Cytoscape: The network visualization tool for GenomeSpace workflows

F1000Research

Volumn 3, Issue , 2014, Pages

  Demchak, Barry ^a   Hull, Tim ^a   Reich, Michael ^b   Liefeld, Ted ^b   Smoot, Michael ^c   Ideker, Trey ^a   Mesirov, Jill P ^b  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^b BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^c QUALCOMM INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

APPLICATION SERVICE PROVIDER; ARTICLE; ARTIFICIAL NEURAL NETWORK; COMPUTER ANALYSIS; COMPUTER NETWORK; COMPUTER PROGRAM; CONTROLLED STUDY; DATA ANALYSIS SOFTWARE; GENETIC DATABASE; GENOME ANALYSIS; INTERNET; PROCESS DEVELOPMENT; SYSTEM ANALYSIS; WEB BROWSER; WORKFLOW;

EID: 84915755892     PISSN: 20461402     EISSN: 1759796X     Source Type: Journal    
DOI: 10.12688/f1000research.4492.2     Document Type: Article

References (13)

1. Wolstencroft K Haines R Fellows D: The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud. Nucleic Acids Res. 2013;41(Web Server issue):W557-61. 23640334 10.1093/nar/gkt328 3692062
2. Altintas I Wang J Crawl D: Challenges and approaches for distributed workflowdriven analysis of large-scale biological data. Proceedings of the Workshop on Data analytics in the Cloud at EDBT/ICDT 2012 Conference, DanaC2012,2012;73-78. 10.1145/2320765.2320791
3. Goecks J Nekrutenko A Taylor J: Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 2010;11(8):R86. 20738864 10.1186/gb-2010-11-8-r86 2945788
4. Rocca-Serra P Brandizi M Maguire E: ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level. Bioinformatics. 2010;26(18):2354-2356. 20679334 10.1093/bioinformatics/btq415 2935443
5. Reich M Liefeld T Gould J: GenePattern 2.0. Nat Genet. 2006;38(5):500-501. 16642009 10.1038/ng0506-500
6. Perez-Llamas C Lopez-Bigas N: Gitools: analysis and visualisation of genomic data using interactive heat-maps. PLoS One. 2011;6(5):e19541. 21602921 10.1371/journal.pone.0019541 3094337
7. Liu T Ortiz JA Taing L: Cistrome: an integrative platform for transcriptional regulation studies. Genome Biol. 2011;12(8):R83. 21859476 10.1186/gb-2011-12-8-r83 3245621
8. Synapse: In L. Sullivan (Ed.), The SAGE glossary of the social and behavioral sciences. (p. 504). Thousand Oaks, CA: SAGE Publications, Inc.2009. 10.4135/9781412972024.n2497
9. Thorvaldsdóttir H Robinson JT Mesirov JP: Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 2013;14(2):178-92. 22517427 10.1093/bib/bbs017 3603213
10. Lotia S Montojo J Dong Y: Cytoscape App Store. Bioinformatics. 2013;29(10):1350-1351. 23595664 10.1093/bioinformatics/btt138 3654709
11. Marinilli M: Java Deployment: with JNLP and WebStart, Sams, Indianapolis, IN 2001. Reference Source
12. Demchak B Hull T Reich M: F1000Research/genomespace-cytoscape-weblaunch. ZENODO. 2014. Data Source
13. Demchak B Hull T Reich M: F1000Research/genomespace-cytoscape. ZENODO. 2014. Data Source