Bioinformatics workflows developed for and used on the St. Jude Cloud project.

scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.

SimTK OpenSim C++ libraries and command-line applications, and Java/Python wrapping.

FinaleToolkit is a package and standalone program to extract fragmentation features of cell-free DNA from paired-end sequencing data.

UCSC Genome Browser source tree. Stable branch: "beta".

Mixed continous/categorical flow-matching model for de novo molecule generation.

Implementations of various simulations for integrate and fire models, as well as conductance based models with synaptic neurotransmission

An interoperable Python framework for biomolecular simulation.

COBRApy is a package for constraint-based modeling of metabolic networks.

Integrated Computational Biology Data Analysis Environment

A comprehensive library for computational molecular biology

Bioinformatics and Computational Biology conference deadline

Mathematical Modeling for Systems Biology

Library for analysing protein structures and sequences

A collection of independent research projects involving various methods involving next generation sequencing (NGS) data analysis, including scRNA-seq, RNA-seq and scATAC-seq data.

This repository provides a demonstration of basic molecular docking using software tools such as AutoDock and ChimeraX. These techniques form part of the curriculum of the Bioinformatics practical course offered by Ahmedabad University, under the course code BIO205.

Graphical simulation of some of the interesting cellular automata.

Ontology of algorithms for analyzing biological models, their parameters, and their outputs

Accurate, easy and integrated suit to compare RNA samples with different degradation levels, quantify decay rates per-transcript and correct for degradation-induced artifacts in differential gene/transcript comparisons

Source code, issues, and discussions for Myokit: A tool for cardiac electrophysiology modelling and simulation