Biology & Genomics

Compile sourced target profiles covering structure, pathways and drug interactions

Parse VCF files and classify variant types, consequences and structural variants

Annotate VCF variants with VEP, ClinVar and gnomAD and rank them in reports

Predict protein and complex structures with AlphaFold2 and ColabFold

Predict protein, nucleic acid and ligand complex structures with Boltz-2

Predict genome-wide expression and chromatin tracks from DNA with Borzoi

Predict antibody, protein and ligand complex structures from FASTA with Chai-1

Dock small molecules into protein pockets with DiffDock-L blind diffusion docking

Fold proteins, DNA, RNA and ligand complexes with ESMFold2 and ESMC models

Score, embed and generate DNA sequences with the Evo 2 genomic model

Embed proteins and score mutations with Meta's ESM-2 model via fair-esm

Redesign residues around a bound ligand or metal site with LigandMPNN

Predict protein, nucleic acid and ligand complex structures with OpenFold3

Design protein sequences onto a backbone with ProteinMPNN inverse folding

Embed and annotate single-cell data with the scGPT foundation model

Integrate scRNA-seq batches and transfer cell labels with scVI and scANVI

Design soluble protein sequences that resist aggregation with SolubleMPNN

Explore iNaturalist observations, wildlife briefings and identification progress

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

Predict absorption, distribution, metabolism and excretion properties of drug candidates

Fetch AlphaFold predicted protein structures and confidence scores by UniProt ID

Plan cell and animal experiments to validate computational or clinical findings

Read and write AnnData .h5ad files for single-cell analysis with scverse tools

Infer gene regulatory networks from expression matrices with GRNBoost2 or GENIE3

Correct batch effects in merged expression matrices and plot before and after QC

Manage Benchling registry, inventory, ELN and workflow data through its API

Test whether gene expression or methylation mediates genetic effects on disease

Detect and correct horizontal pleiotropy in Mendelian randomization analyses

Convert gene and protein identifiers and fetch pathways and orthologs via bioDBnet

Search BioGRID ORCS CRISPR screens and retrieve gene scores by organism

Extract the bioinformatics pipeline of a paper and design a customized analysis plan

Parse sequences and structures and automate NCBI and BLAST workflows with Biopython

Run advanced Biopython motif, population genetics and clustering analyses

Run pairwise and multiple sequence alignments with Biopython Bio.Align

Search and fetch PubMed and GenBank records via NCBI E-utilities with Bio.Entrez

Read, prune, reroot and plot phylogenetic trees with Biopython Bio.Phylo

Read, write and convert FASTA, GenBank and FASTQ sequence files with Biopython

Parse protein PDB and mmCIF structures and compare them with Biopython

Query UniProt, KEGG, ChEMBL and Reactome through one consistent Python API

Pull enzyme kinetics, reactions and properties from BRENDA by EC number or substrate

Calculate buffer recipes for PBS, RIPA and TAE with mass, volume and pH steps

Design integrated bulk transcriptomics, proteomics and metabolomics study plans

Look up cell line identities, accessions and release info in the Cellosaurus database

Query CZ CELLxGENE Census single-cell expression across tissues, diseases and cell types

Build a ceRNA regulatory network from a gene list using miRNA and lncRNA databases

Run ChEA3 transcription factor enrichment on a gene set and fetch TF metadata

Query ChEMBL for bioactive molecules, targets, bioactivities and approved drugs

Estimate immune cell infiltration from bulk data with CIBERSORT-style deconvolution

Query ClinVar for variant significance, phenotypes and VCF annotations