Libraries and tools for viewing and editing biological maps in SBGN
Siper, Metin Can
Please cite this item using this persistent URLhttp://hdl.handle.net/11693/33522
Information about cellular processes and pathways is becoming increasingly available in detailed, computable standard formats including Systems Biology Graphical Notation (SBGN). E ective visualization of this information is a key recurring requirement for biological data analysis, especially for -omic data. Biological data analysis is rapidly migrating to web based platforms; thus there is a substantial need for sophisticated web based pathway viewing and editing tools that support these platforms and other use cases. We propose to develop a modular software architecture to meet this need. This proposed architecture includes reusable web based libraries and easily customizable and embeddable tools developed using these libraries. Our libraries include SBGNViz.js, a Cytoscape.js based library providing a renderer and an API to develop tools visualizing pathway models represented by SBGN Diagrams, and ChiSE.js, an SBGNViz.js based library to visualize and construct pathway models represented in SBGN Diagrams, and miscellaneous Cytoscape.js extensions. Our tools are built using these libraries and include SBGNViz Viewer and Newt, which are sample applications for SBGNViz.js and ChiSE.js, respectively. Newt is being developed to become a rst web based, open source SBGN editor with full support for compound structures such as molecular complexes and compartment, advanced diagramming facilities including grid and alignment guidelines, static and incremental layout, and complexity management of large maps.
Showing items related by title, author, creator and subject.
Bahceci I.; Dogrusoz U.; La K.C.; Babur O.; Gao J.; Schultz N. (Oxford University Press, 2017)Motivation: While existing network visualization tools enable the exploration of cancer genomics data, most biologists prefer simplified, curated pathway diagrams, such as those featured in many manuscripts from The Cancer ...
Dilek, A.; Belviranli, M.E.; Dogrusoz, U. (2010)With recent advancements in techniques for cellular data acquisition, information on cellular processes has been increasing at a dramatic rate. Visualization is critical to analyzing and interpreting complex information; ...
Kim H.; Atalay, R.; Gelenbe, E. (2012)Gene expression centered gene regulatory networks studies can provide insight into the dynamics of pathway activities that depend on changes in their environmental conditions. Thus we propose a new pathway analysis approach ...