GSoC 2016 – National Resource of Network Biology: GraphSpace

My proposal has been accepted by National Resource of Network Biology under the Google Summer of Code 2016 program. Yay!!!

I’ll be working on GraphSpace with my mentor T. M. Murali over the summer to extend its import and export capabilities. I’ll be updating this blog regularly with my progress. Coding period starts from 23rd May and I plan to study various network representation formats during the community bonding period.

Looking forward to a fun summer 🙂

My proposal abstract:

GraphSpace is a tool for storing, sharing, and visualising graphs in order to help collaborative research. Users can upload graphs and share it with other collaborators. Most of its users work in computational biology. One may represent biological interactions through the use of nodes and edges. For example, a node may be thought of as a protein. If there exists an edge between two nodes in the graph, this may indicate that the two proteins interact.Currently GraphSpace can import JSON and .cyjs (Cytsocape JSON) files. It has a REST API to allow automatic uploads of multiple files in these formats. The overall goal of this project is to expand the user communities for GraphSpace by extending its import and export capabilities.The first part of this project will focus on adding import (and export) functionality for various graph file formats like GraphML, GPML, BioPAX to allow a much wider set of graphs to be imported into GraphSpace. The second part of this project will deal with enhancing the Cytoscape JSON parser such that it can store the various properties of the layout like x, y coordinates, color, shape, etc. The third part of this project will be to add a PDF exporter.

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