Libraries and tools for viewing and editing biological maps in SBGN
Siper, Metin Can
Item Usage Stats
MetadataShow full item record
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.
Web based tools
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)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 Genome Atlas ...
Analysis of the Wnt/B-catenin/TCF4 pathway using SAGE, genome-wide microarray and promoter analysis: identification of BRI3 and HSF2 as novel targets Kavak, E.; Najafov, A.; Ozturk, N.; Seker, T.; Cavusoglu, K.; Aslan, T.; Duru, A. D.; Saygili, T.; Hoxhaj, G.; Hiz, M. C.; Unal, D. O.; Birgül-Iyison, N.; Ozturk, M.; Koman, A. (Elsevier, 2010)The Wnt signaling pathway is involved in many differentiation events during embryonic development and can lead to tumor formation after aberrant activation of its components. β-catenin, a cytoplasmic component, plays a ...
NOx storage and reduction pathways on zirconia and titania functionalized binary and ternary oxides as NOx storage and reduction (NSR) systems Say, Z.; Tohumeken, M.; Ozensoy, E. (Elsevier, 2014-08-01)Binary and ternary oxide materials, ZrO2/TiO2 (ZT) and Al2O3/ZrO2/TiO2 (AZT), as well as their Ptfunctionalized counterparts were synthesized and characterized via XRD, Raman spectroscopy, BET, in situ FTIR and TPD ...