Now showing items 1-11 of 11

    • 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 ...
    • catcher: a software program to detect answer copying in multiple-choice tests based on nominal response model 

      Kalender, I. (SAGE Publications, 2012-08-16)
      catcher is a software program designed to compute the v index, a common statistical index for the identification of collusions (cheating) among examinees taking an educational or psychological test. It requires (a) ...
    • ChiBE: interactive visualization and manipulation of BioPAX pathway models 

      Babur, Özgün; Doğrusöz, Uğur; Demir, Emek; Sander, C. (Oxford University Press, 2010-02-01)
      SUMMARY: Representing models of cellular processes or pathways in a graphically rich form facilitates interpretation of biological observations and generation of new hypotheses. Solving biological problems using large ...
    • Identification of relative protein bands in polyacrylamide gel electrophoresis (PAGE) using a multi-resolution snake algorithm 

      Gürcan, M. N.; Koyutürk, M.; Yildiz, H. S.; Çetin-Atalay R.; Çetin, A. Enis (Informa Healthcare, 1999-06)
      In polyacrylamide gel electrophoresis (PAGE) image analysis, it is important to determine the percentage of the protein of interest of a protein mixture. This study presents reliable computer software to determine this ...
    • Integrating biological pathways and genomic profiles with ChiBE 2 

      Babur, O.; Dogrusoz, U.; Çakır, M.; Aksoy, B. A.; Schultz, N.; Sander, C.; Demir, E. (BioMed Central Ltd., 2014)
      Background: Dynamic visual exploration of detailed pathway information can help researchers digest and interpret complex mechanisms and genomic datasets.Results: ChiBE is a free, open-source software tool for visualizing, ...
    • Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal 

      Gao J.; Aksoy, B. A.; Dogrusoz, U.; Dresdner, G.; Gross, B.; Sumer, S. O.; Sun, Y.; Jacobsen, A.; Sinha, R.; Larsson, E.; Cerami, E.; Sander, C.; Schultz, N. (American Association for the Advancement of Science (A A A S), 2013)
      The cBioPortal for Cancer Genomics (http://cbioportal.org) provides a Web resource for exploring, visualizing, and analyzing multidimensional cancer genomics data. The portal reduces molecular profiling data from cancer ...
    • An ontology for collaborative construction and analysis of cellular pathways 

      Demir, Emek; Babur, Özgün; Doğrusöz, Uğur; Gürsoy, Atilla; Ayaz, Aslı; Güleşır, Gürcan; Nişancı, Gürkan; Çetin Atalay, Rengül (Oxford University Press, 2004-02-12)
      Motivation: As the scientific curiosity in genome studies shifts toward identification of functions of the genomes in large scale, data produced about cellular processes at molecular level has been accumulating with an ...
    • PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways 

      Demir, Emek; Babur, Özgün; Doğrusöz, Uğur; Gürsoy, Atilla; Nişancı, Gürkan; Çetin Atalay, Rengül; Öztürk, Mehmet (Oxford University Press, 2002-06)
      Motivation: Availability of the sequences of entire genomes shifts the scientific curiosity towards the identification of function of the genomes in large scale as in genome studies. In the near future, data produced about ...
    • PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways 

      Demir, Emek; Babur, Özgün; Doğrusöz, Uğur; Gürsoy, Atilla; Nişancı, Gürkan; Çetin Atalay, Rengül; Öztürk, Mehmet (American Society for Biochemistry and Molecular Biology(ASBMB), 2002-09)
    • 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, Emek; 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.; Doğrusöz, Uğur; 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 ...