Now showing items 1-6 of 6

    • Efficient querying of SBGN maps stored in a graph database 

      Karaca, Mustafa Enes (Bilkent University, 2019-02)
      Graph visualization is an important research area that endeavors to make graphs more understandable and easier to analyze. In various domains, graph visualization techniques and standards are developed to effectively ...
    • Libraries and tools for viewing and editing biological maps in SBGN 

      Siper, Metin Can (Bilkent University, 2017-08)
      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 ...
    • PATIKAweb: a Web interface for analyzing biological pathways through advanced querying and visualization 

      Dogrusoz, U.; Erson, E. Z.; Giral, E.; Demir, E.; Babur, O.; Cetintas, A.; Colak, R. (Oxford University Press, 2006-02-01)
      Summary: PATIKAweb provides a Web interface for retrieving and analyzing biological pathways in the PATIKA database, which contains data integrated from various prominent public pathway databases. It features a user-friendly ...
    • Semantic validation of biological maps in SBGN 

      Çalış, Umut Utku (Bilkent University, 2019-09)
      Graph visualization is a research field where relational information is graphically represented in the form of graphs or networks. It is applicable in numerous areas from computer network systems, to biology, to software ...
    • Software support for SBGN maps: SBGN-ML and LibSBGN 

      Iersel, Martijn P. van; Villéger, A. C.; Czauderna, T.; Boyd, S. E.; Bergmann, F. T.; Luna, A.; Demir, E.; Sorokin, A.; Dogrusoz, U.; Matsuoka, Y.; Funahashi, A.; Aladjem, M. I.; Mi, H.; Moodie, S. L.; Kitano, H.; Le novère, N.; Schreiber, F. (Oxford University Press, 2012)
      Motivation: LibSBGN is a software library for reading, writing and manipulating Systems Biology Graphical Notation (SBGN) maps stored using the recently developed SBGN-ML file format. The library (available in C++ and Java) ...
    • The systems biology graphical notation 

      Le Novère, N.; Hucka, M.; Mi, H.; Moodie, S.; Schreiber, F.; Sorokin, A.; Demir, E.; Wegner, K.; Aladjem, M. I.; Wimalaratne, S. M.; Bergman, F. T.; Gauges, R.; Ghazal, P.; Kawaji, H.; Li, L.; Matsuoka, Y.; Villéger, A.; Boyd, S. E.; Calzone, L.; Courtot, M.; Dogrusoz, U.; Freeman, T. C.; Funahashi, A.; Ghosh, S.; Jouraku, A.; Kim, S.; Kolpakov, F.; Luna, A.; Sahle, S.; Schmidt, E.; Watterson, S.; Wu, G.; Goryanin, I.; Kell, D. B.; Sander, C.; Sauro, H.; Snoep, J. L.; Kohn, K.; Kitano, H. (Nature Publishing Group, 2009-08)
      Circuit diagrams and Unified Modeling Language diagrams are just two examples of standard visual languages that help accelerate work by promoting regularity, removing ambiguity and enabling software tool support for ...