GSoC/GCI Archive
Google Summer of Code 2013 National Resource for Network Biology (NRNB)

IDEA 25: Specialized Layout Algorithm for SBGN Process Description Diagrams

by Istemi Bahceci for National Resource for Network Biology (NRNB)

This project involves customizing CoSE (Compound Spring Embedder) layout algorithm [3] for biological network drawings using Process Description language of SBGN (Systems Biology Graphical Notation) [2]. A number of customizations could be implemented, including layout algorithm to consider things like substrates and products of process nodes on opposite sides and tiling of members properly inside a molecular complex. This work would improve the SBGN-ML support in BioPAX-Paxtools[4] as well as improving the layout in the network view of cBio Cancer Genomics portal [7]. Besides the improvements on BioPAX-Paxtools[4] and cBioPortal[7], more general hope for the project is providing a common usable asset for the tools that supports SBGN Process Description language.