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Bioinformatics workflow management system
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<h2 id="examples">Examples</h2> <p>In alphabetical order, some examples of bioinformatics workflow management systems include: </p> <ul><li><a href="/facts/Anduril_(workflow_engine)/ePzjrt8b">Anduril</a> bioinformatics and image analysis<a class="footnote-ref" id="fnref:4" href="#fn:4"><sup>4</sup></a><a class="footnote-ref" id="fnref:5" href="#fn:5"><sup>5</sup></a></li> <li><a href="/facts/BioBIKE/1kb2s5Rf">BioBIKE</a>: a <a href="/facts/Web_application/BLkF3BIN">Web-based</a>, programmable, integrated biological knowledge base<a class="footnote-ref" id="fnref:6" href="#fn:6"><sup>6</sup></a></li> <li><a href="/facts/CLC_bio/GvTDDdGC">CLC bio</a>, a bioinformatics analysis and workflow management platform from <a href="/facts/Qiagen/zpepVIfc">QIAGEN Digital Insights</a>.</li> <li><a href="/facts/Clone_manager/sRujkLHu">Clone Manager</a> from Sci-Ed.</li> <li><a href="/facts/Cuneiform_(programming_language)/R9QQ1SrL">Cuneiform</a>: A functional workflow language for large-scale data analysis<a class="footnote-ref" id="fnref:7" href="#fn:7"><sup>7</sup></a></li> <li><a href="/facts/Discovery_Net/Yrm0KI2U">Discovery Net</a>: one of the earliest examples of a scientific workflow system, later commercialized as InforSense which was then acquired by IDBS.</li> <li><a href="/facts/Galaxy_(computational_biology)/sQbA61Qy">Galaxy</a>: initially targeted at <a href="/facts/Genomics/pVU3BGpL">genomics</a><a class="footnote-ref" id="fnref:8" href="#fn:8"><sup>8</sup></a></li> <li><a href="/facts/GenePattern/sh0LuEw9">GenePattern</a>: A powerful scientific workflow system that provides access to hundreds of genomic analysis tools.<a class="footnote-ref" id="fnref:9" href="#fn:9"><sup>9</sup></a></li> <li><a href="/facts/KNIME/232lez5G">KNIME</a> the Konstanz Information Miner<a class="footnote-ref" id="fnref:10" href="#fn:10"><sup>10</sup></a></li> <li><a href="/facts/OnlineHPC/z8MnWJUY">OnlineHPC</a> Online workflow designer based on <a href="/facts/Taverna_workbench/Y2v63Cax">Taverna</a></li> <li>Playbook Workflow Builder Flexible workflow builder for bioinformatics applications based on API services. Initially developed for the NIH CFDE Common Fund program </li> <li><a href="/facts/UGENE/mjzAH719">UGENE</a> provides a workflow management system that is installed on a local computer<a class="footnote-ref" id="fnref:11" href="#fn:11"><sup>11</sup></a></li> <li><a href="/facts/VisTrails/5rLvNxhj">VisTrails</a><a class="footnote-ref" id="fnref:12" href="#fn:12"><sup>12</sup></a></li></ul> <h2 id="comparisons-between-workflow-systems">Comparisons between workflow systems</h2> <p>With a large number of bioinformatics workflow systems to choose from,<a class="footnote-ref" id="fnref:13" href="#fn:13"><sup>13</sup></a> 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: </p> <ul><li>The paper "Scientific workflow systems-can one size fit all?",<a class="footnote-ref" id="fnref:14" href="#fn:14"><sup>14</sup></a> which provides a high-level framework for comparing workflow systems based on their control flow and data flow properties. The systems compared include <a href="/facts/Discovery_Net/Yrm0KI2U">Discovery Net</a>, <a href="/facts/Taverna_workbench/Y2v63Cax">Taverna</a>, Triana, <a href="/facts/Kepler_scientific_workflow_system/x2PphRu1">Kepler</a> as well as Yawl and <a href="/facts/Business_Process_Execution_Language/HUmdnJEb">BPEL</a>.</li> <li>The paper "Meta-workflows: pattern-based interoperability between Galaxy and Taverna"<a class="footnote-ref" id="fnref:15" href="#fn:15"><sup>15</sup></a> which provides a more user-oriented comparison between <a href="/facts/Taverna_workbench/Y2v63Cax">Taverna</a> and <a href="/facts/Galaxy_(computational_biology)/sQbA61Qy">Galaxy</a> in the context of enabling interoperability between both systems.</li></ul> <ul><li>The infrastructure paper "Delivering ICT Infrastructure for Biomedical Research"<a class="footnote-ref" id="fnref:16" href="#fn:16"><sup>16</sup></a> compares two workflow systems, <a href="/facts/Anduril_(workflow_engine)/ePzjrt8b">Anduril</a> and Chipster,<a class="footnote-ref" id="fnref:17" href="#fn:17"><sup>17</sup></a> in terms of infrastructure requirements in a cloud-delivery model.</li></ul> <ul><li>The paper "A review of bioinformatic pipeline frameworks"<a class="footnote-ref" id="fnref:18" href="#fn:18"><sup>18</sup></a> 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".</li></ul> <h2 id="references">References</h2> <ol> <li id="fn:1"><p>Oinn, T.; Greenwood, M.; Addis, M.; Alpdemir, M. N.; Ferris, J.; Glover, K.; Goble, C.; Goderis, A.; Hull, D.; Marvin, D.; Li, P.; Lord, P.; Pocock, M. R.; Senger, M.; Stevens, R.; Wipat, A.; Wroe, C. (2006). "Taverna: Lessons in creating a workflow environment for the life sciences" (PDF). Concurrency and Computation: Practice and Experience. 18 (10): 1067–1100. doi:10.1002/cpe.993. S2CID 10219281. <a href="/wiki/Carole_Goble" target="_blank">/wiki/Carole_Goble</a> <a href="#fnref:1" class="footnote-back-ref">↩</a></p></li> <li id="fn:2"><p>Yu, J.; Buyya, R. (2005). "A taxonomy of scientific workflow systems for grid computing". ACM SIGMOD Record. 34 (3): 44. CiteSeerX 10.1.1.63.3176. doi:10.1145/1084805.1084814. S2CID 538714. <a href="/wiki/CiteSeerX_(identifier)" target="_blank">/wiki/CiteSeerX_(identifier)</a> <a href="#fnref:2" class="footnote-back-ref">↩</a></p></li> <li id="fn:3"><p>Curcin, V.; Ghanem, M. (2008). "Scientific workflow systems - can one size fit all?". 2008 Cairo International Biomedical Engineering Conference. pp. 1–9. doi:10.1109/CIBEC.2008.4786077. ISBN 978-1-4244-2694-2. S2CID 1885579. <a href="978-1-4244-2694-2" target="_blank">978-1-4244-2694-2</a> <a href="#fnref:3" class="footnote-back-ref">↩</a></p></li> <li id="fn:4"><p>"Anduril workflow website". <a href="http://www.anduril.org" target="_blank">http://www.anduril.org</a> <a href="#fnref:4" class="footnote-back-ref">↩</a></p></li> <li id="fn:5"><p>Ovaska, Kristian; Laakso, Marko; Haapa-Paananen, Saija; Louhimo, Riku; Chen, Ping; Aittomäki, Viljami; Valo, Erkka; Núñez-Fontarnau, Javier; Rantanen, Ville (2010-09-07). "Large-scale data integration framework provides a comprehensive view on glioblastoma multiforme". Genome Medicine. 2 (9): 65. doi:10.1186/gm186. ISSN 1756-994X. PMC 3092116. PMID 20822536. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3092116" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3092116</a> <a href="#fnref:5" class="footnote-back-ref">↩</a></p></li> <li id="fn:6"><p>Elhai, J.; Taton, A.; Massar, J.; Myers, J. K.; Travers, M.; Casey, J.; Slupesky, M.; Shrager, J. (2009). "BioBIKE: A Web-based, programmable, integrated biological knowledge base". Nucleic Acids Research. 37 (Web Server issue): W28 – W32. doi:10.1093/nar/gkp354. PMC 2703918. PMID 19433511. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703918" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703918</a> <a href="#fnref:6" class="footnote-back-ref">↩</a></p></li> <li id="fn:7"><p>Brandt, Jörgen; Bux, Marc N.; Leser, Ulf (2015). "Cuneiform: A functional language for large scale scientific data analysis" (PDF). Proceedings of the Workshops of the EDBT/ICDT. 1330: 17–26. <a href="http://ceur-ws.org/Vol-1330/paper-03.pdf" target="_blank">http://ceur-ws.org/Vol-1330/paper-03.pdf</a> <a href="#fnref:7" class="footnote-back-ref">↩</a></p></li> <li id="fn:8"><p>Goecks, J.; Nekrutenko, A.; Taylor, J.; Galaxy Team, T. (2010). "Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences". Genome Biology. 11 (8): R86. doi:10.1186/gb-2010-11-8-r86. PMC 2945788. PMID 20738864. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2945788" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2945788</a> <a href="#fnref:8" class="footnote-back-ref">↩</a></p></li> <li id="fn:9"><p>Reich, Michael; et al. (2006). "GenePattern 2.0". Nature Genetics. 38 (1): 500–5001. doi:10.1038/ng0506-500. PMID 16642009. S2CID 5503897. <a href="/wiki/Doi_(identifier)" target="_blank">/wiki/Doi_(identifier)</a> <a href="#fnref:9" class="footnote-back-ref">↩</a></p></li> <li id="fn:10"><p>Tiwari, Abhishek; Sekhar, Arvind K.T. (2007). "Workflow based framework for life science informatics". Computational Biology and Chemistry. 31 (5–6): 305–319. doi:10.1016/j.compbiolchem.2007.08.009. PMID 17931570. <a href="/wiki/Doi_(identifier)" target="_blank">/wiki/Doi_(identifier)</a> <a href="#fnref:10" class="footnote-back-ref">↩</a></p></li> <li id="fn:11"><p>Okonechnikov, K; Golosova, O; Fursov, M; Ugene, Team (2012). "Unipro UGENE: A unified bioinformatics toolkit". Bioinformatics. 28 (8): 1166–7. doi:10.1093/bioinformatics/bts091. PMID 22368248. <a href="https://doi.org/10.1093%2Fbioinformatics%2Fbts091" target="_blank">https://doi.org/10.1093%2Fbioinformatics%2Fbts091</a> <a href="#fnref:11" class="footnote-back-ref">↩</a></p></li> <li id="fn:12"><p>Bavoil, L.; Callahan, S.P.; Crossno, P.J.; Freire, J.; Scheidegger, C.E.; Silva, C.T.; Vo, H.T. (2005). "VisTrails: Enabling Interactive Multiple-View Visualizations". VIS 05. IEEE Visualization, 2005. pp. 135–142. doi:10.1109/VISUAL.2005.1532788. ISBN 978-0-7803-9462-9. <a href="978-0-7803-9462-9" target="_blank">978-0-7803-9462-9</a> <a href="#fnref:12" class="footnote-back-ref">↩</a></p></li> <li id="fn:13"><p>"Existing Workflow systems". Common Workflow Language wiki. Archived from the original on 2019-10-17. Retrieved 2019-10-17. <a href="https://s.apache.org/existing-workflow-systems" target="_blank">https://s.apache.org/existing-workflow-systems</a> <a href="#fnref:13" class="footnote-back-ref">↩</a></p></li> <li id="fn:14"><p>Curcin, V.; Ghanem, M. (2008). "Scientific workflow systems - can one size fit all?". 2008 Cairo International Biomedical Engineering Conference. pp. 1–9. doi:10.1109/CIBEC.2008.4786077. ISBN 978-1-4244-2694-2. S2CID 1885579. <a href="978-1-4244-2694-2" target="_blank">978-1-4244-2694-2</a> <a href="#fnref:14" class="footnote-back-ref">↩</a></p></li> <li id="fn:15"><p>Abouelhoda, M.; Alaa, S.; Ghanem, M. (2010). "Meta-workflows". Proceedings of the 1st International Workshop on Workflow Approaches to New Data-centric Science - Wands '10. p. 1. doi:10.1145/1833398.1833400. ISBN 9781450301886. S2CID 17343728. <a href="9781450301886" target="_blank">9781450301886</a> <a href="#fnref:15" class="footnote-back-ref">↩</a></p></li> <li id="fn:16"><p>Nyrönen, TH; Laitinen, J; et al. (2012), Delivering ICT infrastructure for biomedical research, Proceedings of the WICSA/ECSA 2012 Companion Volume (WICSA/ECSA '12), ACM, pp. 37–44, doi:10.1145/2361999.2362006, ISBN 9781450315685, S2CID 18199745 <a href="9781450315685" target="_blank">9781450315685</a> <a href="#fnref:16" class="footnote-back-ref">↩</a></p></li> <li id="fn:17"><p>Kallio, M. A.; Tuimala, J. T.; Hupponen, T; Klemelä, P; Gentile, M; Scheinin, I; Koski, M; Käki, J; Korpelainen, E. I. (2011). "Chipster: User-friendly analysis software for microarray and other high-throughput data". BMC Genomics. 12: 507. doi:10.1186/1471-2164-12-507. PMC 3215701. PMID 21999641. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3215701" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3215701</a> <a href="#fnref:17" class="footnote-back-ref">↩</a></p></li> <li id="fn:18"><p>Leipzig J (2016). "A review of bioinformatic pipeline frameworks". Briefings in Bioinformatics. 18 (3): 530–536. doi:10.1093/bib/bbw020. PMC 5429012. PMID 27013646. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5429012" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5429012</a> <a href="#fnref:18" class="footnote-back-ref">↩</a></p></li> </ol>