Merged timeline of 188 items — blog publish times and listing timestamps, cut at midnight . Page 3 of 4.
### Diffdock - name: "diffdock" - description: "Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for aff…
### Markdown Mermaid Writing - name: "markdown-mermaid-writing" - description: "Comprehensive markdown and Mermaid diagram writing skill. Use when creating any scientific document, report, analysis, or visualization. Es…
### Market Research Reports - name: "market-research-reports" - description: "Generate comprehensive market research reports (50+ pages) in the style of top consulting firms (McKinsey, BCG, Gartner). Features profession…
### Labarchive Integration - name: "labarchive-integration" - description: "Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/RE…
### Dhdna Profiler - name: "dhdna-profiler" - description: "Extract cognitive patterns and thinking fingerprints from any text. Use this skill when the user wants to analyze how someone thinks, understand cognitive styl…
### Iso 13485 Certification - name: "iso-13485-certification" - description: "Comprehensive toolkit for preparing ISO 13485 certification documentation for medical device Quality Management Systems. Use when users need…
### Latchbio Integration - name: "latchbio-integration" - description: "Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/Lat…
### Citation Management - name: "citation-management" - description: "Comprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract accurate metadata, validate citations,…
### Histolab - name: "histolab" - description: "Lightweight WSI tile extraction and preprocessing. Use for basic slide processing, tissue detection, tile extraction, and stain normalization for H&E images. Best for simp…
### Database Lookup - name: "database-lookup" - description: "Search 78 public scientific, biomedical, materials science, and economic databases via REST APIs. Covers physics/astronomy (NASA, NIST, SDSS, SIMBAD), earth/…
### Imaging Data Commons - name: "imaging-data-commons" - description: "Query and download public cancer imaging data from NCI Imaging Data Commons using idc-index. Use for accessing large-scale radiology (CT, MR, PET)…
### Hypothesis Generation - name: "hypothesis-generation" - description: "Structured hypothesis formulation from observations. Use when you have experimental observations or data and need to formulate testable hypothese…
### Infographics - name: "infographics" - description: "Create professional infographics using Nano Banana Pro AI with smart iterative refinement. Uses Gemini 3 Pro for quality review. Integrates research-lookup and web…
### Deeptools - name: "deeptools" - description: "NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization."
### Esm - name: "esm" - description: "Comprehensive toolkit for EvolutionaryScale protein language models including ESM3 (generative multimodal design across sequence, structure, and function) and ESM C (efficient embed…
### Cirq - name: "cirq" - description: "Google quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or running quantum characterization experiments. Best for Google…
### Hypogenic - name: "hypogenic" - description: "Automated LLM-driven hypothesis generation and testing on tabular datasets. Use when you want to systematically explore hypotheses about patterns in empirical data (e.g.…
### Dask - name: "dask" - description: "Distributed computing for larger-than-RAM pandas/NumPy workflows. Use when you need to scale existing pandas/NumPy code beyond memory or across clusters. Best for parallel file pr…
### Ginkgo Cloud Lab - name: "ginkgo-cloud-lab" - description: "Submit and manage protocols on Ginkgo Bioworks Cloud Lab (cloud.ginkgo.bio), a web-based interface for autonomous lab execution on Reconfigurable Automatio…
### Hugging Science - name: "hugging-science" - description: "Use when the user is doing AI/ML work in a scientific domain such as biology, chemistry, physics, astronomy, climate, genomics, materials, medicine, ecology,…
### Depmap - name: "depmap" - description: "Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivity data, and gene effect profiles. Use for identifying can…
### Gtars - name: "gtars" - description: "High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokeni…
### Gget - name: "gget" - description: "Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST searches, AlphaFold structures, enrichment analysis. Best for interactive explorat…
### Geomaster - name: "geomaster" - description: "Comprehensive geospatial science skill covering remote sensing, GIS, spatial analysis, machine learning for earth observation, and 30+ scientific domains. Supports satel…
### Glycoengineering - name: "glycoengineering" - description: "Analyze and engineer protein glycosylation. Scan sequences for N-glycosylation sequons (N-X-S/T), predict O-glycosylation hotspots, and access curated glyc…
### Generate Image - name: "generate-image" - description: "Generate or edit images using AI models (FLUX, Nano Banana 2). Use for general-purpose image generation including photos, illustrations, artwork, visual assets…
### Etetoolkit - name: "etetoolkit" - description: "Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogen…
### Geniml - name: "geniml" - description: "This skill should be used when working with genomic interval data (BED files) for machine learning tasks. Use for training region embeddings (Region2Vec, BEDspace), single-cel…
### Consciousness Council - name: "consciousness-council" - description: "Run a multi-perspective Mind Council deliberation on any question, decision, or creative challenge. Use this skill whenever the user wants divers…
### Fluidsim - name: "fluidsim" - description: "Framework for computational fluid dynamics simulations using Python. Use when running fluid dynamics simulations including Navier-Stokes equations (2D/3D), shallow water e…
### Literature Search Openalex - name: "literature-search-openalex" - description: "Query the OpenAlex scholarly database for research papers, authors, institutions, topics, sources, publishers, funders, geo-locations,…
### Dbsnp Database - name: "dbsnp-database" - description: "Use when you want to look up, map, and search for short genetic variants (SNPs, indels) in NCBI's dbSNP database. Resolves between rsIDs, genomic coordinates i…
### Jaspar Database - name: "jaspar-database" - description: "Query the JASPAR database for Transcription Factor (TF) binding profiles. Use when retrieving Position Frequency Matrices (PFMs) or Position Weight Matrices…
### Biopython - name: "biopython" - description: "Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez)…
### Bioservices - name: "bioservices" - description: "Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent…
### Cellxgene Census - name: "cellxgene-census" - description: "Query the CELLxGENE Census (61M+ cells) programmatically. Use when you need expression data across tissues, diseases, or cell types from the largest curate…
### Aeon - name: "aeon" - description: "This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity sea…
### Astropy - name: "astropy" - description: "Core Python library for astronomy and astrophysics workflows that need Astropy APIs, including units/quantities, coordinates, FITS I/O, tables, time systems, WCS, and cosmol…
### Bulk Rnaseq - name: "bulk-rnaseq" - description: "End-to-end bulk RNA-seq orchestrator — takes raw FASTQ reads through QC and trimming (FastQC, fastp/Trim Galore), alignment and quantification (STAR, Salmon, feature…
### Literature Search Europepmc - name: "literature-search-europepmc" - description: "Search Europe PMC for scientific literature and download open-access full texts and PDFs. Retrieve full-text XML/plain text by PMCID,…
### Benchling Integration - name: "benchling-integration" - description: "Benchling Python SDK and REST API integration for registry entities, inventory, ELN entries, workflows, Benchling Apps, and Data Warehouse querie…
### Bgpt Paper Search - name: "bgpt-paper-search" - description: "Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server. Returns 25+ fields per paper…
### Arboreto - name: "arboreto" - description: "Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, singl…
### Adaptyv - name: "adaptyv" - description: "How to use the Adaptyv Bio Foundry API and Python SDK for protein experiment design, submission, and results retrieval. Use this skill whenever the user mentions Adaptyv, Fo…
### Autoskill - name: "autoskill" - description: "Observe the user's screen via screenpipe, detect repeated research workflows, match them against existing scientific-agent-skills, and draft new skills (or composition r…
### Bids - name: "bids" - description: "Use this skill when working with Brain Imaging Data Structure (BIDS) datasets: organizing neuroscience and biomedical data (MRI, EEG, MEG, iEEG, PET, microscopy, NIRS, motion capt…
### Alphafold Database Fetch And Analyze - name: "alphafold-database-fetch-and-analyze" - description: "Retrieve and analyze AlphaFold predicted structures for a protein. Use when the user provides a specific UniProt Ac…
### Clinvar Database - name: "clinvar-database" - description: "Use when needing clinical significance, pathogenicity classifications (e.g., Pathogenic, Benign, VUS), clinical evidence rationales, or finding "hard posit…
### Anndata - name: "anndata" - description: "Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for…
### Uniprot Database - name: "uniprot-database" - description: "Access protein metadata, function, taxonomy, and sequences across UniProtKB, UniParc, and UniRef. Use when searching for proteins, mapping identifiers, or…
