Editing Bioinformatics (section)

==Software and tools==
[[List of bioinformatics software|Software tools for bioinformatics]] include simple command-line tools, more complex graphical programs, and standalone web-services. They are made by [[bioinformatics companies]] or by public institutions.

===Open-source bioinformatics software===
{{Main| List of open-source bioinformatics software}}
{{See also|List of bioinformatics software}}

Many [[free and open-source software]] tools have existed and continued to grow since the 1980s.<ref name="obf-main">{{cite web |title=Open Bioinformatics Foundation: About us |url=http://www.open-bio.org/wiki/Main_Page |website=Official website |publisher=[[Open Bioinformatics Foundation]] |access-date=10 May 2011 |archive-date=12 May 2011 |archive-url=https://web.archive.org/web/20110512022059/http://open-bio.org/wiki/Main_Page |url-status=live }}</ref> The combination of a continued need for new [[algorithm]]s for the analysis of emerging types of biological readouts, the potential for innovative ''[[in silico]]'' experiments, and freely available [[open code]] bases have created opportunities for research groups to contribute to both bioinformatics regardless of [[Funding of science|funding]]. The open source tools often act as incubators of ideas, or community-supported [[Plug-in (computing)|plug-ins]] in commercial applications. They may also provide ''[[de facto]]'' standards and shared object models for assisting with the challenge of bioinformation integration.

Open-source bioinformatics software includes [[Bioconductor]], [[BioPerl]], [[Biopython]], [[BioJava]], [[BioJS]], [[BioRuby]], [[Bioclipse]], [[EMBOSS]], .NET Bio, [[Orange (software)|Orange]] with its bioinformatics add-on, [[Apache Taverna]], [[UGENE]] and [[GenoCAD]].

The non-profit [[Open Bioinformatics Foundation]]<ref name="obf-main" /> and the annual [[Bioinformatics Open Source Conference]] promote open-source bioinformatics software.<ref name="obf-bosc">{{cite web |title=Open Bioinformatics Foundation: BOSC |url=http://www.open-bio.org/wiki/BOSC |website=Official website |publisher=[[Open Bioinformatics Foundation]] |access-date=10 May 2011 |archive-date=18 July 2011 |archive-url=https://web.archive.org/web/20110718175922/http://www.open-bio.org/wiki/BOSC |url-status=live }}</ref>

===Web services in bioinformatics===
[[SOAP]]- and [[REST]]-based interfaces have been developed to allow client computers to use algorithms, data and computing resources from servers in other parts of the world. The main advantage are that end users do not have to deal with software and database maintenance overheads.

Basic bioinformatics services are classified by the [[European Bioinformatics Institute|EBI]] into three categories: [[Sequence alignment software|SSS]] (Sequence Search Services), [[Multiple sequence alignment|MSA]] (Multiple Sequence Alignment), and [[#Sequence analysis|BSA]] (Biological Sequence Analysis).<ref>{{Cite book | vauthors = Nisbet R, Elder IV J, Miner G |title=Handbook of Statistical Analysis and Data Mining Applications |chapter-url=https://books.google.com/books?id=U5np34a5fmQC&q=bioinformatics%20service%20categories%20EBI&pg=PA328|publisher=Academic Press |year=2009 |page=328 |chapter=Bioinformatics |isbn=978-0-08-091203-5 }}</ref> The availability of these [[Service-orientation|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 web-based interface, to integrative, distributed and extensible [[bioinformatics workflow management systems]].

==== Bioinformatics workflow management systems ====
{{main|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, and
* enable scientists to track the [[provenance]] of the workflow execution results and the workflow creation steps.

Some of the platforms giving this service: [[Galaxy (computational biology)|Galaxy]], [[Kepler scientific workflow system|Kepler]], [[Apache Taverna|Taverna]], [[UGENE]], [[Anduril (workflow engine)|Anduril]], [[High-performance Integrated Virtual Environment|HIVE]].
<!-- This is like saying there are different kinds of websites, some of which are convert-PNG-to-PDF.com, and others which are Wikipedia. Plus a lot of jargon. Consider cutting down further.  -->

=== BioCompute and BioCompute Objects ===
In 2014, the [[US Food and Drug Administration]] sponsored a conference held at the [[National Institutes of Health]] Bethesda Campus to discuss reproducibility in bioinformatics.<ref>{{Cite web|url=https://www.fda.gov/ScienceResearch/SpecialTopics/RegulatoryScience/ucm389561.htm|title=Advancing Regulatory Science – Sept. 24–25, 2014 Public Workshop: Next Generation Sequencing Standards|author=Office of the Commissioner|website=www.fda.gov|language=en|access-date=2017-11-30|archive-date=14 November 2017|archive-url=https://web.archive.org/web/20171114200347/https://www.fda.gov/ScienceResearch/SpecialTopics/RegulatoryScience/ucm389561.htm|url-status=dead}}</ref> Over the next three years, a consortium of stakeholders met regularly to discuss what would become BioCompute paradigm.<ref>{{cite journal | vauthors = Simonyan V, Goecks J, Mazumder R | title = Biocompute Objects-A Step towards Evaluation and Validation of Biomedical Scientific Computations | journal = PDA Journal of Pharmaceutical Science and Technology | volume = 71 | issue = 2 | pages = 136–146 | date = 2017 | pmid = 27974626 | pmc = 5510742 | doi = 10.5731/pdajpst.2016.006734 }}</ref> These stakeholders included representatives from government, industry, and academic entities. Session leaders represented numerous branches of the FDA and NIH Institutes and Centers, non-profit entities including the [[Human Variome Project]] and the [[European Federation for Medical Informatics]], and research institutions including [[Stanford]], the [[New York Genome Center]], and the [[George Washington University]].

It was decided that the BioCompute paradigm would be in the form of digital 'lab notebooks' which allow for the reproducibility, replication, review, and reuse, of bioinformatics protocols. This was proposed to enable greater continuity within a research group over the course of normal personnel flux while furthering the exchange of ideas between groups. The US FDA funded this work so that information on pipelines would be more transparent and accessible to their regulatory staff.<ref>{{Cite web|url=https://www.fda.gov/ScienceResearch/SpecialTopics/RegulatoryScience/ucm491893.htm|title=Advancing Regulatory Science – Community-based development of HTS standards for validating data and computation and encouraging interoperability|author=Office of the Commissioner|website=www.fda.gov|language=en|access-date=2017-11-30|archive-date=26 January 2018|archive-url=https://web.archive.org/web/20180126133504/https://www.fda.gov/ScienceResearch/SpecialTopics/RegulatoryScience/ucm491893.htm|url-status=dead}}</ref>

In 2016, the group reconvened at the NIH in Bethesda and discussed the potential for a [[BioCompute Object]], an instance of the BioCompute paradigm. This work was copied as both a "standard trial use" document and a preprint paper uploaded to bioRxiv. The BioCompute object allows for the JSON-ized record to be shared among employees, collaborators, and regulators.<ref>{{cite journal | vauthors = Alterovitz G, Dean D, Goble C, Crusoe MR, Soiland-Reyes S, Bell A, Hayes A, Suresh A, Purkayastha A, King CH, Taylor D, Johanson E, Thompson EE, Donaldson E, Morizono H, Tsang H, Vora JK, Goecks J, Yao J, Almeida JS, Keeney J, Addepalli K, Krampis K, Smith KM, Guo L, Walderhaug M, Schito M, Ezewudo M, Guimera N, Walsh P, Kahsay R, Gottipati S, Rodwell TC, Bloom T, Lai Y, Simonyan V, Mazumder R | title = Enabling precision medicine via standard communication of HTS provenance, analysis, and results | journal = PLOS Biology | volume = 16 | issue = 12 | pages = e3000099 | date = December 2018 | pmid = 30596645 | doi = 10.1371/journal.pbio.3000099 | pmc = 6338479 | doi-access = free }}</ref><ref>{{Citation|title=BioCompute Object (BCO) project is a collaborative and community-driven framework to standardize HTS computational data. 1. BCO Specification Document: user manual for understanding and creating B.|date=2017-09-03|url=https://github.com/biocompute-objects/HTS-CSRS|publisher=biocompute-objects|access-date=30 November 2017|archive-date=27 June 2018|archive-url=https://web.archive.org/web/20180627081221/https://github.com/biocompute-objects/HTS-CSRS|url-status=live}}</ref>