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Items: 1 to 20 of 151

1.

BioContainers: an open-source and community-driven framework for software standardization.

da Veiga Leprevost F, Grüning BA, Alves Aflitos S, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Vera Alvarez R, Griss J, Nesvizhskii AI, Perez-Riverol Y.

Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192.

2.

OLS Client and OLS Dialog: Open Source Tools to Annotate Public Omics Datasets.

Perez-Riverol Y, Ternent T, Koch M, Barsnes H, Vrousgou O, Jupp S, Vizcaíno JA.

Proteomics. 2017 Oct;17(19). doi: 10.1002/pmic.201700244.

3.

Community-driven computational biology with Debian Linux.

Möller S, Krabbenhöft HN, Tille A, Paleino D, Williams A, Wolstencroft K, Goble C, Holland R, Belhachemi D, Plessy C.

BMC Bioinformatics. 2010 Dec 21;11 Suppl 12:S5. doi: 10.1186/1471-2105-11-S12-S5.

4.

Goldilocks: a tool for identifying genomic regions that are 'just right'.

Nicholls SM, Clare A, Randall JC.

Bioinformatics. 2016 Jul 1;32(13):2047-9. doi: 10.1093/bioinformatics/btw116. Epub 2016 Mar 7.

5.

Bioclipse: an open source workbench for chemo- and bioinformatics.

Spjuth O, Helmus T, Willighagen EL, Kuhn S, Eklund M, Wagener J, Murray-Rust P, Steinbeck C, Wikberg JE.

BMC Bioinformatics. 2007 Feb 22;8:59.

6.

Bringing numerous methods for expression and promoter analysis to a public cloud computing service.

Polanski K, Gao B, Mason SA, Brown P, Ott S, Denby KJ, Wild DL.

Bioinformatics. 2018 Mar 1;34(5):884-886. doi: 10.1093/bioinformatics/btx692.

7.

Dugong: a Docker image, based on Ubuntu Linux, focused on reproducibility and replicability for bioinformatics analyses.

Menegidio FB, Jabes DL, Costa de Oliveira R, Nunes LR.

Bioinformatics. 2018 Feb 1;34(3):514-515. doi: 10.1093/bioinformatics/btx554.

PMID:
28968637
8.

The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud.

Wolstencroft K, Haines R, Fellows D, Williams A, Withers D, Owen S, Soiland-Reyes S, Dunlop I, Nenadic A, Fisher P, Bhagat J, Belhajjame K, Bacall F, Hardisty A, Nieva de la Hidalga A, Balcazar Vargas MP, Sufi S, Goble C.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W557-61. doi: 10.1093/nar/gkt328. Epub 2013 May 2.

9.

ms-data-core-api: an open-source, metadata-oriented library for computational proteomics.

Perez-Riverol Y, Uszkoreit J, Sanchez A, Ternent T, Del Toro N, Hermjakob H, Vizcaíno JA, Wang R.

Bioinformatics. 2015 Sep 1;31(17):2903-5. doi: 10.1093/bioinformatics/btv250. Epub 2015 Apr 24.

10.

Scalable computing for evolutionary genomics.

Prins P, Belhachemi D, Möller S, Smant G.

Methods Mol Biol. 2012;856:529-45. doi: 10.1007/978-1-61779-585-5_22.

PMID:
22399474
11.

Visual Omics Explorer (VOE): a cross-platform portal for interactive data visualization.

Kim B, Ali T, Hosmer S, Krampis K.

Bioinformatics. 2016 Jul 1;32(13):2050-2. doi: 10.1093/bioinformatics/btw119. Epub 2016 Mar 7.

12.

CoreFlow: a computational platform for integration, analysis and modeling of complex biological data.

Pasculescu A, Schoof EM, Creixell P, Zheng Y, Olhovsky M, Tian R, So J, Vanderlaan RD, Pawson T, Linding R, Colwill K.

J Proteomics. 2014 Apr 4;100:167-73. doi: 10.1016/j.jprot.2014.01.023. Epub 2014 Feb 3.

PMID:
24503186
13.

RepExplore: addressing technical replicate variance in proteomics and metabolomics data analysis.

Glaab E, Schneider R.

Bioinformatics. 2015 Jul 1;31(13):2235-7. doi: 10.1093/bioinformatics/btv127. Epub 2015 Feb 25.

14.

GUIdock-VNC: using a graphical desktop sharing system to provide a browser-based interface for containerized software.

Mittal V, Hung LH, Keswani J, Kristiyanto D, Lee SB, Yeung KY.

Gigascience. 2017 Apr 1;6(4):1-6. doi: 10.1093/gigascience/giw013.

15.

Reproducible bioinformatics project: a community for reproducible bioinformatics analysis pipelines.

Kulkarni N, Alessandrì L, Panero R, Arigoni M, Olivero M, Ferrero G, Cordero F, Beccuti M, Calogero RA.

BMC Bioinformatics. 2018 Oct 15;19(Suppl 10):349. doi: 10.1186/s12859-018-2296-x.

16.

An architecture for genomics analysis in a clinical setting using Galaxy and Docker.

Digan W, Countouris H, Barritault M, Baudoin D, Laurent-Puig P, Blons H, Burgun A, Rance B.

Gigascience. 2017 Nov 1;6(11):1-9. doi: 10.1093/gigascience/gix099.

17.

TOGGLE: toolbox for generic NGS analyses.

Monat C, Tranchant-Dubreuil C, Kougbeadjo A, Farcy C, Ortega-Abboud E, Amanzougarene S, Ravel S, Agbessi M, Orjuela-Bouniol J, Summo M, Sabot F.

BMC Bioinformatics. 2015 Nov 9;16:374. doi: 10.1186/s12859-015-0795-6.

18.

JMS: An Open Source Workflow Management System and Web-Based Cluster Front-End for High Performance Computing.

Brown DK, Penkler DL, Musyoka TM, Bishop ÖT.

PLoS One. 2015 Aug 17;10(8):e0134273. doi: 10.1371/journal.pone.0134273. eCollection 2015.

19.

Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics.

Giacomoni F, Le Corguillé G, Monsoor M, Landi M, Pericard P, Pétéra M, Duperier C, Tremblay-Franco M, Martin JF, Jacob D, Goulitquer S, Thévenot EA, Caron C.

Bioinformatics. 2015 May 1;31(9):1493-5. doi: 10.1093/bioinformatics/btu813. Epub 2014 Dec 19.

20.

Phenopolis: an open platform for harmonization and analysis of genetic and phenotypic data.

Pontikos N, Yu J, Moghul I, Withington L, Blanco-Kelly F, Vulliamy T, Wong TLE, Murphy C, Cipriani V, Fiorentino A, Arno G, Greene D, Jacobsen JOB, Clark T, Gregory DS, Nemeth AM, Halford S, Inglehearn CF, Downes S, Black GC, Webster AR, Hardcastle AJ; UKIRDC, Plagnol V.

Bioinformatics. 2017 Aug 1;33(15):2421-2423. doi: 10.1093/bioinformatics/btx147.

PMID:
28334266

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