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Items: 1 to 20 of 111

1.

XiP: a computational environment to create, extend and share workflows.

Nagasaki M, Fujita A, Sekiya Y, Saito A, Ikeda E, Li C, Miyano S.

Bioinformatics. 2013 Jan 1;29(1):137-9. doi: 10.1093/bioinformatics/bts630. Epub 2012 Oct 25.

2.

JUICE: a data management system that facilitates the analysis of large volumes of information in an EST project workflow.

Latorre M, Silva H, Saba J, Guziolowski C, Vizoso P, Martinez V, Maldonado J, Morales A, Caroca R, Cambiazo V, Campos-Vargas R, Gonzalez M, Orellana A, Retamales J, Meisel LA.

BMC Bioinformatics. 2006 Nov 23;7:513.

3.

Taverna: a tool for building and running workflows of services.

Hull D, Wolstencroft K, Stevens R, Goble C, Pocock MR, Li P, Oinn T.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W729-32.

4.

Workflows for microarray data processing in the Kepler environment.

Stropp T, McPhillips T, Ludäscher B, Bieda M.

BMC Bioinformatics. 2012 May 17;13:102. doi: 10.1186/1471-2105-13-102.

5.

Applications of the pipeline environment for visual informatics and genomics computations.

Dinov ID, Torri F, Macciardi F, Petrosyan P, Liu Z, Zamanyan A, Eggert P, Pierce J, Genco A, Knowles JA, Clark AP, Van Horn JD, Ames J, Kesselman C, Toga AW.

BMC Bioinformatics. 2011 Jul 26;12:304. doi: 10.1186/1471-2105-12-304.

6.

TOPP--the OpenMS proteomics pipeline.

Kohlbacher O, Reinert K, Gröpl C, Lange E, Pfeifer N, Schulz-Trieglaff O, Sturm M.

Bioinformatics. 2007 Jan 15;23(2):e191-7.

PMID:
17237091
7.

Constructing computational pipelines.

Halling-Brown M, Shepherd AJ.

Methods Mol Biol. 2008;453:451-70. doi: 10.1007/978-1-60327-429-6_24.

PMID:
18712319
8.

A lightweight, flow-based toolkit for parallel and distributed bioinformatics pipelines.

Cieślik M, Mura C.

BMC Bioinformatics. 2011 Feb 25;12:61. doi: 10.1186/1471-2105-12-61.

9.

Pegasys: software for executing and integrating analyses of biological sequences.

Shah SP, He DY, Sawkins JN, Druce JC, Quon G, Lett D, Zheng GX, Xu T, Ouellette BF.

BMC Bioinformatics. 2004 Apr 19;5:40.

10.

Proteomics to go: Proteomatic enables the user-friendly creation of versatile MS/MS data evaluation workflows.

Specht M, Kuhlgert S, Fufezan C, Hippler M.

Bioinformatics. 2011 Apr 15;27(8):1183-4. doi: 10.1093/bioinformatics/btr081. Epub 2011 Feb 16.

PMID:
21325302
11.

The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button.

Swertz MA, Dijkstra M, Adamusiak T, van der Velde JK, Kanterakis A, Roos ET, Lops J, Thorisson GA, Arends D, Byelas G, Muilu J, Brookes AJ, de Brock EO, Jansen RC, Parkinson H.

BMC Bioinformatics. 2010 Dec 21;11 Suppl 12:S12. doi: 10.1186/1471-2105-11-S12-S12.

12.

synbreed: a framework for the analysis of genomic prediction data using R.

Wimmer V, Albrecht T, Auinger HJ, Schön CC.

Bioinformatics. 2012 Aug 1;28(15):2086-7. doi: 10.1093/bioinformatics/bts335. Epub 2012 Jun 10.

PMID:
22689388
13.

TOPPAS: a graphical workflow editor for the analysis of high-throughput proteomics data.

Junker J, Bielow C, Bertsch A, Sturm M, Reinert K, Kohlbacher O.

J Proteome Res. 2012 Jul 6;11(7):3914-20. doi: 10.1021/pr300187f. Epub 2012 May 24.

PMID:
22583024
14.

PREDA: an R-package to identify regional variations in genomic data.

Ferrari F, Solari A, Battaglia C, Bicciato S.

Bioinformatics. 2011 Sep 1;27(17):2446-7. doi: 10.1093/bioinformatics/btr404. Epub 2011 Jul 7.

PMID:
21742634
15.

A graph-based approach for designing extensible pipelines.

Rodrigues MR, Magalhães WC, Machado M, Tarazona-Santos E.

BMC Bioinformatics. 2012 Jul 12;13:163. doi: 10.1186/1471-2105-13-163.

16.

BioMAJ: a flexible framework for databanks synchronization and processing.

Filangi O, Beausse Y, Assi A, Legrand L, Larré JM, Martin V, Collin O, Caron C, Leroy H, Allouche D.

Bioinformatics. 2008 Aug 15;24(16):1823-5. doi: 10.1093/bioinformatics/btn325. Epub 2008 Jun 30.

17.

Data partitioning enables the use of standard SOAP Web Services in genome-scale workflows.

Sztromwasser P, Puntervoll P, Petersen K.

J Integr Bioinform. 2011 Jul 26;8(2):163. doi: 10.2390/biecoll-jib-2011-163.

PMID:
21788681
18.

CalcTav--integration of a spreadsheet and Taverna workbench.

Sroka J, Krupa Ł, Kierzek AM, Tyszkiewicz J.

Bioinformatics. 2011 Sep 15;27(18):2618-9. doi: 10.1093/bioinformatics/btr425. Epub 2011 Jul 19.

PMID:
21775305
19.

RGG: a general GUI Framework for R scripts.

Visne I, Dilaveroglu E, Vierlinger K, Lauss M, Yildiz A, Weinhaeusel A, Noehammer C, Leisch F, Kriegner A.

BMC Bioinformatics. 2009 Mar 2;10:74. doi: 10.1186/1471-2105-10-74.

20.

Bpipe: a tool for running and managing bioinformatics pipelines.

Sadedin SP, Pope B, Oshlack A.

Bioinformatics. 2012 Jun 1;28(11):1525-6. doi: 10.1093/bioinformatics/bts167. Epub 2012 Apr 12.

PMID:
22500002

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