List of open source bioinformatics software
Encyclopedia
This is a list of open source
bioinformatics
software with articles in Wikipedia.
Open source
The term open source describes practices in production and development that promote access to the end product's source materials. Some consider open source a philosophy, others consider it a pragmatic methodology...
bioinformatics
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
software with articles in Wikipedia.
| Software | Description | Resources | Platform | License | Developer |
|---|---|---|---|---|---|
| Anduril Anduril (workflow engine) Anduril is an open source component-based workflow framework for scientific data analysis developed at the Computational Systems Biology Laboratory, University of Helsinki.... |
Component-based workflow Workflow A workflow consists of a sequence of connected steps. It is a depiction of a sequence of operations, declared as work of a person, a group of persons, an organization of staff, or one or more simple or complex mechanisms. Workflow may be seen as any abstraction of real work... framework for data analysis |
Website | Linux Linux Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds... , Mac OS X Mac OS X Mac OS X is a series of Unix-based operating systems and graphical user interfaces developed, marketed, and sold by Apple Inc. Since 2002, has been included with all new Macintosh computer systems... , Windows |
GPL | University of Helsinki University of Helsinki The University of Helsinki is a university located in Helsinki, Finland since 1829, but was founded in the city of Turku in 1640 as The Royal Academy of Turku, at that time part of the Swedish Empire. It is the oldest and largest university in Finland with the widest range of disciplines available... |
| AutoDock Protein-ligand docking Protein–ligand docking is a molecular modelling technique. The goal of protein-ligand docking is to predict the position and orientation of a ligand when it is bound to a protein receptor or enzyme... |
suite of automated docking tools | Website | Platform | License | Developer |
| Biochemical Algorithms Library (BALL) BALL The open source project BALL consists of the versatile C++ class framework BALL , a library of algorithms and data structures targeting molecular modelling and computational structural bioinformatics, a Python interface to this library and the open source graphical interface to BALL, the molecular... |
C++ library and framework for molecular modeling and visualization designed for rapid prototyping | Website - Articles | Linux Linux Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds... , Mac OS X Mac OS X Mac OS X is a series of Unix-based operating systems and graphical user interfaces developed, marketed, and sold by Apple Inc. Since 2002, has been included with all new Macintosh computer systems... , Windows |
LGPL | BALL project team |
| Bioclipse Bioclipse The Bioclipse project is a Java-based, open source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform... |
Visual platform for chemo Cheminformatics Cheminformatics is the use of computer and informational techniques, applied to a range of problems in the field of chemistry. These in silico techniques are used in pharmaceutical companies in the process of drug discovery... - and bioinformatics Bioinformatics Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software... based on the Eclipse Eclipse (software) Eclipse is a multi-language software development environment comprising an integrated development environment and an extensible plug-in system... Rich Client Platform (RCP). |
Website | Platform | Eclipse Public License Eclipse Public License The Eclipse Public License is an open source software license used by the Eclipse Foundation for its software. It replaces the Common Public License and removes certain terms relating to litigations related to patents.... |
The Bioclipse Project |
| Bioconductor Bioconductor Bioconductor is a free, open source and open development software project for the analysis and comprehension of genomic data generated by wet lab experiments in molecular biology.... |
R (programming language) R (programming language) R is a programming language and software environment for statistical computing and graphics. The R language is widely used among statisticians for developing statistical software, and R is widely used for statistical software development and data analysis.... language toolkit |
Website - Articles | Linux Linux Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds... , Mac OS X Mac OS X Mac OS X is a series of Unix-based operating systems and graphical user interfaces developed, marketed, and sold by Apple Inc. Since 2002, has been included with all new Macintosh computer systems... , Windows |
Artistic License 2.0 Artistic License The Artistic License refers most commonly to the original Artistic License , a software license used for certain free and open source software packages, most notably the standard Perl implementation and most CPAN modules, which are dual-licensed under the Artistic License and the GNU General Public... |
Fred Hutchinson Cancer Research Center Fred Hutchinson Cancer Research Center The Fred Hutchinson Cancer Research Center, is one of the world’s leading cancer research institutes... |
| Bioinformatics Learning Tutorial (BLT) | Educational interactive tutorials and 3D animations for Replication, Transcription, and Translation | Project Home - Download for Windows | Windows (stand-alone Stand-alone Standalone software can mean:* Computer software that can work offline, i.e. does not necessarily require network connection to function* Software that is not a part of some software bundle... ), Linux Linux Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds... & Mac OS X Mac OS X Mac OS X is a series of Unix-based operating systems and graphical user interfaces developed, marketed, and sold by Apple Inc. Since 2002, has been included with all new Macintosh computer systems... (source code Source code In computer science, source code is text written using the format and syntax of the programming language that it is being written in. Such a language is specially designed to facilitate the work of computer programmers, who specify the actions to be performed by a computer mostly by writing source... only with Qt QT - Units and measurements :* Quart, a measure of volume in traditional systems of units* Quarter, a unit of mass in Imperial units, equal to 2 stones or a quarter of a long hundredweight; one quarter = 12.70058636 kg* QT interval, a measurement used in cardiology... libraries) |
Academic Free License Academic Free License The Academic Free License is a permissive free software license written in 2002 by Lawrence E. Rosen, the general counsel of the Open Source Initiative .... |
Collaborative project |
| BioHaskell | Haskell (programming language) Haskell (programming language) Haskell is a standardized, general-purpose purely functional programming language, with non-strict semantics and strong static typing. It is named after logician Haskell Curry. In Haskell, "a function is a first-class citizen" of the programming language. As a functional programming language, the... |
Project web site - Bioinformatics software in Haskell] |
Linux Linux Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds... , Mac OS X Mac OS X Mac OS X is a series of Unix-based operating systems and graphical user interfaces developed, marketed, and sold by Apple Inc. Since 2002, has been included with all new Macintosh computer systems... , Windows |
GPL, LGPL, and BSD | Collaborative project |
| BioJava BioJava The BioJava Project is an open source project dedicated to providing Java tools for processing biological data. This includes include objects for manipulating sequences, protein structures, file parsers, CORBA interoperability, DAS, access to AceDB, dynamic programming, and simple statistical... |
Java (programming language) Java (programming language) Java is a programming language originally developed by James Gosling at Sun Microsystems and released in 1995 as a core component of Sun Microsystems' Java platform. The language derives much of its syntax from C and C++ but has a simpler object model and fewer low-level facilities... |
Website | Linux Linux Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds... , Mac OS X Mac OS X Mac OS X is a series of Unix-based operating systems and graphical user interfaces developed, marketed, and sold by Apple Inc. Since 2002, has been included with all new Macintosh computer systems... , Windows |
LGPL v2.1 | Open Bioinformatics Foundation Open Bioinformatics Foundation The Open Bioinformatics Foundation is a non profit, volunteer run organization focused on supporting open source programming in bioinformatics.... |
| BioMOBY BioMOBY BioMOBY is a registry of web services used in bioinformatics. It allows interoperability between biological data hosts and analytical services by annotating services with terms taken from standard ontologies.- The BioMOBY project :... |
registry of web services | Website - Articles | Web | License | Open Bioinformatics Foundation Open Bioinformatics Foundation The Open Bioinformatics Foundation is a non profit, volunteer run organization focused on supporting open source programming in bioinformatics.... |
| BioPerl BioPerl BioPerl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It has played an integral role in the Human Genome Project.... |
Perl Perl Perl is a high-level, general-purpose, interpreted, dynamic programming language. Perl was originally developed by Larry Wall in 1987 as a general-purpose Unix scripting language to make report processing easier. Since then, it has undergone many changes and revisions and become widely popular... language toolkit |
Website | Cross-platform | Artistic License Artistic License The Artistic License refers most commonly to the original Artistic License , a software license used for certain free and open source software packages, most notably the standard Perl implementation and most CPAN modules, which are dual-licensed under the Artistic License and the GNU General Public... & GPL |
Open Bioinformatics Foundation Open Bioinformatics Foundation The Open Bioinformatics Foundation is a non profit, volunteer run organization focused on supporting open source programming in bioinformatics.... |
| BioPHP BioPHP BioPHP is a package of Open Source PHP code, with classes for DNA and protein sequence analysis, alignment, database parsing, and other Bioinformatics tools.-External links:**... |
PHP PHP PHP is a general-purpose server-side scripting language originally designed for web development to produce dynamic web pages. For this purpose, PHP code is embedded into the HTML source document and interpreted by a web server with a PHP processor module, which generates the web page document... language toolkit |
Website | Platform | License | Open Bioinformatics Foundation Open Bioinformatics Foundation The Open Bioinformatics Foundation is a non profit, volunteer run organization focused on supporting open source programming in bioinformatics.... |
| Biopython BioPython The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology, as well as bioinformatics.-References:*refer to the Biopython website for other , and a list of over one hundred .... |
Python Python (programming language) Python is a general-purpose, high-level programming language whose design philosophy emphasizes code readability. Python claims to "[combine] remarkable power with very clear syntax", and its standard library is large and comprehensive... language toolkit |
Website | Cross-platform | Biopython License | Open Bioinformatics Foundation Open Bioinformatics Foundation The Open Bioinformatics Foundation is a non profit, volunteer run organization focused on supporting open source programming in bioinformatics.... |
| BioRails BioRails BioRails is a data management system designed to support researchers in drug discovery. It facilitates the capture of structured end-point data that can be queried and data mined in a relational database... |
a data management system designed to support researchers in drug discovery Drug discovery In the fields of medicine, biotechnology and pharmacology, drug discovery is the process by which drugs are discovered or designed.In the past most drugs have been discovered either by identifying the active ingredient from traditional remedies or by serendipitous discovery... |
Website | Platform | License | Developer |
| BioRuby BioRuby BioRuby is a package of Open Source Ruby code, with classes for DNA and protein sequence analysis, alignment, database parsing, and other Bioinformatics tools. Recently, tools for structural biology have been added.-External links:* ,*... |
Ruby Ruby (programming language) Ruby is a dynamic, reflective, general-purpose object-oriented programming language that combines syntax inspired by Perl with Smalltalk-like features. Ruby originated in Japan during the mid-1990s and was first developed and designed by Yukihiro "Matz" Matsumoto... language toolkit |
Website | Platform | License | Open Bioinformatics Foundation Open Bioinformatics Foundation The Open Bioinformatics Foundation is a non profit, volunteer run organization focused on supporting open source programming in bioinformatics.... |
| caCORE | ontologic representation environment | Website - Articles | Platform | License | National Cancer Institute National Cancer Institute The National Cancer Institute is part of the National Institutes of Health , which is one of 11 agencies that are part of the U.S. Department of Health and Human Services. The NCI coordinates the U.S... |
| caArray | ontologic representation environment | http://caarray.nci.nih.gov/documentation - https://cabig-kc.nci.nih.gov/Molecular/KC/index.php/CaArray | Platform | License | National Cancer Institute National Cancer Institute The National Cancer Institute is part of the National Institutes of Health , which is one of 11 agencies that are part of the U.S. Department of Health and Human Services. The NCI coordinates the U.S... |
| EMBOSS EMBOSS EMBOSS is an acronym for European Molecular Biology Open Software Suite. EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology and bioinformatics user community... |
Suite of packages for sequencing, searching, etc. | Website | Platform | General Public Licence (GPL) and Library GPL | Collaborative project |
| Galaxy Galaxy (computational biology) Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience... |
Scientific workflow Scientific workflow system A Scientific Workflow Systems is a specialized form of a workflow management system designed specifically to compose and execute a series of computational or data manipulation steps, or a workflow, in a scientific application... and data integration Data integration Data integration involves combining data residing in different sources and providing users with a unified view of these data.This process becomes significant in a variety of situations, which include both commercial and scientific domains... system |
Website | Unix-like Unix-like A Unix-like operating system is one that behaves in a manner similar to a Unix system, while not necessarily conforming to or being certified to any version of the Single UNIX Specification.... |
License | Penn State and Emory University Emory University Emory University is a private research university in metropolitan Atlanta, located in the Druid Hills section of unincorporated DeKalb County, Georgia, United States. The university was founded as Emory College in 1836 in Oxford, Georgia by a small group of Methodists and was named in honor of... |
| GMOD Generic Model Organism Database The Generic Model Organism Database Project began as an effort to create reusable software tools for developing Model Organism Databases . MODs describe genome and other information about important experimental organisms in the life sciences... |
Toolkit for addressing many common challenges at biological databases. | Website | Unix-like Unix-like A Unix-like operating system is one that behaves in a manner similar to a Unix system, while not necessarily conforming to or being certified to any version of the Single UNIX Specification.... (server), Web browser Web browser A web browser is a software application for retrieving, presenting, and traversing information resources on the World Wide Web. An information resource is identified by a Uniform Resource Identifier and may be a web page, image, video, or other piece of content... (client) |
Varies depending on tool | Collaborative project |
| GENtle GENtle (software) - Features :GENtle is an equivalent to the proprietary Vector NTI, a handy tool for molecular biologists to analyze and edit DNA sequence files. Invitrogens removal of the free-of-cost academic licence for Vector NTI v11 has had a severe impact on many molecular biology labs that have come to rely... |
An equivalent to the proprietary Vector NTI Vector NTI Vector NTI is a bioinformatics software package. The current versions are v11.5.1 for Windows/PCs and v7.1 for Macs, but only supporting Mac OS X v10.3 .- Features :* create, annotate, analyse, and share DNA/protein sequences... , a tool to analyze and edit DNA DNA Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in... sequence files |
Website | Platform | GPL | Magnus Manske |
| Integrated Genome Browser Integrated Genome Browser Integrated Genome Browser is an open source genome browser, a visualization tool used to observe biologically-interesting patterns in genomic data sets, including sequence data, gene models, alignments, and data from DNA microarrays.- History :... |
Java-based desktop genome browser Genome browser A genome browser is a graphical interface for display of information from a biological database for genomic data. Genome browsers enable researchers to visualize and browse entire genomes with annotated data including gene prediction and structure, proteins, expression, regulation, variation,... |
Website | Linux Linux Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds... , Mac OS X Mac OS X Mac OS X is a series of Unix-based operating systems and graphical user interfaces developed, marketed, and sold by Apple Inc. Since 2002, has been included with all new Macintosh computer systems... , Windows |
CPL 1.0 Common Public License In computing, the CPL is a free software / open-source software license published by IBM. The Free Software Foundation and Open Source Initiative have approved the license terms of the CPL.... |
GenoViz |
| IntAct Intact Intact can refer to:*Intact , a Romanian media trust*Intact and "Intact" by Ned's Atomic Dustbin*Intacto, a film*Entire , describing an animal that has not been spayed or neutered*Genital integrity... |
molecular interaction database | Website - Articles | Platform | License | European Bioinformatics Institute European Bioinformatics Institute The European Bioinformatics Institute is a centre for research and services in bioinformatics, and is part of European Molecular Biology Laboratory... |
| Java Treeview | microarray data viewer | Website - Articles | Cross-platform | License | Developer |
| LabKey Server LabKey Server LabKey Server is free, open source software available for scientists to integrate, analyze, and share biomedical research data. The platform provides a secure data repository that allows web-based querying, reporting, and collaborating across a range of data sources... |
platform for integrating, analyzing and sharing data | Website | Linux Linux Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds... , Mac OS X Mac OS X Mac OS X is a series of Unix-based operating systems and graphical user interfaces developed, marketed, and sold by Apple Inc. Since 2002, has been included with all new Macintosh computer systems... , Windows |
Apache License Apache License The Apache License is a copyfree free software license authored by the Apache Software Foundation . The Apache License requires preservation of the copyright notice and disclaimer.... |
LabKey Software Foundation |
| OpenClinica | software for capturing and managing data in clinical trials | Website | Linux Linux Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds... , Windows |
LGPL | OpenClinica |
| REDCRAFT | software for determining tertiary protein structure given assigned Residual Dipolar Coupling data | Website | Linux Linux Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds... , Mac OS X Mac OS X Mac OS X is a series of Unix-based operating systems and graphical user interfaces developed, marketed, and sold by Apple Inc. Since 2002, has been included with all new Macintosh computer systems... , Windows |
GPL v3 | REDCRAFT |
| SAM Tools | Data format (SAM) and accompanying tool suite, for storing large nucleotide sequence alignments | Website | Linux Linux Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds... |
BSD, MIT License MIT License The MIT License is a free software license originating at the Massachusetts Institute of Technology . It is a permissive license, meaning that it permits reuse within proprietary software provided all copies of the licensed software include a copy of the MIT License terms... |
1000 Genomes Project |
| Taverna workbench Taverna workbench Taverna Workbench is an open source software tool for designing and executing workflows, created by the myGrid project and funded through the OMII-UK... |
Tool for designing and executing workflows | Website | Linux Linux Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds... , Mac OS X Mac OS X Mac OS X is a series of Unix-based operating systems and graphical user interfaces developed, marketed, and sold by Apple Inc. Since 2002, has been included with all new Macintosh computer systems... , Windows |
LGPL | myGrid MyGrid The myGrid consortium is a multi-institutional, multi-disciplinary internationally leading research group focussing on the challenges of eScience... |
| UGENE UGENE UGENE is free open-source cross-platform bioinformatics software.It integrates dozens of well-known biological tools and algorithms, providing both graphical user and command line interfaces... |
integrated bioinformatics tools | Website - Podcast | Linux Linux Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds... , Mac OS X Mac OS X Mac OS X is a series of Unix-based operating systems and graphical user interfaces developed, marketed, and sold by Apple Inc. Since 2002, has been included with all new Macintosh computer systems... , Windows |
GPL2 License | Unipro |
See also
- List of sequence alignment software
- List of open source healthcare software
- List of freeware health software
- List of molecular graphics systems
- List of software for molecular mechanics modeling
External links
- Bio-Informatics software - SourceForgeSourceForgeSourceForge Enterprise Edition is a collaborative revision control and software development management system. It provides a front-end to a range of software development lifecycle services and integrates with a number of free software / open source software applications .While originally itself...
- Free Biology Software - Free Software DirectoryFree Software DirectoryThe Free Software Directory is a project of the Free Software Foundation . It catalogs free software that runs under free operating systems - particularly GNU and Linux. The project was formerly co-run by UNESCO....
- Free Software FoundationFree Software FoundationThe Free Software Foundation is a non-profit corporation founded by Richard Stallman on 4 October 1985 to support the free software movement, a copyleft-based movement which aims to promote the universal freedom to create, distribute and modify computer software... - Bioinformatics Links Directory