Methods and tools for visualization and management of SBGN process description maps

Ankara : The Department of Computer Engineering and the Graduate School of Engineering and Science of Bilkent University, 2014.Thesis (Master's) -- Bilkent University, 2014.Includes bibliographical references leaves 70-71.Graphs are commonly used to model relational information in many areas such as relational databases, software engineering, biological and social networks. In visualization of graphs, automatic layout, interactive editing and complexity management of crowded graphs are essential for effective utilization of underlying information. Advances in graphical user interfaces have given rise and value to interactive editing and diagramming techniques in graph visualization. As the size of the information to be visualized vastly increased, it became harder to analyze such networks, making use of relational information needed to be acquired. To overcome this problem, sophisticated and domain-specific complexity management techniques should be provided. The Systems Biology Graphical Notation (SBGN) has been developed over a number of years by biochemists and computer scientists to standardize visual representation of biochemical and cellular processes. SBGN introduces a concrete, detailed set of symbols for scientists to represent network of interactions, in a way that is not open to more than one interpretation. It also describes the manner, in which such graphical information should be interpreted. The SBGN Process Description (PD) language shows how entities are influenced by processes, which are represented by several reaction types in a biological pathway. It can be used to show all the molecular interactions taking place in a network of biochemical entities, with the same entity appearing multiple times in the same diagram. We developed methods and tools to effectively visualize and manage SBGNPD diagrams. Specifically, we introduced new algorithms for proper management of complexity of large SBGN-PD diagrams. These algorithms strive to keep SBGN-PD diagrams intact as complexity management takes places. In addition, we provided software components and web-based tools that implement these methods. These tools use state-of-the-art web technologies and libraries.Sarı, MecitM.S

New Energetic Copper(II) Complexes With Pyrazolyl Type Ligands

Aksu, Mecit/0000-0002-9864-727XWOS: 000287942300013Nine Cu-II complexes (I-IX) containing the azide ion and bis-2,6-(pyrazol-1-yl)pyridine (pp), bis-2,6-(pyrazol-1-yl)pyridine (dmpp), and 2-(pyrazol-1-yl)-6-(3,5-dirnethylpyrazol-1-yl)pyridine (mpp), which are derivatives of pyrazolylpyridine, were prepared in nonaqueous medium. These complexes were characterized by elemental analyses and IR spectroscopy. Crystals of one of these complexes [CumppClN(3) (VII)] were prepared in suitable size, and a molecular structure of this complex was obtained with X-ray diffraction method. Complexes were examined by thermogravimetry and differential scanning calorimetry methods. Thermal decomposition was observed in complexes including two azide groups similar to that seen in explosives. In the complexes containing one azide group, formation of the Cu-1 complexes was observed after thermal decomposition of the azide group.Ankara University Research FundAnkara University [07B4240001]The authors thank to acknowledge the financial support of the Ankara University Research Fund (Project No: 07B4240001