Aditya Bharadwaj1, Divit P Singh1, Anna Ritz2, Allison N Tegge1,3, Christopher L Poirel4, Pavel Kraikivski5, Neil Adames6, Kurt Luther1,7, Shiv D Kale8, Jean Peccoud6, John J Tyson5, T M Murali1,9. 1. Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA. 2. Biology Department, Reed College, Portland, OR 97202, USA. 3. Department of Statistics, Virginia Tech, Blacksburg, VA 24061, USA. 4. RedOwl Analytics, Baltimore, MD 21230, USA. 5. Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA. 6. Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523, USA. 7. Center for Human-Computer Interaction, Virginia Tech, Blacksburg, VA 24061, USA. 8. Biocomplexity Institute. 9. ICTAS Centre for Systems Biology of Engineered Tissues, Virginia Tech, Blacksburg, VA 24061, USA.
Abstract
SUMMARY: Networks have become ubiquitous in systems biology. Visualization is a crucial component in their analysis. However, collaborations within research teams in network biology are hampered by software systems that are either specific to a computational algorithm, create visualizations that are not biologically meaningful, or have limited features for sharing networks and visualizations. We present GraphSpace, a web-based platform that fosters team science by allowing collaborating research groups to easily store, interact with, layout and share networks. AVAILABILITY AND IMPLEMENTATION: Anyone can upload and share networks at http://graphspace.org. In addition, the GraphSpace code is available at http://github.com/Murali-group/graphspace if a user wants to run his or her own server. CONTACT: murali@cs.vt.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
SUMMARY: Networks have become ubiquitous in systems biology. Visualization is a crucial component in their analysis. However, collaborations within research teams in network biology are hampered by software systems that are either specific to a computational algorithm, create visualizations that are not biologically meaningful, or have limited features for sharing networks and visualizations. We present GraphSpace, a web-based platform that fosters team science by allowing collaborating research groups to easily store, interact with, layout and share networks. AVAILABILITY AND IMPLEMENTATION: Anyone can upload and share networks at http://graphspace.org. In addition, the GraphSpace code is available at http://github.com/Murali-group/graphspace if a user wants to run his or her own server. CONTACT: murali@cs.vt.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Christopher L Poirel; Richard R Rodrigues; Katherine C Chen; John J Tyson; T M Murali Journal: J Comput Biol Date: 2013-05 Impact factor: 1.479
Authors: Dexter Pratt; Jing Chen; David Welker; Ricardo Rivas; Rudolf Pillich; Vladimir Rynkov; Keiichiro Ono; Carol Miello; Lyndon Hicks; Sandor Szalma; Aleksandar Stojmirovic; Radu Dobrin; Michael Braxenthaler; Jan Kuentzer; Barry Demchak; Trey Ideker Journal: Cell Syst Date: 2015-10-28 Impact factor: 10.304
Authors: Anna Ritz; Christopher L Poirel; Allison N Tegge; Nicholas Sharp; Kelsey Simmons; Allison Powell; Shiv D Kale; T M Murali Journal: NPJ Syst Biol Appl Date: 2016-03-03