Google Summer of Code 2013: Co-publication App
Short Description (from Cytoscape GSoc wiki)
Goal
Develop a visual summary of how individuals are connected.
Description
Biological networks can be visualized and analyzed using Cytoscape. Often researchers want to go beyond the network of proteins or genes and also look at the inter-connectedness between colleagues and instituions. Who tends to publish together? What institutions are most collaborative? Are there inter-disciplinary connections in my institution?
Goal: We want to build a cytoscape App that given a set of publications builds a co-publication network where node and edge types are flexible and can be selected by the users. Networks generated portray and highlight with appropriate weights important nodes and edges.
This functionality can be applied to several data types outside academia, whenever relationships and how everyone connects together is of interest. An example is professional social networks (e.g. linked-in), where individuals are connected by who they have worked with in the past or the twitter-verse where individuals are connected when they each reference the same (#) hash tag.
Language and Skills
Java, XML
Input/Output Description
This functionality should be implemented as a cytoscape plugin.
The plugin will receive as input:
- A name of an individual OR
- A name of an institution OR
- A mesh term OR
- a set of publications
The user can choose what a node represents {Author, institution, paper...} and edge represents {Co-publication, shared mesh terms...}
If the user specified a name, institution, or mesh term the plugin will query PubMed for the relevant information and retrieve the set of results as XML.
For every input a graphical or visual summary of the network will have to be generated and displayed within the cytoscape panel using attributes to highlight differences in weights in the relationships generated.
Going Beyond Simple Solutions
We would like applicants to be creative, and come up with new or different ways to generalize the plugin created so that it is applicable for more than just publications.
Environment: Cytoscape
- We want the plugin to be implemented as a Cytoscape 3.0 plugin
- Cytoscape plug-ins are coded in Java using the Cytoscape API
About
This project was started by
We are part of Gary Bader's lab at University of Toronto - CCBR (Toronto, ON Canada). Our lab is strongly engaged in biological network research. Feel free to have a look at our home page for more details on the lab research areas, and at our home-pages for our own research interests.