Bioinformatics workflow management system: Difference between revisions

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{{Redirect|IDBS||IDB (disambiguation){{!}}IDB}}{{Merging|target=Scientific workflow system|discuss=Talk:Bioinformatics workflow management system#Merge_to_Scientific_workflow_system|spacetype=article|dir=to}}{{Example farm|date=February 2012}}

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. | author-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 | 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 | citeseerx = 10.1.1.63.3176 | s2cid = 538714 }}</ref><ref name="CIBEC 2008">{{Cite book | last1 = Curcin | first1 = V. | last2 = Ghanem | first2 = M. | title = 2008 Cairo International Biomedical Engineering Conference | chapter = Scientific workflow systems - can one size fit all? | doi = 10.1109/CIBEC.2008.4786077 | pages = 1–9 | year = 2008 | isbn = 978-1-4244-2694-2 | s2cid = 1885579 }}</ref>

==Examples==

In alphabetical order, some examples of bioinformatics workflow management systems include:

* [[Anduril (workflow engine)|Anduril]] bioinformatics and image analysis<ref>{{Cite web|url=http://www.anduril.org|title=Anduril workflow website}}</ref><ref>{{Cite journal|last1=Ovaska|first1=Kristian|last2=Laakso|first2=Marko|last3=Haapa-Paananen|first3=Saija|last4=Louhimo|first4=Riku|last5=Chen|first5=Ping|last6=Aittomäki|first6=Viljami|last7=Valo|first7=Erkka|last8=Núñez-Fontarnau|first8=Javier|last9=Rantanen|first9=Ville|date=2010-09-07|title=Large-scale data integration framework provides a comprehensive view on glioblastoma multiforme|journal=Genome Medicine|volume=2|issue=9|pages=65|doi=10.1186/gm186|issn=1756-994X|pmc=3092116|pmid=20822536 |doi-access=free }}</ref>

* [[BioBIKE]]: a [[Web application|Web-based]], programmable, integrated biological knowledge base<ref>{{Cite journal

| last1 = Elhai | first1 = J.

| last2 = Taton | first2 = A.

| last3 = Massar | first3 = J.

| last4 = Myers | first4 = J. K.

| last5 = Travers | first5 = M.

| last6 = Casey | first6 = J.

| last7 = Slupesky | first7 = M.

| last8 = Shrager | first8 = J.

| doi = 10.1093/nar/gkp354

| title = BioBIKE: A Web-based, programmable, integrated biological knowledge base

| journal = Nucleic Acids Research

| volume = 37

| issue = Web Server issue

| pages = W28–W32

| year = 2009

| pmid = 19433511

| pmc =2703918

}}</ref>

*[[CLC bio]], a bioinformatics analysis and workflow management platform from [[Qiagen|QIAGEN Digital Insights]].

*[[Clone manager|Clone Manager]] from Sci-Ed.

*[[Cuneiform (programming language)|Cuneiform]]: A functional workflow language for large-scale data analysis<ref>{{Cite journal

| last1 = Brandt | first1 = Jörgen

| last2 = Bux | first2 = Marc N.

| last3 = Leser | first3 = Ulf

| title = Cuneiform: A functional language for large scale scientific data analysis

| journal = Proceedings of the Workshops of the EDBT/ICDT

| volume = 1330

| pages = 17–26

| year = 2015

| url = http://ceur-ws.org/Vol-1330/paper-03.pdf

}}</ref>

* [[Discovery Net]]: one of the earliest examples of a scientific workflow system, later commercialized as InforSense which was then acquired by IDBS.{{citation needed|date=September 2016}}

*[[Galaxy (computational biology)|Galaxy]]: initially targeted at [[genomics]]<ref>{{Cite journal

| last1 = Goecks | first1 = J.

| 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

| doi-access = free

}}</ref>

* [[GenePattern]]: A powerful scientific workflow system that provides access to hundreds of genomic analysis tools.<ref>{{Cite journal

| pmid = 16642009

| year = 2006

| last1 = Reich

| first1 = Michael

| title = GenePattern 2.0

| journal = Nature Genetics

| volume = 38

| issue = 1

| pages = 500–5001

| doi = 10.1038/ng0506-500

| s2cid = 5503897

|display-authors=etal}}</ref>

* [[KNIME]] the Konstanz Information Miner<ref>{{Cite journal | doi = 10.1016/j.compbiolchem.2007.08.009| pmid = 17931570| title = Workflow based framework for life science informatics| journal = Computational Biology and Chemistry| year = 2007| volume=31| issue = 5–6| pages=305–319| last1 = Tiwari| first1 = Abhishek| last2 = Sekhar| first2 = Arvind K.T.}}</ref>

* [[OnlineHPC]] Online workflow designer based on [[Taverna workbench|Taverna]]{{citation needed|date=September 2016}}

* [[Playbook Workflow Builder]] Flexible workflow builder for bioinformatics applications based on API services. Initially developed for the NIH CFDE Common Fund program {{citation needed|date=September 2023}}

*[[UGENE]] provides a workflow management system that is installed on a local computer<ref>{{Cite journal

| pmid = 22368248

| year = 2012

| last1 = Okonechnikov

| first1 = K

| title = Unipro UGENE: A unified bioinformatics toolkit

| journal = Bioinformatics

| volume = 28

| issue = 8

| pages = 1166–7

| last2 = Golosova

| first2 = O

| last3 = Fursov

| first3 = M

| last4 = Ugene

| first4 = Team

| doi = 10.1093/bioinformatics/bts091

| doi-access = free

}}</ref>

* [[VisTrails]]<ref>{{Cite book | doi = 10.1109/VISUAL.2005.1532788 | year = 2005 | pages = 135–142| last1 = Bavoil| first1 = L.| last2 = Callahan| first2 = S.P.| last3 = Crossno| first3 = P.J.| last4 = Freire| first4 = J.| last5 = Scheidegger| first5 = C.E.| last6 = Silva| first6 = C.T.| last7 = Vo| first7 = H.T.| title = VIS 05. IEEE Visualization, 2005| chapter = VisTrails: Enabling Interactive Multiple-View Visualizations| isbn = 978-0-7803-9462-9}}</ref>

==Comparisons between workflow systems==

With a large number of bioinformatics workflow systems to choose from,<ref>{{cite web|url=https://s.apache.org/existing-workflow-systems|title=Existing Workflow systems|website=Common Workflow Language wiki|archive-url=https://web.archive.org/web/20191017094453/https://github.com/common-workflow-language/common-workflow-language/wiki/Existing-Workflow-systems|archive-date=2019-10-17|url-status=live|access-date=2019-10-17}}</ref> 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 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 | 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>

{{Citation

| last1 = Nyrönen | first1 = TH

| last2 = Laitinen | first2 = J

| title = Delivering ICT infrastructure for biomedical research

| pages = 37–44

| series = Proceedings of the WICSA/ECSA 2012 Companion Volume (WICSA/ECSA '12)

| year = 2012

| publisher = ACM

| doi = 10.1145/2361999.2362006

|display-authors=etal| isbn = 9781450315685

| s2cid = 18199745

}}

</ref> compares two workflow systems, [[Anduril (workflow engine)|Anduril]] and Chipster,<ref name=chipster>{{Cite journal

| pmid = 21999641

| pmc = 3215701

| year = 2011

| last1 = 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

| doi-access = free

}}</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 |journal=Briefings in Bioinformatics |volume=18 |issue=3 |pages=530–536 |doi=10.1093/bib/bbw020 |pmid=27013646 |pmc=5429012 |name-list-style=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==

{{Reflist}}

[[Category:Bioinformatics software]]

[[Category:Workflow applications]]

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