Here is a list that covers many of the most widely used open source tools for bio scientific research, If anyone has any additional tools to suggest or experiences using open source tools for their research, please feel free to share them with the community.

Genomics and Genetics

  • Bioconductor: An open source and open development software project for the analysis and comprehension of genomic data.
  • Galaxy: A web-based platform for data-intensive biomedical research that includes tools for genomic data analysis.
  • Ensembl: A genome browser and annotation database for vertebrate genomes.
  • UCSC Genome Browser: A web-based genome browser developed by the University of California, Santa Cruz.
  • Samtools: A suite of programs for interacting with high-throughput sequencing data.
  • GATK: A toolkit for analyzing high-throughput sequencing data for germline and somatic variants.
  • NCBI Genome Data Viewer: A web-based genome browser developed by the National Center for Biotechnology Information.


  • ProteomeXchange: A repository for proteomics data.
  • MaxQuant: An open source software suite for the quantitative analysis of mass spectrometry data.
  • Skyline: A software suite for targeted proteomics data analysis.
  • OpenMS: An open source software suite for mass spectrometry-based proteomics.

Structural Biology

  • PyMOL: An open source molecular visualization system.
  • Chimera: A molecular visualization program for displaying, modeling, and analyzing molecular structures.
  • Phenix: A software suite for macromolecular crystallography.
  • Rosetta: A software suite for macromolecular modeling, design, and docking.


  • NEST: A simulator for large-scale networks of spiking neurons.
  • Brainstorm: A software suite for the analysis of neurophysiological and neuroimaging data.
  • OpenEphys: An open source platform for electrophysiology research.
  • NeuroML: A markup language for describing neuronal models and simulations.
  • Allen Brain Atlas: An online public resource of the Allen Institute for Brain Science that provides gene expression data and anatomical information for the mouse brain.

Bioinformatics and Computational Biology

  • Biopython: A set of tools for biological computation in Python.
  • BioPerl: A set of Perl modules for bioinformatics.
  • BioJava: A set of Java libraries for bioinformatics.
  • BioSQL: A database schema for storing biological sequence data.
  • EMBOSS: A suite of open source software for sequence analysis.