Browsing by Subject "Pathway visualization"

Now showing 1 - 4 of 4

Open Access
Integrating biological pathways and genomic profiles with ChiBE 2
(2013) Çakır, Merve
Biological pathways store information about spatial and temporal organization of interactions taking place in an organism. They hold valuable information that can assist scientific community in understanding the details of a particular mechanism or deciphering the reasons of disruption when the system goes wrong. However, extracting knowledge from these pathways is not trivial as they can be huge and complicated. Additionally, simple visualization of pathways will only reveal limited knowledge, whereas their integration with experimental results can identify distinct and intriguing relationships. Therefore, it is critical to have tools that are specialized in analyzing and understanding biological pathways. ChiBE is one such tool that can visualize, manipulate and analyze pathway data stored in BioPAX format. While preparing the second version of the tool, there have been improvements regarding pathway searches, high throughput data integration, and database connections. Visual notation has also been updated in order to follow standards in visualizations defined by the SBGN community. Previously defined pathway query algorithms have been adapted to be compatible with the BioPAX model. New query types have also been designed to offer a wider range of options. With these queries, ChiBE now offers a variety of ways of pathway decomposition and thorough analysis of complex pathway views. There has also been improvements in integration of high throughput experimental results. To offer easy access to expression microarrays, a gateway to the GEO database has been added. The cBio Cancer Genomics Portal is also now reachable within ChiBE in order to obtain information about genomic status of various cancer cells. After simply asking for an identifier of a particular experiment, ChiBE retrieves the results from databases and then integrates them with the available pathway view through color codes. Furthermore, a connection to DAVID database is available, in case users want to annotate a list of genes with respect to biological terms associated with them. With these new features and improvements, ChiBE 2 has become a comprehensive tool that offers a wide range of analysis options with a genomics-oriented workflow to deepen our understanding of biological pathways.
Open Access
A layout algorithm for signaling pathways
(Elsevier, 2006-01-20) Genç, Burkay; Doğrusöz, Uğur
Visualization is crucial to the effective analysis of biological pathways. A poorly laid out pathway confuses the user, while a well laid out one improves the user's comprehension of the underlying biological phenomenon. We present a new, elegant algorithm for layout of biological signaling pathways. Our algorithm uses a force-directed layout scheme, taking into account directional and rectangular regional constraints enforced by different molecular interaction types and subcellular locations in a cell. The algorithm has been successfully implemented as part of a pathway visualization and analysis toolkit named Patika, and results with respect to computational complexity and quality of the layout have been found satisfactory. The algorithm may be easily adapted to be used in other applications with similar conventions and constraints as well. Patika version 1.0 beta is available upon request at http://www.patika.org. © 2004 Elsevier Inc. All rights reserved.
Open Access
Patika Web : a Web service for accessing and visualizing pathway data in patika database
(2005) Erson, Emine Zeynep
After completion of Human Genome Project, there has been an exponential increase in the available biological data. Although there has been an enormous effort for creating ontologies, standards and tools, current bioinformatics infrastructure is far from coping with this data. The Patika Project aims to provide the community an integrated environment for modeling, analyzing and integrating cellular processes. Patika project develops software tools providing access, visualization and analysis on the data in Patika database. In this thesis, we present analysis, design and implementation of Patikaweb, a Web-service having a user-friendly interface without requiring any registrations, installations. To achieve an enhanced data analysis , Patikaweb provides a multiple-view schema , compartments and compound graphs for visualizing molecular complexes, pathways and black-box reactions. Querying component supports SQL-like queries and an array of graphtheoretic queries for finding feedback loops, common targets and regulators, or interesting subgraphs based on user’s genes of interest. Constructed models can be saved in XML, exported to standard formats such as BioPAX, SBML or converted to static images. A highly interactive and user friendly querying interface is supported with Patikaweb. Visual representation of complex information in pathway research is very important. The information should be presented with high coverage, while providing a user friendly interface. In this thesis we also present a new approach to visualize complex pathway information coping with the limitations introduced by ontology and graphical representation. Patikaweb ’s unique visualization and querying features fill an important gap in the pool of currently available tools and databases.
Open Access
VISIBIOweb : a web-based visualization and layout service for biological pathways
(2009) Dilek, Alptuğ
A biological pathway is a representation of biological reactions between molecules in a living cell. At present, there are hundreds of Internet-accessible databases storing biological pathway data. Exchanging, handling, and storing this data are crucial in terms of both providing understandability and allowing further enhancements on the gathered data. As a result of this necessity, many biological models were developed to cluster the data in a meaningful manner under a semantically reasonable hierarchy. As the amount and complexity of the data increases, visualization of pathways becomes inevitable. Graphs are inherently suitable for modeling pathways. The task of creating a visual representation for pathways dynamically requires methods from the area of graph visualization. As a result, many software systems, which can interpret the pathway data with a graph structure and visualize the constructed graph, emerged. However, many of these software systems are insufficient due to poor complexity handling of the underlying model, lack of visual standardization or long installation steps. In this thesis, we introduce VISIBIOweb, a new open-source and web-based visualization service for biological pathway models stored in BioPAX (Biological Pathways Exchange Language) format. VISIBIOweb runs on Apache Tomcat server and is implemented in Java based on Eclipse GEF (Graphical Editing Framework). Google Maps API is used on the client side as the core component to visualize the representation constructed on the server. VISIBIOweb supports basic graph viewing functionalities such as zooming, scrolling, and selection of graph objects. The inspector window is provided to view the properties of the selected graph object. Once the view for the uploaded biological model is created, it can be stored as a static image. The biological models can also be persisted and embedded within other web sites just like Google Maps. The layout information of the constructed graph is also provided in an XML-based format. The introduction of such a format is a good starting point to develop an official layout extension for BioPAX format.