#acl All:read
= Google Summer of Code 2013: Co-authorship social network App =
== Short Description (from Cytoscape GSoc wiki) ==
'''Goal''' <<BR>> 
Create a visual summary of how individuals are connected.

'''Description''' <<BR>> 

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 will help identify important nodes and edges which could be people, publications or research topics.  For example, a co-publication network will have people (authors) as nodes and connections between people who have co-published together.

This functionality can be applied to several data types outside academia, whenever relationships between people 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.  This project will start with support for co-publication networks and extend to other networks like twitter and linked-in as time permits.

'''Language and Skills''' <<BR>> 
Java, XML 

==== Input/Output Description ====
This functionality should be implemented as a cytoscape app.

The app will receive as basic input:
  1. A name of an individual OR 
  1. A name of an institution OR
  1. A mesh term OR
  1. 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 specifies a name, institution, or mesh term, the app 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 be generated and displayed within the Cytoscape panel using attributes to highlight differences in weights in the relationships generated. 

== Example Co-publication Network ==
{{attachment:gdb_network.png}}
=== Legend ===
 * set of 88 publications 
 * Node Colour -> total citations (limited to 88 publications analyzed)
 * Node size -> number of publications (limited to 88 publications analyzed)
 * Edge weight -> number of co-publication
 * Edge Opacity -> number of co-publications (<2 less visible)
 * Node Label Opacity -> number of publications (<2 less visible)

=== Going Beyond Simple Solutions ===
We would like applicants to be creative, and come up with new or different ways to generalize their proposed app so that it is applicable for more than just publications.

=== Environment: Cytoscape ===
 * We want the plugin to be implemented as a Cytoscape 3.0 app
 * Cytoscape apps are coded in Java using the Cytoscape API
== About ==
Potential members:
 * [[RuthIsserlin|Ruth Isserlin]]
 * [[GaryBader|Gary Bader]]

We are part of [[Home|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|home page]] for more details on the lab research areas, and at our home-pages for our own research interests.