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#REDIRECT [[Scientific workflow system]] {{R from merge}}
{{Example farm|date=February 2012}}
A '''bioinformatics workflow management system''' is a specialized form of [[Workflow#Workflow management system|workflow management system]] designed specifically to compose and execute a series of computational or data manipulation steps, or a [[workflows|workflow]], in a specific ___domain of science, [[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.
==Examples==
* [[Anduril (workflow engine)|Anduril]] bioinformatics and image analysis
* [[BioBIKE]]
* [http://chipster.csc.fi/ Chipster]
* [[Discovery Net]]: one of the earliest examples of a scientific workflow system, later commercialized as InforSense which then acquired by IDBS.
* [[Galaxy (computational biology)|Galaxy]]: initially targeted at [[genomics]]
* [[OnlineHPC]] Online workflow designer based on [[Taverna workbench|Taverna]]
* [http://www.tavaxy.org Tavaxy]:<ref>{{cite doi|10.1186/1471-2105-13-77}}</ref> A cloud-based bioinformatics workflow system that integrates features from both Taverna and Galaxy for NGS data analysis.
* [[Taverna workbench]]:<ref>{{cite doi|10.1093/bioinformatics/bth361}}</ref> an early e-Science system widely used in bioinformatics
* [[VisTrails]]
==Comparisons between workflow systems==
With a large number of bioinformatics workflow systems to chose from, it becomes difficult to understand and compare the features of the different workflow systems. There has been little work conducted in evaluating and comparing the systems from a bioinformatician's perspective, especially when it comes to comparing the data types they can deal with, the in-built functionalities that are provided to the user or even their performance or usability. Examples of existing comparisons include
* The paper "Scientific workflow systems-can one size fit all?",<ref>
{{Citation
| last1 = Curcin | first1 = V
| last2 = Ghanem| first2 = M
| title = Scientific workflow systems - can one size fit all?
| series = Biomedical Engineering Conference, 2008. CIBEC 2008
| year = 2008
| publisher = IEEE
| doi = 10.1109/CIBEC.2008.4786077
| url = http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=4786077
}}
</ref> 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>
{{Citation
| last1 = Abouelhoda | first1 = M
| last2 = Ghanem| first2 = M
| last3 = Alaa| first3 = S
| title = Meta-workflows: pattern-based interoperability between Galaxy and Taverna
| series = Wands '10 Proceedings of the 1st International Workshop on Workflow Approaches to New Data-centric Science
| year = 2010
| publisher = ACM
| doi = 10.1145/1833398.1833400
}}
</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>
{{Citation
| last1 = Nyrönen | first1 = TH
| last2 = Laitinen | first2 = J et al.
| title = Delivering ICT infrastructure for biomedical research
| series = Proceedings of the WICSA/ECSA 2012 Companion Volume (WICSA/ECSA '12)
| year = 2012
| publisher = ACM
| url = http://dl.acm.org/citation.cfm?id=2362006
| doi = 10.1145/2361999.2362006
}}
</ref> compares two workflow systems, [[Anduril (workflow engine)|Anduril]] and [http://chipster.csc.fi/ Chipster], in terms of infrastructure requirements in a cloud-delivery model.
== See also ==
{{Empty section|date=July 2013}}
==References==
{{Reflist}}
==External links==
* {{cite doi|10.1002/cpe.993}}
* {{cite doi|10.1145/1084805.1084814}} from the ACM [[SIGMOD]] Record
* {{cite doi|10.1109/CIBEC.2008.4786077}} paper in CIBEC'08 comparing multiple workflow systems for bioinformatics applications
{{DEFAULTSORT:Bioinformatics workflow management systems}}
[[Category:Bioinformatics]]
[[Category:Bioinformatics software]]
[[Category:Lists of software]]
[[Category:Workflow technology]]
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