GSoC/GCI Archive
Google Summer of Code 2012 National Resource for Network Biology (NRNB)

Understanding Complex Pathways using User Data and Web Services in PathVisio

by Jake Fried for National Resource for Network Biology (NRNB)

IDEA 8: Understanding Complex Pathways using User Data and Web Services in PathVisio The goal is to produce a user-friendly mechanism to filter/highlight nodes in PathVisio, a tool to draw biological pathways. Users would be able to upload text data from a variety of external sources (e.g. protein-drug or protein-biological pathway data; PharmGKB or DrugBank) or experimental data and then filter out nodes in a biological pathway based on a combination of this information. In addition to user-uploaded data, the tool might also pull data directly from pre-selected databases using web services; BioCatalogue provides directory of biology-oriented web services. An example query is that a user might like to know what proteins in a particular biological pathway are involved in cell division, are known targets to the cancer drug doxorubicin, and are also over-expressed in some experiment the user has performed. One example of a tool that already does this well for textual data is Google Refine (http://www.youtube.com/watch?v=LovigIDl634). This tool would help biologists navigate large, complicated pathways. Language and Skills: Java Potential Mentors: Augustin Luna Contact: wikipathways-discuss@googlegroups.com