haleyyew
commented
6 years ago I want to work on this project. I worked with NRNB last summer, the project was SBML to SBGN interconversion, and my mentors were Nicolas Rodriguez and Sarah Keating. My project repository can be found here
The first 2 goals of this project seems easy, because I already have experience with SBGN-PD and I implemented a converter in Java. The converter between BioPAX and SBGN-PD should be similar. What I'm highly interested in is building a web service that also supports diagram editing and graph querying. However, by looking at SBGNViz I realize that a web service has already been build for SBGN-PD. What I'm wondering is if we can visualize BioPAX directly without converting to SBGN-PD first? For example, can I build a web tool similar to ChiBE, that supports similar operations? Which projects do you suggest me to look into to understand the scope of this project?
After completing the project last summer, I took a step further to explore more about SBML. I downloaded the dataset here and implemented a graph navigation tool as a school project. The incomplete version of the project can be found here. I used D3.js as my library for data visualization, and several simple algorithms in the backend for graph querying and data filtering. Therefore I think I'm highly qualified to work on this project.
However, I need to point out that I'm a first year M.Sc student and I might have other commitments with my supervisor this summer. Therefore I might not be able to work on this project full-time. However, I would dedicate sufficient amount of time in this project due to my passion for building a web service for data visualization.
ozgunbabur
khanspers
Background
BioPAX is a widely used pathway modeling and exchange standard language, supported by many pathway databases and used as an integration medium by Pathway Commons. SBGN language (specifically the Process Description dialect, or SBGN-PD) is a standard for pathway visualization, which has been successfully used to visualize BioPAX models by several tools including SBGNViz and ChiBE.
Ideally, we would like to have web-based pathway editors that can generate/edit BioPAX models, and visualize them using SBGN-PD notation. This ideal is challenged by the fact that the BioPAX software stack, most specifically Paxtools, is implemented in Java and not easily accessible to web-based tools. To bridge between BioPAX and SBGN, we need a web service that will provide a both-ways mapping and conversion, as well as provide an interface for major BioPAX operations that Paxtools provide, including graph queries.
Goal
Build a web-server that will:
Difficulty Level 1
Relatively easy project for a candidate with experience in building web servers.
Skills
Required: Javascript, Java, building Java-based web services. Optional: BioPAX, SBGN.
Public Repository
A new repository needs to be generated.
Potential Mentors
Ozgun Babur (please add your name)
Contact
Ozgun Babur