GraphSpace: Stimulating interdisciplinary collaborations in network biology

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

Transcript

1. GraphSpace: Stimulating interdisciplinary collaborations in network biology Aditya Bharadwaj, Divit P. Singh, Anna Ritz, Allison N. Tegge, Christopher L. Poirel, Pavel Kraikivski, Neil Adames, Kurt Luther, Shiv D. Kale, Jean Peccoud, John J. Tyson and T. M. Murali Bioinformatics, in press, 2017 July 22nd , 2017 Aditya Bharadwaj Ph.D. Student Department of Computer Science Virginia Tech, Blacksburg, USA
2. Networks are Ubiquitous in Systems Biology Ritz et al., Pathways on demand: automated reconstruction of human signaling networks. npj Systems Biology and Applications, 2 (2016): 16002.
3. Research is increasingly collaborative Olivier H. Beauchesne, Map of scientific collaboration (Redux!), 2008-2012
4. Research is increasingly interdisciplinary Biology DATA NETWORK Computer Science Mathematics Genomics Network Analysis Proteomics Metabolomics
5. But collaboration is still painful! SHARE PUBLISH LAYOUT SEARCH Challenges faced by interdisciplinary research teams in network biology GROUPS
6. GraphSpace Features GROUPS Create groups and add/invite your collaborators. SHARE Share your networks and layouts with one or more groups. graphspace.org PUBLISH Share your networks with the scientific community. LAYOUT Use a powerful layout editor to move nodes, edit network style and save new layouts. Search for networks with a given property or that contain a specific node or collection of nodes. SEARCH
7. Free to use at www.graphspace.org
8. Easy to upload graphs
9. Access networks via unique URLs
10. Create groups Researcher graphspace.org Collaborators Group X Group Y Group Z
11. Add/Invite collaborators Researcher graphspace.org Collaborators
12. Share networks Researcher graphspace.org Collaborators
13. An online collaborative platform Researcher graphspace.org Collaborators Scientific Community
14. Use GraphSpace as a service CyGraphSpace App GraphCrowd graphspace-python GraphSpace R ESTful AP I
15. Poster A-151 GraphSpace is growing • 21000+ Graphs • 300+ Users • 90+ Groups Contact Information • Mail: adb@vt.edu • Website: adityabharadwaj.in PUBLISH Share your networks with the scientific community SHARE Share your networks and layouts with one or more groups GROUPS Create groups and add/invite your collaborators URL PNG JSON LAYOUT Use a powerful layout editor to move nodes, edit network styles, and save new layouts INTERACT Sequentially step through subgraphs of the entire network Share your networks and layouts with one or more groups. VISUALIZE Visually explore your network Search for networks with a given property or that contain a specific node or collection of nodes SEARCH Save your networks online and access them anytime, anywhere, and on any device STORE GraphSpace exposes its functionality via easy-to-use RESTful APIs API REST SERVICE 21,000+ Graphs 300+ Users 90+ Groups What is GraphSpace? GraphSpace is a web-based platform that fosters team science by allowing collaborators to easily store, share, interact with, and lay out networks. BACKGROUND Despite the existence of several software systems and interfaces to analyze and view networks, interdisciplinary research teams in network biology find it challenging to share, explore, and interpret computed networks in their collaborations. FUTURE DIRECTIONS • Plug and play algorithms providing a single platform for algorithm development. • Automated personalized layouts generated by learning user preferences from previous layouts. • Crowdsourced layouts generated by citizen scientist via integration with plaforms like Zooniverse and MTurk. GET INVOLVED • Web: http://bioinformatics.cs.vt.edu/ murali/ • Email: murali@cs.vt.edu • Github: https://github.com/Murali-group/GraphSpace/ FUNDING DBI 1062380 R01 GM095955, UH2CA203768 GRAPHSPACE FEATURES Stimulating interdisciplinary collaborations in network biology Aditya Bharadwaj, Divit P. Singh, Anna Ritz, Allison N. Tegge, Christopher L. Poirel, Pavel Kraikivski, Neil Adames, Kurt Luther, Shiv D. Kale, Jean Peccoud, John J. Tyson, and T. M. Murali GraphSpace www.graphspace.org CyGraphSpace App GraphCrowd graphspace-python GraphSpace R ESTful AP I Filter nodes and edges Network Dissemination Researcher Collaborating Groups Collaboration among We would like to thank NRNB and Google Summer of Code. ACKNOWLEDGEMENTS