Browsing by Author "Çivril, Ali"
Now showing 1 - 2 of 2
Results Per Page
Sort Options
Item Open Access A compound graph layout algorithm for biological pathways(Springer, Berlin, Heidelberg, 2004-09-10) Doğrusöz, Uğur; Giral, Erhan; Çetintaş, Ahmet; Çivril, Ali; Demir, EmekWe 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 within PATIKA, a pathway analysis tool for drawing complicated biological pathways with compartimental constraints and arbitrary nesting relations to represent molecular complexes and pathway abstractions. Experimental results show that execution times and quality of the produced drawings with respect to commonly accepted layout criteria and pathway drawing conventions are quite satisfactory. © Springer-Verlag Berlin Heidelberg 2004.Item Open Access PATIKA: An informatics infrastructure for cellular networks(ISCB Org, 2004) 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, HilmiThe 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 an extensive ontology and data integration mechanisms. It also features advanced database querying, microarray data analysis, and automatic layout components.