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Items: 1 to 20 of 215

1.

Creating reusable tools from scripts: the Galaxy Tool Factory.

Lazarus R, Kaspi A, Ziemann M; Galaxy Team.

Bioinformatics. 2012 Dec 1;28(23):3139-40. doi: 10.1093/bioinformatics/bts573. Epub 2012 Sep 28.

2.

BioBlend.objects: metacomputing with Galaxy.

Leo S, Pireddu L, Cuccuru G, Lianas L, Soranzo N, Afgan E, Zanetti G.

Bioinformatics. 2014 Oct;30(19):2816-7. doi: 10.1093/bioinformatics/btu386. Epub 2014 Jun 12.

3.

Analysis of next-generation sequencing data using Galaxy.

Blankenberg D, Hillman-Jackson J.

Methods Mol Biol. 2014;1150:21-43. doi: 10.1007/978-1-4939-0512-6_2.

PMID:
24743989
4.

Osiris: accessible and reproducible phylogenetic and phylogenomic analyses within the Galaxy workflow management system.

Oakley TH, Alexandrou MA, Ngo R, Pankey MS, Churchill CK, Chen W, Lopker KB.

BMC Bioinformatics. 2014 Jul 2;15:230. doi: 10.1186/1471-2105-15-230.

5.

Updating annotations with the distributed annotation system and the automated sequence annotation pipeline.

Speier W, Ochs MF.

Bioinformatics. 2012 Nov 1;28(21):2858-9. doi: 10.1093/bioinformatics/bts530. Epub 2012 Sep 3.

6.

ballaxy: web services for structural bioinformatics.

Hildebrandt AK, Stöckel D, Fischer NM, de la Garza L, Krüger J, Nickels S, Röttig M, Schärfe C, Schumann M, Thiel P, Lenhof HP, Kohlbacher O, Hildebrandt A.

Bioinformatics. 2015 Jan 1;31(1):121-2. doi: 10.1093/bioinformatics/btu574. Epub 2014 Sep 2.

PMID:
25183489
7.

Galaxy LIMS for next-generation sequencing.

Scholtalbers J, Rößler J, Sorn P, de Graaf J, Boisguérin V, Castle J, Sahin U.

Bioinformatics. 2013 May 1;29(9):1233-4. doi: 10.1093/bioinformatics/btt115. Epub 2013 Mar 11.

PMID:
23479349
8.

The missing graphical user interface for genomics.

Schatz MC.

Genome Biol. 2010;11(8):128. doi: 10.1186/gb-2010-11-8-128. Epub 2010 Aug 25.

9.

Automated programming for bioinformatics algorithm deployment.

Alterovitz G, Jiwaji A, Ramoni MF.

Bioinformatics. 2008 Feb 1;24(3):450-1. doi: 10.1093/bioinformatics/btm602. Epub 2008 Jan 3.

PMID:
18174185
10.
11.

Phylesystem: a git-based data store for community-curated phylogenetic estimates.

McTavish EJ, Hinchliff CE, Allman JF, Brown JW, Cranston KA, Holder MT, Rees JA, Smith SA.

Bioinformatics. 2015 Sep 1;31(17):2794-800. doi: 10.1093/bioinformatics/btv276. Epub 2015 May 4.

12.

CloudDOE: a user-friendly tool for deploying Hadoop clouds and analyzing high-throughput sequencing data with MapReduce.

Chung WC, Chen CC, Ho JM, Lin CY, Hsu WL, Wang YC, Lee DT, Lai F, Huang CW, Chang YJ.

PLoS One. 2014 Jun 4;9(6):e98146. doi: 10.1371/journal.pone.0098146. eCollection 2014.

13.

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
14.

cl-dash: rapid configuration and deployment of Hadoop clusters for bioinformatics research in the cloud.

Hodor P, Chawla A, Clark A, Neal L.

Bioinformatics. 2016 Jan 15;32(2):301-3. doi: 10.1093/bioinformatics/btv553. Epub 2015 Oct 1.

15.

Analyzing HT-SELEX data with the Galaxy Project tools--A web based bioinformatics platform for biomedical research.

Thiel WH, Giangrande PH.

Methods. 2016 Mar 15;97:3-10. doi: 10.1016/j.ymeth.2015.10.008. Epub 2015 Oct 23.

16.

OntologyWidget - a reusable, embeddable widget for easily locating ontology terms.

Beauheim CC, Wymore F, Nitzberg M, Zachariah ZK, Jin H, Skene JH, Ball CA, Sherlock G.

BMC Bioinformatics. 2007 Sep 13;8:338.

17.

BioMAJ2Galaxy: automatic update of reference data in Galaxy using BioMAJ.

Bretaudeau A, Monjeaud C, Le Bras Y, Legeai F, Collin O.

Gigascience. 2015 May 9;4:22. doi: 10.1186/s13742-015-0063-8. eCollection 2015.

18.

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.

19.

deepTools2: a next generation web server for deep-sequencing data analysis.

Ramírez F, Ryan DP, Grüning B, Bhardwaj V, Kilpert F, Richter AS, Heyne S, Dündar F, Manke T.

Nucleic Acids Res. 2016 Jul 8;44(W1):W160-5. doi: 10.1093/nar/gkw257. Epub 2016 Apr 13.

20.

SED-ED, a workflow editor for computational biology experiments written in SED-ML.

Adams RR.

Bioinformatics. 2012 Apr 15;28(8):1180-1. doi: 10.1093/bioinformatics/bts101. Epub 2012 Feb 25.

PMID:
22368254

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