Bioinformatics workflow management system: Difference between revisions

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A '''bioinformatics workflow management system''' is a specialized form of [[workflow management system]] designed specifically to compose and execute a series of computational or data manipulation steps, or a [[workflows|workflow]], that relate to [[bioinformatics]].

There are currently many different workflow systems. Some have been developed more generally as [[scientific workflow system]]s for use by scientists from many different disciplines like [[astronomy]] and [[earth science]]. All such systems are based on an abstract representation of how a computation proceeds in the form of a directed graph, where each node represents a task to be executed and edges represent either data flow or execution dependencies between different tasks. Each system typically provides visual front-end allowing the user to build and modify complex applications with little or no programming expertise.<ref>{{citeCite journal doi| last1 = Oinn | first1 = T. | last2 = Greenwood | first2 = M. | last3 = Addis | first3 = M. | last4 = Alpdemir | first4 = M. N. | last5 = Ferris | first5 = J. | last6 = Glover | first6 = K. | last7 = Goble | first7 = C. | authorlink7 = Carole Goble| last8 = Goderis | first8 = A. | last9 = Hull | first9 = D. | doi = 10.1002/cpe.993 |noedit last10 = Marvin | first10 = D. | last11 = Li | first11 = P. | last12 = Lord | first12 = P. | last13 = Pocock | first13 = M. R. | last14 = Senger | first14 = M. | last15 = Stevens | first15 = R. | last16 = Wipat | first16 = A. | last17 = Wroe | first17 = C. | title = Taverna: Lessons in creating a workflow environment for the life sciences | journal = Concurrency and Computation: Practice and Experience | volume = 18 | issue = 10 | pages = 1067–1100 | year = 2006 | pmid = | pmc = }}</ref><ref>{{citeCite journal doi| last1 = Yu | first1 = J. | last2 = Buyya | first2 = R. | doi = 10.1145/1084805.1084814 |noedit title = A taxonomy of scientific workflow systems for grid computing | journal = ACM SIGMOD Record | volume = 34 | issue = 3 | pages = 44 | year = 2005 | pmid = | pmc = }}</ref><ref>{{cite doi|10.1109/CIBEC.2008.4786077|noedit}}</ref>

==Examples==

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* [[OnlineHPC]] Online workflow designer based on [[Taverna workbench|Taverna]]

* SeqWare: Hadoop Oozie-based workflow system focused on genomics data analysis in cloud environments{{citation needed|date=October 2014}}.

* Tavaxy<ref>{{citeCite journal doi| last1 = Abouelhoda | first1 = M. | last2 = Issa | first2 = S. | last3 = Ghanem | first3 = M. | title = Tavaxy: Integrating Taverna and Galaxy workflows with cloud computing support | doi = 10.1186/1471-2105-13-77 |noedit journal = BMC Bioinformatics | volume = 13 | pages = 77 | year = 2012 | pmid = 22559942| pmc =3583125 }}</ref> A cloud-based bioinformatics workflow system that integrates features from both Taverna and Galaxy for NGS data analysis.

* [[Taverna workbench]]:<ref>{{Cite journal | last1 = Oinn | first1 = T. | last2 = Addis | first2 = M. | last3 = Ferris | first3 = J. | last4 = Marvin | first4 = D. | last5 = Senger | first5 = M. | last6 = Greenwood | first6 = M. | last7 = Carver | first7 = T. | last8 = Glover | first8 = K. | last9 = Pocock | first9 = M. R. | last10 = Wipat | doi = 10.1093/bioinformatics/bth361 | first10 = A. | last11 = Li | first11 = P. | title = Taverna: A tool for the composition and enactment of bioinformatics workflows | journal = Bioinformatics | volume = 20 | issue = 17 | pages = 3045–3054 | year = 2004 | pmid = 15201187 | pmc = }}</ref><ref>{{Cite journal | last1 = Hull | first1 = D.| authorlink = | last2 = Wolstencroft | first2 = K. | last3 = Stevens | first3 = R. | authorlink3 = Robert David Stevens | last4 = Goble | first4 = C. A. | authorlink4 = Carole Goble | last5 = Pocock | first5 = M. R. | last6 = Li | first6 = P. | last7 = Oinn | first7 = T. | title = Taverna: A tool for building and running workflows of services | doi = 10.1093/nar/gkl320 | journal = [[Nucleic Acids Research]] | volume = 34 | issue = Web Server issue | pages = W729–W732 | year = 2006 | pmc = 1538887 | pmid = 16845108}} {{open access}}</ref> an early ___domain-independent system widely used in bioinformatics and other areas of [[e-Science]]

* [[Taverna workbench]]:<ref>{{cite doi|10.1093/bioinformatics/bth361|noedit}}</ref><ref>{{cite doi|10.1093/nar/gkl320|noedit}}</ref> an early ___domain-independent system widely used in bioinformatics and other areas of [[e-Science]]

* [[VisTrails]]<ref>{{cite doi|10.1109/VISUAL.2005.1532788|noedit}}</ref>

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* The paper "Meta-workflows: pattern-based interoperability between Galaxy and Taverna" <ref>

{{Cite doibook | last1 = Abouelhoda | first1 = M. | last2 = Alaa | first2 = S. | last3 = Ghanem | first3 = M. | doi = 10.1145/1833398.1833400 | chapter = Meta-workflows | title = Proceedings of the 1st International Workshop on Workflow Approaches to New Data-centric Science - Wands '10 | pages = 1 | year = 2010 | isbn = 9781450301886 | pmid = |noedit pmc = }}</ref> which provides a more user-oriented comparison between [[Taverna workbench|Taverna]] and [[Galaxy (computational biology)|Galaxy]] in the context of enabling interoperability between both systems.

* The infrastructure paper "Delivering ICT Infrastructure for Biomedical Research" <ref>