Electrostatics / Apbs Pdb2pqr

The Chemistry Development Kit

This library tackles the construction and efficient execution of computational chemistry workflows

A curated list of Cheminformatics libraries and software.

Therapeutics Data Commons: Machine Learning Datasets and Tasks for Therapeutics

Pegasus Workflow Management System - Automate, recover, and debug scientific computations.

Code for the paper: Benhenda, M. 2017. ChemGAN challenge for drug discovery: can AI reproduce natural chemical diversity? arXiv preprint arXiv:1708.08227.

Demonstrating best practices for bioinformatics command line tools

✏️ A versatile DNA sequence optimizer

An efficient FASTQ manipulation suite

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

SortMeRNA: next-generation sequence filtering and alignment tool

A Python library which allows construction and manipulation of complex molecules, as well as automatic molecular design and the creation of molecular databases.

A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)

Inference of ploidy and heterozygosity structure using whole genome sequencing data

UGENE is free open-source cross-platform bioinformatics software

Antimicrobial Resistance Identification By Assembly

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.

Benchmarking programming languages/implementations for common tasks in Bioinformatics

A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)

A collection of scripts and notes related to genomics and bioinformatics