debt, government spending, revenue, interest rates, exchange rates, and savings bonds. Use when working with U.S. federal fiscal data, national debt tracking (Debt to the Penny), Daily Treasury Statements, Monthly Treasury Statements, Treasury securities auctions, interest rates on Treasury securities, foreign exchange rates, savings bonds, or ...Votes: 0GitHub stars: 68
- Alterlab BenchlingIntegrates 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.Votes: 0GitHub stars: 68
- Alterlab DnanexusDevelops 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/@ta...Votes: 0GitHub stars: 68
- Alterlab Ginkgo CloudSubmits 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.Votes: 0GitHub stars: 68
- Alterlab LabarchiveIntegrates 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.Votes: 0GitHub stars: 68
- Alterlab LatchbioBuilds 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 ...Votes: 0GitHub stars: 68
- Alterlab OmeroManages 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.Votes: 0GitHub stars: 68
- Alterlab OpentronsWrites 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.Votes: 0GitHub stars: 68
- Alterlab ProtocolsioWorks with protocols.io through its REST API (v3 and v4 endpoints) and official MCP server — search and retrieve protocols by keyword, URI, or DOI; create private protocols, edit their metadata and steps, and publish them with a DOI; manage protocol and step discussions, workspaces, file-manager items, file uploads, experiment records, and organization exports. Use when discovering, drafting, publishing, or citing protocols.io protocols, recording protocol runs, or wiring protocols.io into la...Votes: 0GitHub stars: 68
- Alterlab PylabrobotPrograms lab automation with PyLabRobot, a vendor-agnostic async Python framework that drives Hamilton STAR/Vantage, Tecan EVO, and Opentrons OT-2 liquid handlers plus plate readers, heater shakers, incubators, centrifuges, pumps, scales, and thermocyclers, with a chatterbox simulator and browser visualizer. Use when writing or simulating liquid-handling protocols in Python, controlling several instrument types from one script, or porting a protocol between robot vendors. For Opentrons-only p...Votes: 0GitHub stars: 68
- Alterlab Bgpt SearchSearch scientific papers and retrieve structured experimental evidence extracted from full-text studies via the BGPT MCP server (`search_papers`, plus `lookup_paper` by DOI), returning 25+ fields per paper (methods, results, sample sizes, quality scores, limitations, 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 Academ...Votes: 0GitHub stars: 68
- Alterlab Mixed MethodsMixed 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 s...Votes: 0GitHub stars: 68
- Alterlab Open ScienceGuidance 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...Votes: 0GitHub stars: 68