GSoC 2016 – Week 1

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.

Cheers!

Advertisements

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s