Advanced Data Visualization Research Articles

386 Improved Identification and Visualization of Emergency Department Patient Visits

386 Improved Identification and Visualization of Emergency Department Patient Visits

SBGN-ED – working with the Systems Biology Graphical Notation

AbstractThe Systems Biology Graphical Notation - SBGN [1] provides a standard for the visual representation of biochemical and cellular processes. SBGN aims to improve information exchange and to support the collaborative creation of large maps based on individual modules. The language contains three views of biological processes covering different levels of detail:(1) Process Description (PD): this sublanguage provides a detailed presentation of the temporal dependencies of biological interactions in a network;(2) Entity Relationship (ER): this sublanguage displays the relationships in which a given entity can participate in a network; and(3) Activity Flow (AF): this sublanguage shows the flow of information between biological entities in an abstract way.SBGN aims to support a more efficient and accurate communication of biological knowledge between different research communities. However, to increase its usage, tools for editing, validating, layouting and translating SBGN maps are desirable.We present novel developments in SBGN-ED [2], a tool which allows the creation of all three types of SBGN maps from scratch or the editing of existing maps, the validation of these maps for syntactical and semantical correctness, the translation of networks from databases such as KEGG into SBGN and the export of SBGN maps into several file and image formats. SBGN-ED is based on the Vanted system [3] for the integration, analysis and visualisation of experimental data within biological networks and functional hierarchies. We furthermore present some applications based on SBGN-ED such as RIMAS [4].SBGN-ED is freely available from http://www.sbgn-ed.org. The web site contains also tutorials and example files.[1] N. Le Novère et al. (2009) The systems biology graphical notation. Nature Biotechnology, 27: 735–741.[2] B.H. Junker, C. Klukas and F. Schreiber (2006) VANTED: a system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics, 7: 109.1–109.13.[3] T. Czauderna, C. Klukas and F. Schreiber (2010) Editing, validating, and translating of SBGN maps. Bioinformatics, 26(18): 2340-2341.[3] A. Junker, A. Hartmann, F. Schreiber, H. Bäumlein (2010) An engineers view on regulation of seed development. Trends in Plant Science 15(6): 303-307.

Novel developments in SBGN-ED and applications

Systems Biology Graphical Notation (SBGN, http://sbgn.org) [1] is an emerging standard for graphical representations of biochemical and cellular processes studied in systems biology. Three different views (Process Description, Entity Relationship, and Activity Flow) cover several aspects of the represented processes in different levels of detail. SBGN helps to communicate biological knowledge more efficient and accurate between different research communities in the life sciences. However, to support SBGN, methods and tools for editing, validating, and translating of SBGN maps are necessary.We present methods for these tasks and novel developments in SBGN-ED (www.sbgn-ed.org) [2], a tool which allows to create all three types of SBGN maps from scratch, to validate these maps for syntactical and semantical correctness, to translate maps from the KEGG database into SBGN, and to export SBGN maps into several file and image formats. SBGN-ED is based on VANTED (Visualization and Analysis of NeTworks containing Experimental Data, http://www.vanted.org) [3].As applications of SBGN and SBGN-ED we present furthermore MetaCrop (http://metacrop.ipk-gatersleben.de) [4], a database that summarizes diverse information about metabolic pathways in crop plants, and RIMAS (Regulatory Interaction Maps of Arabidopsis Seed Development, http://rimas.ipk-gatersleben.de) [5], an information portal that provides a comprehensive overview of regulatory pathways and genetic interactions during Arabidopsis embryo and seed development.[1] Le Novère, N. et al. (2009) The Systems Biology Graphical Notation. Nature Biotechnology, 27, 735-741.[2] Czauderna, T., Klukas, C., Schreiber, F. (2010) Editing, validating, and translating of SBGN maps. Bioinformatics, 26 (18), 2340-2341.[3] Junker, B.H., Klukas, C., Schreiber, F. (2006) VANTED: A system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics, 7, 109+.[4] Grafahrend-Belau, E., Weise, S., Koschützki, D., Scholz, U., Junker, B.H., Schreiber, F. (2008) MetaCrop - A detailed database of crop plant metabolism. Nucleic Acids Research, 36, D954-D958.[5] Junker, A., Hartmann, A., Schreiber, F., Bäumlein, H. (2010) An engineer's view on regulation of seed development. Trends in Plant Science, 15(6), 303-307.

Novel developments in SBGN-ED and applications

AbstractSystems Biology Graphical Notation (SBGN, http://sbgn.org) [1] is an emerging standard for graphical representations of biochemical and cellular processes studied in systems biology. Three different views (Process Description, Entity Relationship, and Activity Flow) cover several aspects of the represented processes in different levels of detail. SBGN helps to communicate biological knowledge more efficient and accurate between different research communities in the life sciences. However, to support SBGN, methods and tools for editing, validating, and translating of SBGN maps are necessary.We present methods for these tasks and novel developments in SBGN-ED (www.sbgn-ed.org) [2], a tool which allows to create all three types of SBGN maps from scratch, to validate these maps for syntactical and semantical correctness, to translate maps from the KEGG database into SBGN, and to export SBGN maps into several file and image formats. SBGN-ED is based on VANTED (Visualization and Analysis of NeTworks containing Experimental Data, http://www.vanted.org) [3].As applications of SBGN and SBGN-ED we present furthermore MetaCrop (http://metacrop.ipk-gatersleben.de) [4], a database that summarizes diverse information about metabolic pathways in crop plants, and RIMAS (Regulatory Interaction Maps of Arabidopsis Seed Development, http://rimas.ipk-gatersleben.de) [5], an information portal that provides a comprehensive overview of regulatory pathways and genetic interactions during Arabidopsis embryo and seed development.[1] Le Novère, N. et al. (2009) The Systems Biology Graphical Notation. Nature Biotechnology, 27, 735-741.[2] Czauderna, T., Klukas, C., Schreiber, F. (2010) Editing, validating, and translating of SBGN maps. Bioinformatics, 26 (18), 2340-2341.[3] Junker, B.H., Klukas, C., Schreiber, F. (2006) VANTED: A system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics, 7, 109+.[4] Grafahrend-Belau, E., Weise, S., Koschützki, D., Scholz, U., Junker, B.H., Schreiber, F. (2008) MetaCrop - A detailed database of crop plant metabolism. Nucleic Acids Research, 36, D954-D958.[5] Junker, A., Hartmann, A., Schreiber, F., Bäumlein, H. (2010) An engineer's view on regulation of seed development. Trends in Plant Science, 15(6), 303-307.

The forecast for predictive analytics: hot and getting hotter

The forecast for predictive analytics: hot and getting hotter

An introduction to data mining and other techniques for advanced analytics

This paper reviews the use of data mining (DM) for extracting patterns from large databases, held by companies such as banks, retailers and telco operators. The DM process is discussed, together with the ideal architecture, for applying this approach in a data warehouse environment. Some related techniques are identified — advanced data visualization tools for converting large volumes of data into pictorial form together with text mining and social network analysis for extracting structured data from unstructured text and relationships. The role of contact optimization is highlighted, as a method for optimizing the business value that a company can achieve from its DM activities. Finally, the paper suggests some initial steps in selecting a DM software product and offers the author's personal guidelines for the types of product that are likely to be most useful in different situations.

VANTED: a system for advanced data analysis and visualization in the context of biological networks.

BackgroundRecent advances with high-throughput methods in life-science research have increased the need for automatized data analysis and visual exploration techniques. Sophisticated bioinformatics tools are essential to deduct biologically meaningful interpretations from the large amount of experimental data, and help to understand biological processes.ResultsWe present VANTED, a tool for the visualization and analysis of networks with related experimental data. Data from large-scale biochemical experiments is uploaded into the software via a Microsoft Excel-based form. Then it can be mapped on a network that is either drawn with the tool itself, downloaded from the KEGG Pathway database, or imported using standard network exchange formats. Transcript, enzyme, and metabolite data can be presented in the context of their underlying networks, e. g. metabolic pathways or classification hierarchies. Visualization and navigation methods support the visual exploration of the data-enriched networks. Statistical methods allow analysis and comparison of multiple data sets such as different developmental stages or genetically different lines. Correlation networks can be automatically generated from the data and substances can be clustered according to similar behavior over time. As examples, metabolite profiling and enzyme activity data sets have been visualized in different metabolic maps, correlation networks have been generated and similar time patterns detected. Some relationships between different metabolites were discovered which are in close accordance with the literature.ConclusionVANTED greatly helps researchers in the analysis and interpretation of biochemical data, and thus is a useful tool for modern biological research. VANTED as a Java Web Start Application including a user guide and example data sets is available free of charge at .

Statistical, Computational and Visualization Methodologies to Unveil Gene Primary Structure Features

Gene sequence features such as codon bias, codon context, and codon expansion (e.g. trinucleotide repeats) can be better understood at the genomic scale level by combining statistical methodologies with advanced computer algorithms and data visualization through sophisticated graphical interfaces. This paper presents the ANACONDA system, a bioinformatics application for gene primary structure analysis. Codon usage tables using absolute metrics and software for multivariate analysis of codon and amino acid usage are available in public databases. However, they do not provide easy computational and statistical tools to carry out detailed gene primary structure analysis on a genomic scale. We propose the usage of several statistical methods--contingency table analysis, residual analysis, multivariate analysis (cluster analysis)--to analyze the codon bias under various aspects (degree of association, contexts and clustering). The developed solution is a software application that provides a user-guided analysis of codon sequences considering several contexts and codon usage on a genomic scale. The utilization of this tool in our molecular biology laboratory is focused on particular genomes, especially those from Saccharomyces cerevisiae, Candida albicans and Escherichia coli. In order to illustrate the applicability and output layouts of the software these species are herein used as examples. The statistical tools incorporated in the system are allowing to obtain global views of important sequence features. It is expected that the results obtained will permit identification of general rules that govern codon context and codon usage in any genome. Additionally, identification of genes containing expanded codons that arise as a consequence of erroneous DNA replication events will permit uncovering new genes associated with human disease.

Adding visualization functions of DAVIS to Jasp: Mixing two Java-based statistical systems

Jasp is an experimental general purpose Java-based statistical system which adopts several new computing technologies. It has a function-based and object-oriented language, an advanced user interface, flexible extensibility and a server/client architecture with distributed computing abilities. DAVIS is, on the other hand, a stand-alone Java-based system, and is designed for providing advanced data visualization functions with easy operations by a GUI. In this paper, it is made possible to use tools of DAVIS from within Jasp, in order that the new integrated system can handle not only data filtering and statistical analysis but also data visualization. We develop a mechanism for extending the server/client system of Jasp to realize an efficient collaboration with DAVIS in the client-side. It is shown that the mechanism is straightforward and simple.

Biological data integration: wrapping data and tools.

Nowadays scientific data is inevitably digital and stored in a wide variety of formats in heterogeneous systems. Scientists need to access an integrated view of remote or local heterogeneous data sources with advanced data accessing, analyzing, and visualization tools. Building a digital library for scientific data requires accessing and manipulating data extracted from flat files or databases, documents retrieved from the Web as well as data generated by software. We present an approach to wrapping web data sources, databases, flat files, or data generated by tools through a database view mechanism. Generally, a wrapper has two tasks: it first sends a query to the source to retrieve data and, second builds the expected output with respect to the virtual structure. Our wrappers are composed of a retrieval component based on an intermediate object view mechanism called search views mapping the source capabilities to attributes, and an eXtensible Markup Language (XML) engine, respectively, to perform these two tasks. The originality of the approach consists of: 1) a generic view mechanism to access seamlessly data sources with limited capabilities and 2) the ability to wrap data sources as well as the useful specific tools they may provide. Our approach has been developed and demonstrated as part of the multidatabase system supporting queries via uniform object protocol model (OPM) interfaces.

Use of Advanced Technology Videotapes in the Delivery of Structural Engineering Courses

A teaching and learning development project is currently under way at Queens-land University of Technology to develop advanced technology videotapes for use with the delivery of structural engineering courses. These tapes consist of integrated computer and laboratory simulations of important concepts, and behaviour of structures and their components for a number of structural engineering subjects. They will be used as part of the regular lectures and thus will not only improve the quality of lectures and learning environment, but also will be able to replace the ever-dwindling laboratory teaching in these subjects. The use of these videotapes, developed using advanced computer graphics, data visualization and video technologies, will enrich the learning process of the current diverse engineering student body. This paper presents the details of this new method, the methodology used, the results and evaluation in relation to one of the structural engineering subjects, steel structures.

Use of Advanced Technology Videotapes in the Delivery of Structural Engineering Courses

Abstract A teaching and learning development project is currently under way at Queens-land University of Technology to develop advanced technology videotapes for use with the delivery of structural engineering courses. These tapes consist of integrated computer and laboratory simulations of important concepts, and behaviour of structures and their components for a number of structural engineering subjects. They will be used as part of the regular lectures and thus will not only improve the quality of lectures and learning environment, but also will be able to replace the ever-dwindling laboratory teaching in these subjects. The use of these videotapes, developed using advanced computer graphics, data visualization and video technologies, will enrich the learning process of the current diverse engineering student body. This paper presents the details of this new method, the methodology used, the results and evaluation in relation to one of the structural engineering subjects, steel structures.

Visualization of n-dimensional analytical data on personal computers

Visualization is the task of creating images that allow important features in the data to be discerned much more readily than from the raw data. In this article we describe our efforts towards using three-dimensional graphics for improved visualization of different data from analytical chemistry. Various available algorithms are used to analyze and visualize data features that are otherwise difficult to grasp. A selection of case studies is presented to demonstrate the capabilities of data visualization. It is shown that, despite some limitations in computing power, it is perfectly feasible to use standard personal computers for advanced data visualization tasks.

Computerization of polymer matrix composite materials data and metadata

The Automotive Composites Consortium and ASTM are active in developing standards for the computerization of composite materials data and metadata. This paper describes the application of these emerging standards for polymer matrix composites and in particular those using graphite, aramid and glass fibres in both thermoset and thermoplastic matrix materials. A first generation advanced materials data visualization and integration system, M/VISION, has been completed for the collection and exchange of composite material properties data. Information is separated into test, design, and analysis categories with all data types stored as relational databases. The use of existing technical data exchange standards including the Automotive Composites Consortium's for collecting test data are discussed.