Browse Tools

PubMed Database — NCBI's comprehensive biomedical literature database providing free access to over 37 million citations from MEDLINE, life science journals, and online books. Query via E-utilities RE

Broad Institute tools — access Terra cloud genomics platform, GSEA/MSigDB gene set enrichment analysis, GenePattern workflow server, Picard sequencing utilities, and FireBrowse TCGA data portal progra

Institute — utilities for discovering, querying, and downloading datasets from major genomics and bioinformatics research institutes, including Broad Institute (gnomAD, Terra, Hail), European Bioinfor

KEGG Database — Direct REST API access to KEGG (Kyoto Encyclopedia of Genes and Genomes) for biological pathway analysis, gene-pathway mapping, metabolic networks, drug interactions, and cross-databas

PrimerBLAST is an NCBI web tool that combines Primer3 for PCR primer design with BLAST-based specificity checking against NCBI databases. Designs primers for a target sequence, checks them for off-tar

AOP-Wiki (Adverse Outcome Pathway Wiki) is the authoring and discovery interface for browsing, searching, exporting, and citing AOP knowledgebase content including AOPs, Key Events (KEs), Key Event Re

AnimalGenome.org data-access skill for livestock genomics workflows using Animal QTLdb and CorrDB. Routes users to REST-style API usage (`iinfo`, `iquery`, `ifetch`), species-level QTL and trait-corre

CompTox Chemicals Dashboard is the U.S. EPA's publicly accessible resource for chemical information, identity resolution, toxicity data, and DSSTox database access. Use this skill for chemical search

InsectBase — comprehensive web database for insect genome sequences, gene annotations, and comparative genomics data covering 138+ insect species. Provides genome assemblies (FASTA), structural annota

LepBase — versatile, scalable search engine and genome database for Lepidoptera (butterflies and moths) assemblies and genomic features. Provides genome browser, BLAST sequence search, REST API for ge

Bioprocess engineering computational tools for bioreactor design, fermentation kinetics, metabolic flux analysis, and bioprocess scale-up. Model bioreactor dynamics (batch, fed-batch, continuous/CSTR)

Brainnetome Atlas — a human brain parcellation of 246 subregions (210 cortical + 36 subcortical) derived from connectivity-based parcellation using diffusion MRI tractography and resting-state fMRI. P

Cryobiology computational tools for cryopreservation protocol design, cell survival modeling, and optimal cooling rate calculation. Implements Mazur's two-factor hypothesis (osmotic injury + intracell

dbGaP tools — NCBI/dbGaP controlled-access retrieval workflow for human genotype, phenotype, and sequence datasets. Covers the Authorized Access portal, PI and downloader roles, dbGaP File Selector, S

This skill provides tools for working with FinnGen data. NOTE: This is a placeholder due to tool access limitations.

Use when working with GlyConnect, the ExPASy glycosylation knowledgebase for contextual glycoprotein evidence, glycan compositions, literature-backed glycosylation sites, and linked search workflows a

mgcv — Mixed GAM Computation Vehicle with Automatic Smoothness Estimation. Fit generalized additive models (GAMs) with penalized regression splines via gam(), large-dataset GAMs with bam(), and genera

Use when working with NetMHCpan 4.1 for MHC class I peptide binding and ligand presentation prediction. NetMHCpan accepts peptide lists or FASTA proteins, scores candidate ligands against up to 20 all

ReefCloud is a tool for marine biology and oceanography, focused on coral reef analysis. It helps researchers analyze images of coral reefs to monitor their health and composition.

rgdal (R) bindings for GDAL and PROJ for legacy sp-class vector/raster IO, layer discovery, and CRS transformation workflows. Trigger this skill for readOGR/writeOGR, ogrListLayers, GDALinfo, and spTr

SemMedDB is a repository of semantic predications (subject-predicate-object triples) extracted from PubMed/MEDLINE citations using the SemRep NLP system. It maps biomedical text to UMLS concepts and s

SimBiology workflows in MATLAB for quantitative systems pharmacology (QSP), physiologically based pharmacokinetic (PBPK), and PK/PD modeling. Use this skill for SimBiology model construction, SBML imp

SpatiaLite extends SQLite with OGC-style spatial SQL, geometry metadata tables, RTree spatial indexing, and import/export helpers for formats such as Shapefile, DBF, and GeoJSON. Use this skill when u

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HostDB routing skill for host-pathogen genomics queries, gene expression analysis, ortholog searches, and comparative genomics on parasitic and tropical disease organisms. Use this skill when users me

Illumina sequencing operations routing skill for BCL Convert, DRAGEN, BaseSpace Sequence Hub, and Illumina Connected Analytics (ICA). Use when a user needs to inspect an Illumina run folder, fix or va

VectorBase — NIAID Bioinformatics Resource Center for invertebrate vectors of human pathogens (mosquitoes, ticks, sandflies, tsetse flies, kissing bugs, and related arthropods). Provides genome assemb

Use this skill when users need AWS Batch for containerized high-throughput compute jobs on AWS. Covers compute environments, job queues, job definitions, submit-job orchestration, array jobs, multi-no

ADMIXTURE for maximum likelihood estimation of individual ancestries from SNP genotype data. Use when working with admixture, ancestry estimation, population structure analysis, K selection via cross-

Google Life Sciences (hpc-cloud) skill for routing genomic and bioinformatics workload execution through the Cloud Life Sciences API and adjacent Google Cloud services. Use this skill when users menti

Use when working with microfluidics, droplet microfluidics, lab-on-chip design, microfluidic flow control, digital PCR analysis, droplet-based single-cell encapsulation, chip layout generation, Fluige

protocols.io — cloud-based platform for creating, sharing, and executing reproducible lab protocols. Provides a REST API for protocol discovery, retrieval, and management. Supports lab automation inte

ScrumPy (Metabolic Modelling in Python) for structural and kinetic metabolic modeling using `.spy` model files, stoichiometric analysis, LP-based flux analysis, and elementary mode workflows. Use this

Use when users need Azure Batch for large-scale parallel or HPC workloads, including pool creation, autoscale policies, job/task submission, container tasks, and operational validation. Routes to offi

Use when working with BioModels, curated systems biology models, SBML model discovery, model metadata retrieval, model file manifests, COMBINE archive downloads, model identifier validation, or buildi

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Generate deep skill for GlyTouCan, a common repository for glycan structures.

Monolix/NONMEM population PK/PD modeling skill for nonlinear mixed-effects workflows across GUI-first MonolixSuite and control-stream-driven NONMEM. Use when users need data formatting for ID/TIME/obs

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Access and analyze climate model data using the Pangeo ecosystem.

This skill provides an interface to the Global Biodiversity Information Facility (GBIF) API through the R package 'rgbif'. It enables querying and retrieving biodiversity data, including occurrence re

"Accesses the U.S. EPA's Computational Toxicology (CTX) APIs to retrieve toxicology and environmental health data, including chemical hazard information, exposure data, and bioactivity profiles."

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PhyloMeasures routing skill for computing phylogenetic diversity indices, community-level phylogenetic structure, and standardized effect sizes from species assemblage matrices and phylogenetic trees.