121 Open Source Computational Biology Software Projects

WebGL accelerated JavaScript molecular graphics library

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

Working with molecular structures in pandas DataFrames

OpenChem: Deep Learning toolkit for Computational Chemistry and Drug Design Research

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

Interactive network visualization in Python and Dash, powered by Cytoscape.js

A high-performance, Pythonic language for bioinformatics

A publicly-editable collection of open computational neuroscience resources

Ten Quick Tips for Deep Learning in Biology

A list of schools and researchers in computational neuroscience

Syntax highlighting for computational biology

Variational Autoencoder for Dimensionality Reduction of Time-Series

Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing

Next generation sequencing reads de novo assembler.

Deep learning meets molecular dynamics.

dna2vec: Consistent vector representations of variable-length k-mers

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.

Race and ethnicity Imputation from Disease history with Deep LEarning

Protein Graph Library

A comprehensive library for computational molecular biology

Python3 binding to mRMR Feature Selection algorithm (currently not maintained)

Clair: Exploring the limit of using deep neural network on pileup data for germline variant calling

Web application for enormous biological heatmaps

Chaste - Cancer Heart And Soft Tissue Environment - main public repository.

Python Programming for Biologists

The Biochemical Algorithms Library

Infectious Disease Sequencing Platform

An R Package for Geneset Enrichment Workflows

Natural language processing of Gene Expression Omnibus data

Various utilities regarding Levenshtein transducers. (Java)

Clustering scRNAseq by genotypes

10x Genomics Reads Simulator

NeoDTI: Neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions

A library to build and execute typed scientific workflows

a modeling environment tailored to parameter estimation in dynamical systems

A Curated List of Computational Biology Datasets Suitable for Machine Learning

Список вакансий в Департаменте Вычислительной Биологии в компании BIOCAD

Predicting protein structure through sequence modeling

An Artificial Neural Network-based discriminator for validating clinically significant genomic variants

The MPI Bioinformatics Toolkit

Collection of scripts for bacterial genomics

A flexible Nextflow-based framework for the definition of sequencing data processing pipelines

A Go package for engineering organisms.

Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model

Super high performance interactive heatmap software

forester is a collection of open source libraries of Java and Ruby software for phylogenomics and evolutionary biology research

A COBRApy extension for genome-scale models of metabolism and expression (ME-models)

A Python-based Effective Feature Generation Tool from DNA, RNA, and Protein Sequences

Code and Data to accompany "Dilated Convolutions for Modeling Long-Distance Genomic Dependencies", presented at the ICML 2017 Workshop on Computational Biology

DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies a series of filters and integrates data across replicate sets to arrive at a precise list of circRNA candidates.

To tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS), most of the existing short-read aligners can be configured to favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging the computational power of both CPU and GPU with optimized algorithms, delivers high speed and sensitivity simultaneously.

Data visualization library for creating interactive graphs and dashboards for bioinformatics etc.

Code and resources for the EPSRC BioSimSpace project.

Smart search engine for all bioinformatics databases worldwide

The Microbiome Interpretable Temporal Rule Engine

SOAPdenovo-Trans, a de novo transcriptome assembler designed specifically for RNA-Seq. We evaluated its performance on transcriptome datasets from rice and mouse.

DeepChem 2017: Deep Learning & NLP for Computational Chemistry, Biology & Nano-materials

📖 Generation and Applications of Knowledge Graphs in Systems and Networks Biology

AI assembly of bioNLP wordnets

ChIP-seq/RNA-seq analysis software suite for gene expression heatmaps

R package for cell type prediction based on SVD and ML approaches

Streamlining SLAM-seq analysis with ultra-high sensitivity

Python API for the Interactive Tree of Life (iTOL)

Ptera Software is a fast, easy-to-use, and open-source software package for analyzing flapping-wing flight.

screenlamp is a Python toolkit for hypothesis-driven virtual screening

This is the main repository for the HackBio'2020 Virtual Internship Experience ❤️

A full-featured bioinformatics software collection for the comprehensive analysis of aptamers in HT-SELEX experiments.

Python implementation of Spatial Analysis of Functional Enrichment (SAFE)

Cross-platform GUI desktop application for making biological heatmaps

Syntax highlighting for computational biology

DeepSEA in TensorFlow

Bio::Phylo - Phyloinformatic analysis using Perl

pyQms, generalized, fast and accurate mass spectrometry data quantification

Towards fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics.

Python library for reading, writing, and converting computational chemistry file formats and generating input files.

Myokit: A simple interface to cardiac cellular electrophysiology

Analysis of non-covalent interactions in MD trajectories

Tools for phylogenetic data analysis including visualization and cluster-computing support.

Genetic Heterogeneity Profiling by Single Cell RNA Sequencing

A standalone program that reads files created with the graphical network editor Escher and converts them to files in community standard formats.

Intelligent System for Analysis, Model Building And Rational Design of biomolecules.

:earth_americas: Review materials for bioinformatics, computational biology, and science in general

Contact map analysis for biomolecules; based on MDTraj

Repository for my research on generative modelling of cell images

Coursera Computational-NeuroScience course of the University of Washington

Repository to host data standards for the ALIFE community.

Ultrafast sequence typing and gene detection from NGS raw reads

A project for exploring differentially active signaling paths related to proteomics datasets

Code repository for the book "Python for the Life Sciences" by Lancaster & Webster

Artisanal 🤣 bioinformatics tools and pipelines in Scala

Nucleic and amino acid primitive types

CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology

Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.

Fitness landscape exploration sandbox for biological sequence design.

:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

Spatial alignment of single cell transcriptomic data.

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

🧬 An R package for visualizing molecular data in 3D

A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction

STAPLE (Shared Tools for Automatic Personalised Lower Extremity modelling) consists of a collection of methods for generating skeletal models from three-dimensional bone geometries, usually segmented from medical images. The methods are currently being expanded to create complete musculoskeletal models.