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==Examples==
In alphabetical order, some examples of bioinformatics workflow management systems include:
* [[Anduril (workflow engine)|Anduril]] bioinformatics and image analysis{{cn}}
* [[BioExtract]]: a web-based system for querying biomolecular sequence data, executing analytic tools on the resulting extracts, and constructing workflows composed of such queries and tools.{{cn}}
* [[Anvaya Workflows]]: Anvaya is a software application consisting of interface to Bioinformatics tools and databases in a workflow environment, to execute the set of analyses tools in series or in parallel.<ref>{{Cite journal
| pmid = 22809419
| year = 2012
| author1 = Limaye
| first1 = B
| title = Anvaya: A workflows environment for automated genome analysis
| journal = Journal of bioinformatics and computational biology
| volume = 10
| issue = 4
| pages = 1250006
| last2 = Banerjee
| first2 = R
| last3 = Datta
| first3 = A
| last4 = Inamdar
| first4 = H
| last5 = Vats
| first5 = P
| last6 = Dahale
| first6 = S
| last7 = Bhandari
| first7 = A
| last8 = Ramakrishnan
| first8 = E. P.
| last9 = Tupakula
| first9 = R
| last10 = Malviya
| first10 = S
| last11 = Bayaskar
| first11 = A
| last12 = Gadhari
| first12 = R
| last13 = Jain
| first13 = S
| last14 = Gavane
| first14 = V
| last15 = Mahajan
| first15 = R
| last16 = Sunitha
| first16 = K
| last17 = Joshi
| first17 = R
| doi = 10.1142/S0219720012500060
}}</ref>
* [[BioExtract]]: a web-based system for querying biomolecular sequence data, executing analytic tools on the resulting extracts, and constructing workflows composed of such queries and tools.
* [[BioBIKE]]: a Web-based, programmable, integrated biological knowledge base<ref>{{Cite journal
| last1 = Elhai | first1 = J.
| pmc =2703918
}}</ref>
* [[Discovery Net]]: one of the earliest examples of a scientific workflow system, later commercialized as InforSense which was then acquired by IDBS.{{cn}}
* [http://bpipe.org Bpipe] - a tool for running and managing bioinformatics pipelines.
* [http://chipster.csc.fi Chipster]: a user-friendly analysis software for microarray data<ref name=chipster>{{Cite journal
| pmid = 21999641
| pmc = 3215701
| year = 2011
| author1 = Kallio
| first1 = M. A.
| title = Chipster: User-friendly analysis software for microarray and other high-throughput data
| journal = BMC Genomics
| volume = 12
| pages = 507
| last2 = Tuimala
| first2 = J. T.
| last3 = Hupponen
| first3 = T
| last4 = Klemelä
| first4 = P
| last5 = Gentile
| first5 = M
| last6 = Scheinin
| first6 = I
| last7 = Koski
| first7 = M
| last8 = Käki
| first8 = J
| last9 = Korpelainen
| first9 = E. I.
| doi = 10.1186/1471-2164-12-507
}}</ref>
* [[Discovery Net]]: one of the earliest examples of a scientific workflow system, later commercialized as InforSense which was then acquired by IDBS.
* [[Galaxy (computational biology)|Galaxy]]: initially targeted at [[genomics]]<ref>{{Cite journal
| last1 = Goecks | first1 = J.
| doi = 10.1038/ng0506-500
|display-authors=etal}}</ref>
* GeneProf: web based functional genomics experiments, e.g. RNA-seq or ChIP-seq<ref>{{Cite journal
| pmid = 22205509
| year = 2011
| author1 = Halbritter
| first1 = F
| title = Gene ''Prof'': Analysis of high-throughput sequencing experiments
| journal = Nature Methods
| volume = 9
| issue = 1
| pages = 7–8
| last2 = Vaidya
| first2 = H. J.
| last3 = Tomlinson
| first3 = S. R.
| doi = 10.1038/nmeth.1809
}}</ref>
* [[KNIME]] the Konstanz Information Miner<ref>{{Cite journal | doi = 10.1016/j.compbiolchem.2007.08.009| title = Workflow based framework for life science informatics| journal = Computational Biology and Chemistry| year = 2007| volume=31| pages=305–319}}</ref>
* [[OnlineHPC]] Online workflow designer based on [[Taverna workbench|Taverna]]{{cn}}
* [http://molquest.com/ MolQuest]: a comprehensive, easy-to-use desktop application for sequence analysis and molecular biology data management.
* [http://nextflow.io Nextflow] - A DSL for parallel and scalable computational pipelines.
* [[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>{{Cite journal | 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 | 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]]
* [[UGENE]] provides a workflow management system that is installed on a local computer<ref>{{Cite journal
| pmid = 22368248
| doi = 10.1145/2361999.2362006
|display-authors=etal}}
</ref> compares two workflow systems, [[Anduril (workflow engine)|Anduril]] and Chipster,<ref name=chipster/>{{Cite in terms of infrastructure requirements in a cloud-delivery model.journal
| pmid = 21999641
| pmc = 3215701
| year = 2011
| author1 = Kallio
| first1 = M. A.
| title = Chipster: User-friendly analysis software for microarray and other high-throughput data
| journal = BMC Genomics
| volume = 12
| pages = 507
| last2 = Tuimala
| first2 = J. T.
| last3 = Hupponen
| first3 = T
| last4 = Klemelä
| first4 = P
| last5 = Gentile
| first5 = M
| last6 = Scheinin
| first6 = I
| last7 = Koski
| first7 = M
| last8 = Käki
| first8 = J
| last9 = Korpelainen
| first9 = E. I.
| doi = 10.1186/1471-2164-12-507
}}</ref> in terms of infrastructure requirements in a cloud-delivery model.
* The paper "A review of bioinformatic pipeline frameworks" <ref>{{cite journal |last=Leipzig |first=J |date=2016 |title=A review of bioinformatic pipeline frameworks |url=http://bib.oxfordjournals.org/content/early/2016/03/23/bib.bbw020.full |journal=Briefings in bioinformatics |access-date=23 March 2016 |doi=10.1093/bib/bbw020 |pmid=27013646 |name-list-format=vanc }}
</ref> attempts to classify workflow management systems based on three dimensions: "using an implicit or explicit syntax, using a configuration, convention or class-based design paradigm and offering a command line or workbench interface".
==References==
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