583 skills found · Page 18 of 20
jamditis / multi-agent-coordinatorUse to coordinate several long-running workers with durable prompts, event-driven watches, review gates, owner updates, and safe cleanup.
jamditis / unattended-agent-runsUse to design or operate recurring newsroom agent work without a person watching each run. Covers a simple process-per-run starter and a persistent supervised session.
Microck / api-test-generatorГенерация полных Python pytest тестов для REST API эндпоинтов с валидацией схемы. Использовать при создании тестов для новых эндпоинтов, добавлении покрытия для CRUD операций или валидации соответствия API с OpenAPI схемами.
Microck / archonInteractive Archon integration for knowledge base and project management via REST API. On first use, asks for Archon host URL
Microck / biopythonPrimary Python toolkit for molecular biology. Preferred for Python-based PubMed/NCBI queries (Bio.Entrez), sequence manipulation, file parsing (FASTA, GenBank, FASTQ, PDB), advanced BLAST workflows, structures, phylogenetics. For quick BLAST, use gget. For direct REST API, use pubmed-database.
Microck / bioservicesPrimary Python tool for 40+ bioinformatics services. Preferred for multi-database workflows: UniProt, KEGG, ChEMBL, PubChem, Reactome, QuickGO. Unified API for queries, ID mapping, pathway analysis. For direct REST control, use individual database skills (uniprot-database, kegg-database).
Microck / backend-ai-guideExpert guide for Backend.AI distributed computing platform. Automatically activates when users ask about: - Backend.AI architecture, components (Manager, Agent, Storage Proxy, Webserver, App Proxy) - Features (session scheduling, Sokovan orchestrator, multi-tenancy, resource allocation) - APIs (REST…
Microck / brightdataProgressive four-tier URL content scraping with automatic fallback strategy. USE WHEN user says "scrape this URL", "fetch this page", "get content from", "can't access this site", "use Bright Data", "pull content from URL", or needs to retrieve web content that may have bot detection or access restr…
arpitg1304 / ros2-web-integrationPatterns and best practices for integrating ROS2 systems with web technologies including REST APIs, WebSocket bridges, and browser-based robot interfaces.
jaechang-hits / scikit-survival-analysisTime-to-event modeling with scikit-survival: Cox PH (elastic net), Random Survival Forests, Boosting, SVMs for censored data. C-index, Brier, time-dependent AUC; Kaplan-Meier, Nelson-Aalen, competing risks. Pipeline/GridSearchCV compatible.
jaechang-hits / arboreto-grn-inferenceGRN inference from expression via GRNBoost2 (gradient boosting) or GENIE3 (Random Forest). Load matrix, filter by TFs, infer TF-target-importance links, save network. Dask-parallelized to single-cell scale. Core SCENIC component.
jaechang-hits / biopython-molecular-biologyMolecular biology toolkit: sequence manipulation, FASTA/GenBank/PDB I/O, NCBI Entrez, BLAST automation, pairwise/MSA alignment, Bio.PDB, phylogenetic trees. Use for batch processing, custom pipelines, format conversion, PubMed/GenBank queries.
jaechang-hits / biopython-sequence-analysisBiopython sequence analysis: parse FASTA/FASTQ/GenBank/GFF (SeqIO), NCBI Entrez (esearch/efetch/elink), remote/local BLAST, pairwise/MSA alignment (PairwiseAligner, MUSCLE/ClustalW), phylogenetic trees (Phylo). Use for gene family studies, phylogenomics, comparative genomics, NCBI pipelines.
jaechang-hits / homer-motif-analysisDe novo and known TF motif enrichment in ChIP-seq/ATAC-seq peaks via HOMER. findMotifsGenome.pl finds over-represented patterns vs background; annotatePeaks.pl assigns context (TSS distance, gene, repeat).
jaechang-hits / protocolsio-integrationprotocols.io REST API: search and fetch wet-lab, bioinformatics, and clinical protocols by keyword, DOI, or category, with steps, reagents, materials, equipment, timing. Public access free; auth needed for private or publishing. Pair with opentrons-protocol-api or benchling-integration to execute.
jaechang-hits / viennarna-structure-predictionPredict RNA secondary structure, MFE folding, base-pair probabilities, RNA-RNA interactions via ViennaRNA Python bindings. Pipeline: sequence → MFE → partition function and pair-probability matrix → dot-bracket → duplex. Use for siRNA/sgRNA targeting, ribozyme design, RNA accessibility.
jaechang-hits / adaptyv-bioAPI + Python SDK for ordering cell-free protein expression and binding assays. Submit sequences for expression (10–100 µg), measure binding affinity (KD) against targets, track status, and retrieve results programmatically — no wet-lab setup.
jaechang-hits / hmdb-databaseParse HMDB (Human Metabolome Database) local XML for metabolite info, chemical properties, biological context, disease links, spectra, and cross-DB mapping. No REST API — uses ~6 GB XML download. Use drugbank-database-access for drugs; pubchem-compound-search for live lookups.
jaechang-hits / interpro-databaseQuery InterPro REST API for protein domain architecture, family classification, and member-DB integration. Search entries, retrieve a protein's domains, list family members, get taxonomic distribution, link to PDB. Unifies Pfam, PANTHER, PIRSF, PRINTS, PROSITE, SMART, CDD, NCBIfam.
jaechang-hits / metabolomics-workbench-databaseQuery Metabolomics Workbench REST API (4,200+ NIH studies) for metabolite ID, study discovery, RefMet standardization, m/z precursor searches, and gene/protein annotations.
jaechang-hits / pride-databaseSearch the PRIDE Archive v3 REST API for proteomics datasets: discover projects by keyword + faceted filters (organism, instrument, disease, software), fetch project metadata, list and download RAW/PEAK/RESULT/FASTA files (with FTP/Aspera URLs), look up which projects mention a UniProt accession, an…
jaechang-hits / uniprot-protein-databaseQuery UniProt REST API: search by gene/protein name, fetch FASTA, map IDs (Ensembl, PDB, RefSeq), access Swiss-Prot annotations. Use bioservices for multi-DB access; alphafold-database-access for structures.
jaechang-hits / umap-learnUMAP dimensionality reduction for visualization, clustering prep, and feature engineering. Fast nonlinear manifold learning preserving local and global structure.
jaechang-hits / uspto-databaseAccess USPTO patent data via PatentsView REST API and Google Patents Public Data (BigQuery). Search by inventor, assignee, CPC, or keywords; download metadata and claims; analyze portfolios; track tech trends.
jaechang-hits / biorxiv-databaseQuery bioRxiv/medRxiv preprints via REST API. Search by DOI, category, or date range; retrieve metadata (title, abstract, authors, category, DOI, version history) and PDFs. No auth. For peer-reviewed biomedical use pubmed-database; broader scholarly search use openalex-database.
jaechang-hits / openalex-databaseQuery OpenAlex REST API for 250M+ scholarly works, authors, institutions, journals, concepts. Search by keyword, author, DOI, ORCID, or ID; filter by year, OA, citations, field; retrieve citations, references, author disambiguation. Free, no auth.
jaechang-hits / pubmed-databaseProgrammatic PubMed access via NCBI E-utilities REST API. Covers Boolean/MeSH queries, field-tagged search, endpoints (ESearch, EFetch, ESummary, EPost, ELink), history server for batches, citation matching, systematic review strategies. Use for biomedical literature search or automated pipelines.
jaechang-hits / alphafold-database-accessAccess AlphaFold DB's 200M+ predicted structures by UniProt ID. Download PDB/mmCIF, analyze pLDDT/PAE, bulk-fetch proteomes via Google Cloud. For experimental structures use PDB; for prediction use ColabFold or ESMFold.
jaechang-hits / chembl-database-bioactivityQuery ChEMBL (2M+ compounds, 19M+ bioactivity measurements, 13K+ targets) via the public REST/JSON API with plain `requests` — no SDK install required. Search compounds, retrieve IC50/Ki/EC50 bioactivities, find target inhibitors, run SAR, access drug mechanism/indication data.
jaechang-hits / dailymed-databaseQuery FDA drug labels (DailyMed) via REST API. Search structured product labels (SPLs) by name, NDC, set ID, or RxCUI; get indications, dosage, warnings, adverse reactions, packaging. No auth. For adverse events use fda-database; for DDIs use ddinter-database.
