Content deleted Content added
added "A review of bioinformatic pipeline frameworks" |
→Examples: Sorting. Added link to Chipster. Added BPipe and Nextflow. |
||
Line 71:
| pmc =2703918
}}</ref>
* [http://bpipe.org Bpipe] - a tool for running and managing bioinformatics pipelines.
* [[UGENE]] provides a workflow management system that is installed on a local computer<ref>{{Cite journal▼
* [http://chipster.csc.fi Chipster]: a user-friendly analysis software for microarray data<ref name=chipster>{{Cite journal▼
| pmid = 22368248▼
| year = 2012▼
| author1 = Okonechnikov▼
| first1 = K▼
| title = Unipro UGENE: A unified bioinformatics toolkit▼
| journal = Bioinformatics (Oxford, England)▼
| volume = 28▼
| issue = 8▼
| pages = 1166–7▼
| last2 = Golosova▼
| first2 = O▼
| last3 = Fursov▼
| first3 = M▼
| last4 = Ugene▼
| first4 = Team▼
| doi = 10.1093/bioinformatics/bts091▼
}}</ref>▼
▲* Chipster: a user-friendly analysis software for microarray data<ref name=chipster>{{Cite journal
| pmid = 21999641
| pmc = 3215701
Line 116 ⟶ 99:
| 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.
Line 163 ⟶ 145:
}}</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>
* [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
▲| year = 2012
▲| author1 = Okonechnikov
▲| first1 = K
▲| title = Unipro UGENE: A unified bioinformatics toolkit
▲| journal = Bioinformatics (Oxford, England)
▲| volume = 28
▲| issue = 8
▲| pages = 1166–7
▲| last2 = Golosova
▲| first2 = O
▲| last3 = Fursov
▲| first3 = M
▲| last4 = Ugene
▲| first4 = Team
▲| doi = 10.1093/bioinformatics/bts091
▲}}</ref>
* [[VisTrails]]<ref>{{Cite journal | doi = 10.1109/VISUAL.2005.1532788 | title = VisTrails: enabling interactive multiple-view visualizations| year = 2005 | journal=VIS 05. IEEE Visualization, 2005.}}</ref>
| |||