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In alphabetical order, some examples of bioinformatics workflow management systems include:
* [[Anduril (workflow engine)|Anduril]] bioinformatics and image analysis
* [[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>{{
| 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
Line 46 ⟶ 89:
| doi = 10.1093/bioinformatics/bts091
}}</ref>
* Chipster: a user-friendly analysis software for microarray data<ref name=chipster>{{
| pmid = 21999641 | | 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>{{
| last1 = Goecks | first1 = J.
* GeneProf: web based functional genomics experiments, e.g. RNA-seq or ChIP-seq<ref>{{cite pmid| 22205509|noedit}}</ref>▼
| last2 = Nekrutenko | first2 = A.
| last3 = Taylor | first3 = J.
| last4 = Galaxy Team | first4 = T.
| title = Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
| doi = 10.1186/gb-2010-11-8-r86
| journal = Genome Biology
| volume = 11
| issue = 8
| pages = R86
| year = 2010
| pmid = 20738864
| pmc =2945788
}}</ref>
▲* GeneProf: web based functional genomics experiments, e.g. RNA-seq or ChIP-seq<ref>{{
| 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 doi|10.1016/j.compbiolchem.2007.08.009|noedit}}</ref>
* [[OnlineHPC]] Online workflow designer based on [[Taverna workbench|Taverna]]
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