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  for biological network drawings using Process Description language of SBGN (Systems Biology Graphical Notation) . 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 as well as improving the layout in the network view of cBio Cancer Genomics portal . Besides the improvements on BioPAX-Paxtools and cBioPortal, more general hope for the project is providing a common usable asset for the tools that supports SBGN Process Description language.