Google Summer of Code 2014: A Web Interface For CAN-VD Database Using Cytoscape.js

Project Full Title

GSoC-Idea7: Developing An Interface For The Cancer Network Altering Variant Database (CAN-VD) Using Cytoscape.js

Background

Cancer is highly associated with genomic mutations. Such mutations in genes affect their protein products resulting in mutated proteins that acquire new function (gain-of-interaction/function), mutants that lose their function (loss-of- interaction/function) or mutants that lose a function and acquire another (switch-of-interaction/function). Identifying mutants that are related to cancer development and interpreting their functional consequences is important for understanding cancer biology and developing diagnostics, prognostics and drug targets.

Focus

We are studying the effects of mutations on protein-protein interaction (PPI) networks in cancer. The effects of over 800,000 missense mutations are being analyzed and stored in the Cancer Network Altering-Variant Database (CNA-VD), a relational database implemented in MySQL. CAN-VD stores the PPI interactions mediated by wildtype and variant protein sequences to build and compare the PPI network in the two conditions and understand the effects of mutations on the network topology and, consequently, the cellular and biological functions of the cancer system.

Goals

1.      Develop a web-based interface for PPI data retrieval with a comprehensive search function.
2.      Develop a visualization and annotation module using Cytoscape.js to visualize the retrieved PPI data as a network with annotations that highlight the mutation effects (the differences between the normal and cancer networks).

Inputs

The student will be provided with the database design and sample data as well as an introduction to the topic and the different possible visualizations and annotations needed. The student will have the freedom to choose among them or to propose other options.

Language and Skills'

OS: Windows 7 64bit
Webserver: IIS 7.5 (Windows 7 default)
Database server: MySQL (V5.1 or later)
Scripting: HTML, Javascipt, PHP and JSON

Candidate Students Acceptance Criteria

Students interested in working in this project will be asked to do an initial project that will be used for evaluation.

For Candidate Students: Please fill in this form.

Links

1- Project description (PDF).

2- Project files.

3- Cytoscap.js Website.

4- JQuery.

5-GeneMania Database.

6-The Rice Proteogenomics Database.

GSoC-Idea7 Mentors

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.