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Items: 1 to 20 of 90

1.

The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows.

O'Connor BD, Yuen D, Chung V, Duncan AG, Liu XK, Patricia J, Paten B, Stein L, Ferretti V.

F1000Res. 2017 Jan 18;6:52. doi: 10.12688/f1000research.10137.1. eCollection 2017.

2.

Building Portable and Reproducible Cancer Informatics Workflows: An RNA Sequencing Case Study.

Kaushik G, Davis-Dusenbery B.

Methods Mol Biol. 2019;1878:39-64. doi: 10.1007/978-1-4939-8868-6_2.

PMID:
30378068
3.

Kronos: a workflow assembler for genome analytics and informatics.

Taghiyar MJ, Rosner J, Grewal D, Grande BM, Aniba R, Grewal J, Boutros PC, Morin RD, Bashashati A, Shah SP.

Gigascience. 2017 Jul 1;6(7):1-10. doi: 10.1093/gigascience/gix042.

4.

Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud.

Afgan E, Sloggett C, Goonasekera N, Makunin I, Benson D, Crowe M, Gladman S, Kowsar Y, Pheasant M, Horst R, Lonie A.

PLoS One. 2015 Oct 26;10(10):e0140829. doi: 10.1371/journal.pone.0140829. eCollection 2015.

5.

Bionimbus: a cloud for managing, analyzing and sharing large genomics datasets.

Heath AP, Greenway M, Powell R, Spring J, Suarez R, Hanley D, Bandlamudi C, McNerney ME, White KP, Grossman RL.

J Am Med Inform Assoc. 2014 Nov-Dec;21(6):969-75. doi: 10.1136/amiajnl-2013-002155. Epub 2014 Jan 24.

6.

Developing reproducible bioinformatics analysis workflows for heterogeneous computing environments to support African genomics.

Baichoo S, Souilmi Y, Panji S, Botha G, Meintjes A, Hazelhurst S, Bendou H, Beste E, Mpangase PT, Souiai O, Alghali M, Yi L, O'Connor BD, Crusoe M, Armstrong D, Aron S, Joubert F, Ahmed AE, Mbiyavanga M, Heusden PV, Magosi LE, Zermeno J, Mainzer LS, Fadlelmola FM, Jongeneel CV, Mulder N.

BMC Bioinformatics. 2018 Nov 29;19(1):457. doi: 10.1186/s12859-018-2446-1.

7.

Yabi: An online research environment for grid, high performance and cloud computing.

Hunter AA, Macgregor AB, Szabo TO, Wellington CA, Bellgard MI.

Source Code Biol Med. 2012 Feb 15;7(1):1. doi: 10.1186/1751-0473-7-1.

8.

DockerBIO: web application for efficient use of bioinformatics Docker images.

Kwon C, Kim J, Ahn J.

PeerJ. 2018 Nov 27;6:e5954. doi: 10.7717/peerj.5954. eCollection 2018.

9.

ClinGen advancing genomic data-sharing standards as a GA4GH driver project.

Dolman L, Page A, Babb L, Freimuth RR, Arachchi H, Bizon C, Brush M, Fiume M, Haendel M, Hansen DP, Milosavljevic A, Patel RY, Pawliczek P, Yates AD, Rehm HL.

Hum Mutat. 2018 Nov;39(11):1686-1689. doi: 10.1002/humu.23625.

PMID:
30311379
10.

BioShaDock: a community driven bioinformatics shared Docker-based tools registry.

Moreews F, Sallou O, Ménager H, Le Bras Y, Monjeaud C, Blanchet C, Collin O.

F1000Res. 2015 Dec 14;4:1443. doi: 10.12688/f1000research.7536.1. eCollection 2015.

11.

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.

12.

Enhanced reproducibility of SADI web service workflows with Galaxy and Docker.

Aranguren ME, Wilkinson MD.

Gigascience. 2015 Dec 3;4:59. doi: 10.1186/s13742-015-0092-3. eCollection 2015.

13.

Genome Annotator Light (GAL): A Docker-based package for genome analysis and visualization.

Panda A, Chaudhari NM, Tripathy S.

Genomics. 2019 Mar 26. pii: S0888-7543(18)30700-6. doi: 10.1016/j.ygeno.2019.03.012. [Epub ahead of print]

14.

Using Docker Compose for the Simple Deployment of an Integrated Drug Target Screening Platform.

List M.

J Integr Bioinform. 2017 Jun 10;14(2). pii: /j/jib.2017.14.issue-2/jib-2017-0016/jib-2017-0016.xml. doi: 10.1515/jib-2017-0016.

15.

Inexpensive and Highly Reproducible Cloud-Based Variant Calling of 2,535 Human Genomes.

Shringarpure SS, Carroll A, De La Vega FM, Bustamante CD.

PLoS One. 2015 Jun 25;10(6):e0129277. doi: 10.1371/journal.pone.0129277. eCollection 2015.

16.

Cloud computing for comparative genomics.

Wall DP, Kudtarkar P, Fusaro VA, Pivovarov R, Patil P, Tonellato PJ.

BMC Bioinformatics. 2010 May 18;11:259. doi: 10.1186/1471-2105-11-259.

17.

The NIH BD2K center for big data in translational genomics.

Paten B, Diekhans M, Druker BJ, Friend S, Guinney J, Gassner N, Guttman M, Kent WJ, Mantey P, Margolin AA, Massie M, Novak AM, Nothaft F, Pachter L, Patterson D, Smuga-Otto M, Stuart JM, Van't Veer L, Wold B, Haussler D.

J Am Med Inform Assoc. 2015 Nov;22(6):1143-7. doi: 10.1093/jamia/ocv047. Epub 2015 Jul 13.

18.

Semantic workflows for benchmark challenges: Enhancing comparability, reusability and reproducibility.

Srivastava A, Adusumilli R, Boyce H, Garijo D, Ratnakar V, Mayani R, Yu T, Machiraju R, Gil Y, Mallick P.

Pac Symp Biocomput. 2019;24:208-219.

19.

Interoperable and scalable data analysis with microservices: Applications in Metabolomics.

Emami Khoonsari P, Moreno P, Bergmann S, Burman J, Capuccini M, Carone M, Cascante M, de Atauri P, Foguet C, Gonzalez-Beltran A, Hankemeier T, Haug K, He S, Herman S, Johnson D, Kale N, Larsson A, Neumann S, Peters K, Pireddu L, Rocca-Serra P, Roger P, Rueedi R, Ruttkies C, Sadawi N, Salek RM, Sansone SA, Schober D, Selivanov V, Thévenot EA, van Vliet M, Zanetti G, Steinbeck C, Kultima K, Spjuth O.

Bioinformatics. 2019 Mar 9. pii: btz160. doi: 10.1093/bioinformatics/btz160. [Epub ahead of print]

PMID:
30851093
20.

PhenoMeNal: processing and analysis of metabolomics data in the cloud.

Peters K, Bradbury J, Bergmann S, Capuccini M, Cascante M, de Atauri P, Ebbels TMD, Foguet C, Glen R, Gonzalez-Beltran A, Günther UL, Handakas E, Hankemeier T, Haug K, Herman S, Holub P, Izzo M, Jacob D, Johnson D, Jourdan F, Kale N, Karaman I, Khalili B, Emami Khonsari P, Kultima K, Lampa S, Larsson A, Ludwig C, Moreno P, Neumann S, Novella JA, O'Donovan C, Pearce JTM, Peluso A, Piras ME, Pireddu L, Reed MAC, Rocca-Serra P, Roger P, Rosato A, Rueedi R, Ruttkies C, Sadawi N, Salek RM, Sansone SA, Selivanov V, Spjuth O, Schober D, Thévenot EA, Tomasoni M, van Rijswijk M, van Vliet M, Viant MR, Weber RJM, Zanetti G, Steinbeck C.

Gigascience. 2019 Feb 1;8(2). pii: giy149. doi: 10.1093/gigascience/giy149.

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