Cytoscape: the network visualization tool for GenomeSpace workflows

Barry Demchak, Tim Hull, Michael Reich, Ted Liefeld, Michael Smoot, Trey Ideker, Jill P. Mesirov
2014 F1000Research  
Modern genomic analysis often requires workflows incorporating multiple best-of-breed tools. GenomeSpace is a web-based visual workbench that combines a selection of these tools with mechanisms that create data flows between them. One such tool is Cytoscape 3, a popular application that enables analysis and visualization of graph-oriented genomic networks. As Cytoscape runs on the desktop, and not in a web browser, integrating it into GenomeSpace required special care in creating a seamless
more » ... experience and enabling appropriate data flows. In this paper, we present the design and operation of the Cytoscape GenomeSpace app, which accomplishes this integration, thereby providing critical analysis and visualization functionality for GenomeSpace users. It has been downloaded over 850 times since the release of its first version in September, 2013. 73-78. Publisher Full Text 3. Goecks J, Nekrutenko A, Taylor J, et al.: Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 2010; 11(8): R86. PubMed Abstract | Publisher Full Text | Free Full Text 4. Rocca-Serra P, Brandizi M, Maguire E, et al.: ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level. Bioinformatics. 2010; 26(18): 2354-2356. PubMed Abstract | Publisher Full Text | Free Full Text 5. Reich M, Liefeld T, Gould J, et al.: GenePattern 2.0. Nat Genet. 2006; 38(5): 500-501. PubMed Abstract | Publisher Full Text 6. Perez-Llamas C, Lopez-Bigas N: Gitools: analysis and visualisation of genomic data using interactive heat-maps. PLoS One. 2011; 6(5): e19541. PubMed Abstract | Publisher Full Text | Free Full Text 7. Liu T, Ortiz JA, Taing L, et al.: Cistrome: an integrative platform for transcriptional regulation studies. Genome Biol. 2011; 12(8): R83. PubMed Abstract | Publisher Full Text | Free Full Text 8. Synapse: In L. Sullivan (Ed.), The SAGE glossary of the social and behavioral sciences. (p. 504). Thousand Oaks, CA: SAGE Publications, Inc. 2009. Publisher Full Text 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. PubMed Abstract | Publisher Full Text | Free Full Text 10. Lotia S, Montojo J, Dong Y, et al.: Cytoscape App Store. Bioinformatics. 2013; 29(10): 1350-1351. PubMed Abstract | Publisher Full Text | Free Full Text 11. Marinilli M: Java Deployment: with JNLP and WebStart, Sams, Indianapolis, IN 2001. Reference Source 12. Demchak B, Hull T, Reich M, et al.: F1000Research/genomespace-cytoscapeweblaunch. ZENODO. 2014. Data Source 13. Demchak B, Hull T, Relch M, et al.: F1000Research/genomespace-cytoscape. ZENODO. 2014. Data Source References
doi:10.12688/f1000research.4492.1 pmid:25165537 pmcid:PMC4133763 fatcat:u2jdqiszbvcc3ekgytd767xp6a