title: An interactive visualization tool and data model for experimental design in systems biology.
abstract: Experimental design is important, but is often under-supported, in systems biology research. To improve experimental design, we extend the visualization of complex sphingolipid pathways to study biosynthetic origin in SphinGOMAP. We use the ganglio-series sphingolipid dataset as a test bed and the Java Universal Network / Graph Framework (JUNG) visualization toolkit. The result is an interactive visualization tool and data model for experimental design in lipid systems biology research. We improve the current SphinGOMAP in terms of interactive visualization by allowing (i) choice of four different network layouts, (ii) dynamic addition / deletion of on-screen molecules and (iii) mouse-over to reveal detailed molecule data. Future work will focus on integrating various lipid-relevant data systematically i.e. SphinGOMAP biosynthetic data, Lipid Bank molecular data (Japan) and Lipid MAPS metabolic pathway data (USA). We aim to build a comprehensive and interactive communication platform to improve experimental design for scientists globally in high-throughput lipid systems biology research.
authors.affiliation: College of Computing, Georgia Institute of Technology, Atlanta, GA 30332, USA. skapoor6@mail.gatech.edu
authors.forename: Shray
authors.initials: S
authors.lastname: Kapoor
authors.forename: Chang Feng
authors.initials: CF
authors.lastname: Quo
authors.forename: Alfred H
authors.initials: AH
authors.lastname: Merrill
authors.forename: May D
authors.initials: MD
authors.lastname: Wang
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D003196:Computer Graphics; D003198:Computer Simulation; D003628:Database Management Systems; D016208:Databases, Factual; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D008055:Lipids / Q000737:chemistry; D053858:Metabolic Networks and Pathways; D015203:Reproducibility of Results; D013107:Sphingolipids / Q000737:chemistry*; D049490:Systems Biology / Q000379:methods*; D018511:Systems Integration; D014584:User-Computer Interface
chemical_list: D008055:Lipids; D013107:Sphingolipids