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UTOPIA (Bioinformatics tools) UTOPIA (User-friendly Tools for OPerating Informatics Applications) is a suite of free tools for visualising and analysing bioinformatics data. Based on an ontology-driven data model, it contains appl. UTOPIA (Bioinformatics tools) - Wikipedia.
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This is a list of computer software which is made for bioinformatics and released under open-source software licenses with articles in Wikipedia.
Software | Description | Platform | License | Developer |
---|---|---|---|---|
.NET Bio | Language-neutral toolkit built using the Microsoft 4.0 .NET Framework to help developers, researchers, and scientists | .NET Framework | Apache | Collaborative project |
AMPHORA | Metagenomics analysis software | Linux | GPL | ? |
Anduril | Component-based workflow framework for data analysis | Linux, macOS, Windows | GPL | University of Helsinki |
Ascalaph Designer | Computer program for general purpose molecular modelling for molecular design and simulations. | ? | GPLv2 | Agile Molecule |
AutoDock | Suite of automated docking tools | ? | GPL | ? |
Avogadro | Molecule editor and visualizer for in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. | ? | GPL | ? |
Bioclipse | Visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP) | ? | Eclipse Public | The Bioclipse Project |
Bioconductor | R (programming language) language toolkit | Linux, macOS, Windows | Artistic 2.0 | Fred Hutchinson Cancer Research Center |
BioJava | Java | Linux, macOS, Windows | LGPL v2.1 | Open Bioinformatics Foundation |
BioJS | JavaScript | Web browser | Apache | ? |
BioMOBY | Registry of web services | Web browser | Artistic | Open Bioinformatics Foundation |
BioPerl | Perl language toolkit | Cross-platform | Artistic, GPL | Open Bioinformatics Foundation |
BioPHP | PHP language toolkit | ? | GPL v2 | Open Bioinformatics Foundation |
Biopython | Python language toolkit | Cross-platform | Biopython[1] | Open Bioinformatics Foundation |
BioRuby | Ruby language toolkit | ? | GPL v2 or Ruby | Open Bioinformatics Foundation |
CP2K | Perform atomistic simulations of solid state, liquid, molecular and biological systems. | ? | GPL and LGPL | Free open source GNU GPLv2 or later |
EMBOSS | Suite of packages for sequencing, searching, etc. | ? | GPL and LGPL | Collaborative project |
Galaxy | Scientific workflow and data integration system | Unix-like | Academic Free | Collaborative project |
GenePattern | Scientific workflow system that provides access to hundreds of genomic analysis tools | Unix-like (public server); Linux, macOS, Windows | MIT | Broad Institute, UC San Diego |
Geworkbench | Genomic data integration platform | Linux, macOS, Windows | GeWorkbench License[2] | Columbia University |
GMOD | Toolkit to address many common challenges at biological databases | Unix-like (server), Web browser (client) | Varies depending on tool | Collaborative project |
GenGIS | Application that allows combining digital map data with information about biological sequences collected from the environment | Windows, macOS | GPL | Collaborative project |
Genomespace | Centralized web application that provides data format transformations and facilitates connections with other bioinformatics tools | Web browser | LGPL | Broad Institute, collaborative project |
GENtle | An equivalent to the proprietary Vector NTI, a tool to analyze and edit DNA sequence files | ? | GPL | Magnus Manske |
GROMACS | Molecular dynamics package mainly designed for simulations of proteins, lipids and nucleic acids. | Linux, macOS, Windows | Common Public 1.0 | GenoViz |
Integrated Genome Browser | Java-based desktop genome browser | Linux, macOS, Windows | Common Public 1.0 | GenoViz |
InterMine | Extensive data warehouse system for the analysis and integration of biological datasets | Cross-platform | LGPL | University of Cambridge |
LabKey Server | Software platform, allows organizations to integrate, analyze, and share complex biomedical data | Linux, macOS, Windows | Apache | LabKey Software Foundation |
LAMMPS | Molecular dynamics program | Linux, macOS, Windows | Apache | Sandia National Laboratories. |
mothur | Software for analysis of the 16S rRNA gene | Linux, macOS, Windows | ? | University of Michigan |
PathVisio | Desktop software for drawing, analysing, and visualizing biological pathways | Linux, macOS, Windows | Apache 2.0 | Maastricht University |
Orange | Component-based data mining and machine learning software suite, featuring a visual programming front-end for exploratory data analysis and interactive visualization, and Python bindings and libraries for scripting | Linux, macOS, Windows | GPL | University of Ljubljana |
Staden Package | Sequence assembly, editing, and analysis, mainly consisting of gap4, gap5, and spin. | Linux, macOS, Windows | BSD | Wellcome Trust Sanger Institute, Medical Research Council |
Taverna workbench | Tool to design and execute workflows | Linux, macOS, Windows | LGPL | myGrid |
UGENE | Integrated bioinformatics tools | Linux, macOS, Windows | GPL 2 | Unipro |
Unipept | Metaproteomics biodiversity analysis | Web browser | MIT | Ghent University |
VOTCA | A Coarse-grained modeling package, | GNU/Linux, macOS, Windows, any other Unix variety | Apache License 2.0 | Max Planck Institute for Polymer Research |
See also[edit]
References[edit]
- ^Biopython License
- ^'GeWorkbench License'. geWorkbench. Columbia University. 15 June 2014.
External links[edit]
![Free bioinformatics software downloads Free bioinformatics software downloads](/uploads/1/2/7/0/127071596/278275305.jpg)
Open Source Bioinformatics
- Free Biology Software – Free Software Directory – Free Software Foundation
Free Bioinformatics Software Download
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