Biology & Genomics

Prepare and launch nf-core pacsomatic tumor-normal PacBio HiFi genomics runs

Track pathogen lineages and weekly sequence shares from public GenSpectrum data

Run and interpret pathway enrichment on gene lists or ranked gene data

Align sequences and build maximum-likelihood phylogenetic trees with IQ-TREE and MAFFT

Join, merge and measure genomic intervals on Polars and read BED, VCF and BAM files

Query the PrimeKG knowledge graph for gene, drug and disease associations

Design and audit PCR and RT-qPCR primers with Primer3 and off-target checks

Read and export protocols.io protocols through its official REST API

Run bulk RNA-seq differential expression analysis with PyDESeq2 and Wald tests

Plan liquid-handling lab automation protocols and offline simulations with PyLabRobot

Process mass spectrometry data for proteomics and metabolomics with pyOpenMS

Read, filter and write SAM, BAM, VCF and FASTQ genomic files with pysam

Load Therapeutics Data Commons datasets, task splits and benchmarks with PyTDC

Turn paired-end 16S amplicon reads into QIIME 2 ASVs and taxonomy assignments

Run and validate RELION cryo-EM refinement and half-map postprocessing

Score laboratory animal severity and forecast welfare endpoints with RELSA and ARIMA

Run cloud molecular modeling for pKa, docking and dynamics with Rowan

Run single-cell RNA-seq QC, clustering, UMAP and marker analysis with Scanpy

Analyze microbiome and sequence data with scikit-bio diversity metrics and trees

Estimate RNA velocity and latent time from spliced and unspliced single-cell counts

Fit scVI, scANVI and totalVI probabilistic models for single-cell omics data

Run AlphaFold, Boltz and other protein design models on Tamarind Bio via API

Simulate biochemical reaction networks from SBML or Antimony models with Tellurium

Store and query genomic variant calls with TileDB-VCF at cohort scale

Build molecular graph models for property prediction and generation with TorchDrug

Embed microbiome samples and fine-tune Waypoint models with the waypoint CLI

Convert lab instrument output files to Allotrope ASM JSON or flat CSV

Run nf-core pipelines for RNA-seq, WGS and ATAC-seq sequencing data

Batch-correct and integrate single-cell data with scVI and totalVI models

Run quality control and MAD filtering on single-cell RNA-seq h5ad data

Set up a bio-research environment and survey connected literature and tools

Work with DNA, RNA and protein sequences, BLAST and phylogenetics using Biopython

Run flux balance analysis and knockout simulations on metabolic models with COBRApy

Analyze flux distributions for gene essentiality, pathways and secretion products

Build or load genome-scale metabolic models from BiGG and export validated JSON files

Validate metabolic models for mass balance, dead ends, thermodynamic loops and GPR rules

Plan a publishable metabolic modeling study with feasible models, analyses and metrics

Run the full metabolic flux analysis pipeline from model loading to publication figures

Look up AlphaFold structure predictions and protein annotations as short summaries

Query Bgee for healthy wild-type gene expression metadata in compact summaries

Look up ligand-target binding data in BindingDB by PDB, UniProt or similarity

Fetch BioBank Japan association results for one genetic variant as a short summary

Search BioStudies and ArrayExpress and pull study records by accession

Check Boltz job status and recover or download results from finished jobs

Install, verify and authenticate the boltz-api CLI and fix common setup errors

Design new protein, peptide and antibody binder candidates for a target with Boltz

Screen and rank existing protein or antibody binders against a target with Boltz

Predict solubility, permeability and logD for small molecules from SMILES strings

Generate novel small-molecule ligands and hits for a target with Boltz