Now showing items 1-7 of 7

    • Algorithms for effective querying of compound graph-based pathway databases 

      Doğrusöz, Uğur; Çetintaş, Ahmet; Demir, Emek; Babur, Özgün (BioMed Central Ltd., 2009-11-16)
      Background: Graph-based pathway ontologies and databases are widely used to represent data about cellular processes. This representation makes it possible to programmatically integrate cellular networks and to investigate ...
    • Algorithms for effective querying of graph-based pathway databases 

      Çetintaş, Ahmet (Bilkent University, 2007)
      As the scientific curiosity shifts toward system-level investigation of genomicscale information, data produced about cellular processes at molecular level has been accumulating with an accelerating rate. Graph-based ...
    • A compound graph layout algorithm for biological pathways 

      Doğrusöz, Uğur; Giral, Erhan; Çetintaş, Ahmet; Çivril, Ali; Demir, Emek (Springer, Berlin, Heidelberg, 2004-09-10)
      We present a new compound graph layout algorithm based on traditional force-directed layout scheme with extensions for nesting and other application-specific constraints. The algorithm has been successfully implemented ...
    • A layout algorithm for undirected compound graphs 

      Doğrusöz, Uğur; Giral, Erhan; Çetintaş, Ahmet; Civril, Ali; Demir, Emek (Elsevier, 2009-03-15)
      We present an algorithm for the layout of undirected compound graphs, relaxing restrictions of previously known algorithms in regards to topology and geometry. The algorithm is based on the traditional force-directed layout ...
    • PATIKA: An informatics infrastructure for cellular networks 

      Aksay, Çağrı; Ayaz, Aslı; Babur, Özgün; Bilgin, C.; Çetintaş, Ahmet; Çivril, Ali; Çolak, Recep; Çözen, G.; Demir, Emek; Doğrusöz, Uğur; Erson, Zeynep; Gerdaneri, Ozan; Giral, Erhan; Güleşır, Gürcan; Nişancı, Gürkan; Sakarya, O.; Yıldırım, Hilmi (ISCB Org, 2004)
      The PATIKA Project aims for an informatics infrastructure to cope with the inherently complex cellular pathway data and provides software tools with sophisticated visualization technology around a central database using ...
    • PATIKAweb: a Web interface for analyzing biological pathways through advanced querying and visualization 

      Doğrusöz, Uğur; Erson, E. Zeynep; Giral, Erhan; Demir, Emek; Babur, Özgün; Çetintaş, Ahmet; Çolak, Recep (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 ...
    • PATIKAweb: a Web service for querying, visualizing and analyzing a graph-based pathway database 

      Aksay, Çağrı; Arık, Fatma; Ataer, Esra; Ayaz, Aslı; Babur, Özgün; Belviranlı, Mehmet E.; Çetintaş, Ahmet; Çolak, Recep; Çözen, G.; Demir, Emek; Dilek, Alptuğ; Doğrusöz, Uğur; Giral, Erhan; Kaya, Engin; Küçük, Evren; Tekin, A. S.; Yıldırım, Hilmi; Erson, Zeynep (ISCB Org, 2005-06)
      PATIKAweb provides a Web service for retrieving and analyzing biological pathways in PATIKA database, which currently contains data integrated from popular public pathway databases like Reactome. It features a user-friendly ...