First Week 🙂
Here it goes!!
After discussion with my mentor, we decided to start working on GPML format which is extensively used as a file format for biological pathways.
We decided to work with sample files available on http://www.wikipathways.org/index.php/WikiPathways. To parse the file we used https://docs.python.org/2/library/xml.etree.elementtree.html and extracted all the information available like various data nodes, interactions, groups, etc.
One major difference is that in formats like cytoscape JSON the edges(interaction) are defined between two nodes but in the case of GPML they are defined only by the coordinates. So we need to create an initial layout for the network so it can be rendered properly by GraphSpace.
GraphSpace uses cytoscape web in the backend to render graphs. To solve the problem of creating groups we can use http://cytoscapeweb.cytoscape.org/tutorial#section/Compound_Nodes provided by cytoscape web.
By next week I plan to have a working prototype of the GPML upload function.