#bioinformatics

Terminal-based plasmid map viewer, sequence editor, and cloning/mutagenesis workbench in pure Python

HBAT 2: A Python Package to analyse Hydrogen Bonds and Other Non-covalent Interactions in Macromolecular Structures https://hbat-web.abhishek-tiwari.com

composable apps for scientific programming

A framework for state-of-the-art pre-trained bio foundation models on genomics and transcriptomics modalities.

SemiBin: metagenomics binning with self-supervised deep learning

This Python package contains a collection of scripts and tools for including in MGnify pipelines

Read UCSC Trix indexes in pure JavaScript

Tablassert turns biomedical spreadsheets (Excel, CSV, TSV) into knowledge graphs ready for NCATS Translator. Declare how your columns map to subject–predicate–object statements in YAML; Tablassert resolves free text to standard CURIEs, attaches provenance and statistical annotations, and emits KGX-compliant nodes and edges.

Services and guidelines for normalizing genes

Search UniProtKB by protein function, fetch curated records, map IDs across databases, and pull reference proteomes, taxonomy, and sequences via MCP. STDIO or Streamable HTTP.

A hybrid assembly and MAG recovery pipeline (and more!)

🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission

Python script to upload bins and MAGs to ENA (European Nucleotide Archive)

a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies

High-performance SASA (Solvent Accessible Surface Area) calculation in Zig with Python bindings

Shared core types and traits for the OpenProteo proteomics reader family.

MCP server exposing PlantCV as a measurement instrument — plant traits plus the segmentation overlay they were measured from