Software and tools

Software tools for bioinformatics range from simple command-line tools, to more complex graphical programs and standalone web-services available from various bioinformatics companies or public institutions.

Open-source bioinformatics software

Many free and open-source software tools have existed and continued to grow since the 1980s.[23] The combination of a continued need for new algorithms for the analysis of emerging types of biological readouts, the potential for innovative in silico experiments, and freely available open code bases have helped to create opportunities for all research groups to contribute to both bioinformatics and the range of open-source software available, regardless of their funding arrangements. The open source tools often act as incubators of ideas, or community-supported plug-ins in commercial applications. They may also provide de facto standards and shared object models for assisting with the challenge of bioinformation integration.

The range of open-source software packages includes titles such as Bioconductor, BioPerl, Biopython, BioJava, BioRuby, Bioclipse, EMBOSS, .NET Bio, Taverna workbench, and UGENE. In order to maintain this tradition and create further opportunities, the non-profit Open Bioinformatics Foundation[23] have supported the annual Bioinformatics Open Source Conference (BOSC) since 2000.[24]

Web services in bioinformatics

SOAP- and REST-based interfaces have been developed for a wide variety of bioinformatics applications allowing an application running on one computer in one part of the world to use algorithms, data and computing resources on servers in other parts of the world. The main advantages derive from the fact that end users do not have to deal with software and database maintenance overheads.

Basic bioinformatics services are classified by the EBI into three categories: SSS (Sequence Search Services), MSA (Multiple Sequence Alignment), and BSA (Biological Sequence Analysis).[citation needed] The availability of these service-oriented bioinformatics resources demonstrate the applicability of web-based bioinformatics solutions, and range from a collection of standalone tools with a common data format under a single, standalone or web-based interface, to integrative, distributed and extensible bioinformatics workflow management systems.

Bioinformatics workflow management systems

Main article: Bioinformatics workflow management systems

A Bioinformatics workflow management system 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 Bioinformatics application. Such systems are designed to

provide an easy-to-use environment for individual application scientists themselves to create their own workflows

provide interactive tools for the scientists enabling them to execute their workflows and view their results in real-time

simplify the process of sharing and reusing workflows between the scientists.

enable scientists to track the provenance of the workflow execution results and the workflow creation steps.

Currently, there are at least four platforms giving this service: Galaxy, Kepler, Taverna and Anduril.

Rosalind

Rosalind[25] is an educational resource and web project for learning bioinformatics through problem solving and computer programming.[26][27][28][29][30] Rosalind users learn bioinformatics concepts through a problem tree that builds up biological, algorithmic, and programming knowledge concurrently or learn by topics, with the topic of Alignment, Combinatorics, Computational Mass Spectrometry, Heredity, Population Dynamics and so on. Each problem is checked automatically, allowing for the project to also be used for automated homework testing in existing classes.

Rosalind is a joint project between the University of California at San Diego and Saint Petersburg Academic University along with the Russian Academy of Sciences. The project's name commemorates Rosalind Franklin, whose X-ray crystallography with Raymond Gosling facilitated the discovery of the DNA double helix by James D. Watson and Francis Crick. It was recognized by Homolog.us as the Best Educational Resource of 2012 in their review of the Top Bioinformatics Contributions of 2012. As of November 2013, it hosts over 13,000 problem solvers.

Rosalind is used to teach the first Bioinformatics Algorithms course on Coursera in 2013,[31] including interactive learning materials hosted on Stepic.[32]