Biology & Genomics

Route life-sciences questions to the right database skills and synthesize evidence

Search Rhea for biochemical reactions and look up reaction IDs

Browse RNAcentral RNA entries and cross-references in concise summaries

Quality-control, annotate and cluster single-cell RNA-seq data with UMAP views

Pull STRING protein interaction partners, networks and enrichment results

Fetch TPMI PheWAS association results for a single variant

Fetch UKB-TOPMed PheWAS association results for a single variant

Look up UniProt protein entries, UniRef clusters and FASTA sequences

Send protein designs to a cloud lab for binding, expression and stability assays

Predict drug ADMET properties like hERG, clearance and Lipinski with RDKit

Map ADMET liabilities to structural causes and biological pathways

Fetch AlphaFold protein structures and pLDDT and PAE confidence by UniProt ID

Work with AnnData .h5ad files for annotated single-cell data matrices

Infer gene regulatory networks from expression data with GRNBoost2 and GENIE3

Connect to Benchling for registry, inventory, ELN entries and workflows

Organize, validate and convert neuroimaging datasets to the BIDS standard

Estimate binding affinity and screen docking scores across compound batches

Segment cells and track objects in microscopy images with Cellpose and trackpy

Run NVIDIA BioNeMo models for protein folding, docking and molecule design

Query 40+ bioinformatics databases like UniProt and KEGG in one Python API

Look up enzyme kinetic parameters like Km and kcat from the BRENDA database

Run bulk RNA-seq from raw FASTQ through QC, alignment and gene counts

Detect somatic mutations, copy number and tumor purity from cancer sequencing

Query the CELLxGENE Census of 61M+ single cells across tissues and diseases

Model metabolic networks with flux balance analysis and gene knockouts

Query COSMIC for somatic cancer mutations, gene census and mutational signatures

Access curated biology datasets like GTEx, COSMIC, GWAS Catalog and MSigDB

Predict spatial gene expression from H&E histology slides with DeepSpot-M

Generate drug-like molecules with scaffold growing and multi-objective filters

Query DepMap for cancer cell line gene dependency and drug sensitivity scores

Predict protein-ligand binding poses with DiffDock from PDB or SMILES input

Draw plasmid maps, sequence logos and GC plots from GenBank and FASTA files

Build and run genomics pipelines and apps on DNAnexus with the dxpy SDK

Chain structure prediction, docking, design and ADMET into one drug pipeline

Look up DrugBank drug properties, targets, interactions and pharmacology data

Fetch DNA and RNA sequences, raw FASTQ reads and assemblies from ENA

Design and embed proteins with ESM3 and ESM C protein language models

Draw and manipulate phylogenetic trees and orthology with the ETE toolkit

Gate flow cytometry data and run proliferation and cell cycle analysis

Parse FCS flow cytometry files and export events to NumPy or CSV

Convert genomic intervals across BED, GFF, VCF and SAM and catch contig mismatches

Predict promoters, splice sites and expression from DNA sequence with hosted models

Run quick CLI and Python lookups for genes, BLAST, AlphaFold and enrichment

Submit protein expression and assay protocols to Ginkgo Cloud Lab robots

Predict N-glycosylation motifs and O-glycosylation hotspots in protein sequences

Scan sequences for N-glycosylation sequons and predict O-glycosylation hotspots

Analyze genomic intervals, BED coverage and fragments with fast Rust bindings

Search GWAS Catalog for SNP-trait associations and summary statistics

Search the Human Metabolome Database for metabolite properties and spectra