Browsing by Subject "Biological process diagrams"
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Item Open Access Automated layout of process description maps drawn in systems biology graphical notation = Systems biology graphical notation kullanılarak çizilen proses diyagramlarının otomatik yerleştirilmesi(2014) Genç, BegümEvolving technology has increased the focus on genomics. The combination of today’s advanced studies with decades of molecular biology research yield in huge amount of pathway data. These models can be used to improve high-throughput data analysis by linking correlation to the causation, shedding light on many complex diseases. In order to prevent ambiguity and ensure regularity of the research, a need for using a standard notation has emerged. Systems Biology Graphical Notation (SBGN) is a visual language developed by a community of biochemists, modellers and computer scientists with the intention of enabling scientists to represent networks, including models of cellular processes, in a standard, unambiguous way. SBGN is formed of three languages: process, entity relationship and activity flow. This research is focused on its process diagram branch. Automated layout is commonly used to clearly visualize the information represented by graphs. Considering the fact that, biological pathways includes nested structures (e.g., nucleoplasms), we have made use of a force-directed automatic layout algorithm called Compound Spring Embedder (CoSE), which supports the compound graph structures. On top of this layout structure, we have developed a specialized layout algorithm called SBGN-PD layout. SBGN-PD layout enhancements mainly include properly tiling of complex members and disconnected molecules, placement of product and substrate edges on the opposite sides of a process node without disturbing the force-directed structure of the algorithm.Item Open Access Systems biology graphical notation markup language (SBGNML) version 0.3(De Gruyter, 2020) Luna, A.; Bergmann, F. T.; Czauderna, T.; Doğrusöz, Uğur; Rougny, A.; Dräger, A.; Touré, V.; Mazein, A.; Mazein, M. L.This document defines Version 0.3 Markup Language (ML) support for the Systems Biology Graphical Notation (SBGN), a set of three complementary visual languages developed for biochemists, modelers, and computer scientists. SBGN aims at representing networks of biochemical interactions in a standard, unambiguous way to foster efficient and accurate representation, visualization, storage, exchange, and reuse of information on all kinds of biological knowledge, from gene regulation, to metabolism, to cellular signaling. SBGN is defined neutrally to programming languages and software encoding; however, it is oriented primarily towards allowing models to be encoded using XML, the eXtensible Markup Language. The notable changes from the previous version include the addition of attributes for better specify metadata about maps, as well as support for multiple maps, sub-maps, colors, and annotations. These changes enable a more efficient exchange of data to other commonly used systems biology formats (e. g., BioPAX and SBML) and between tools supporting SBGN (e. g., CellDesigner, Newt, Krayon, SBGN-ED, STON, cd2sbgnml, and MINERVA). More details on SBGN and related software are available at http://sbgn.org. With this effort, we hope to increase the adoption of SBGN in bioinformatics tools, ultimately enabling more researchers to visualize biological knowledge in a precise and unambiguous manner.