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 a visual front-end, allowing the user to build and modify complex applications with little or no programming expertise.<ref>{{Cite journal | 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. | authorlink7author-link7 = Carole Goble| last8 = Goderis | first8 = A. | last9 = Hull | first9 = D. | doi = 10.1002/cpe.993 | 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 = | s2cid = 10219281 | url = https://eprints.soton.ac.uk/260908/1/taverna-ccpe-reviewed.pdf }}</ref><ref>{{Cite journal | last1 = Yu | first1 = J. | last2 = Buyya | first2 = R. | doi = 10.1145/1084805.1084814 | title = A taxonomy of scientific workflow systems for grid computing | journal = ACM SIGMOD Record | volume = 34 | issue = 3 | pages = 44 | year = 2005 | pmid = | pmc = | citeseerx = 10.1.1.63.3176 | s2cid = 538714 }}</ref><ref name="CIBEC 2008">{{Cite book | last1 = Curcin | first1 = V. | last2 = Ghanem | first2 = M. | title = Scientific workflow systems - can one size fit all? | doi = 10.1109/CIBEC.2008.4786077 | pages = 1–9 | year = 2008 | pmid = | pmc = | journal=2008 Cairo International Biomedical Engineering Conference| isbn = 978-1-4244-2694-2 | s2cid = 1885579 }}</ref>

==Examples==

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* The paper "Scientific workflow systems-can one size fit all?",<ref name="CIBEC 2008"/> which provides a high-level framework for comparing workflow systems based on their control flow and data flow properties. The systems compared include [[Discovery Net]], [[Taverna workbench|Taverna]], Triana, [[Kepler scientific workflow system|Kepler]] as well as Yawl and [[Business Process Execution Language|BPEL]].

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

{{Cite book | 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 = | pmc = | s2cid = 17343728 }}</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>