12 research outputs found

    A new dynamical layout algorithm for complex biochemical reaction networks

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    BACKGROUND: To study complex biochemical reaction networks in living cells researchers more and more rely on databases and computational methods. In order to facilitate computational approaches, visualisation techniques are highly important. Biochemical reaction networks, e.g. metabolic pathways are often depicted as graphs and these graphs should be drawn dynamically to provide flexibility in the context of different data. Conventional layout algorithms are not sufficient for every kind of pathway in biochemical research. This is mainly due to certain conventions to which biochemists/biologists are used to and which are not in accordance to conventional layout algorithms. A number of approaches has been developed to improve this situation. Some of these are used in the context of biochemical databases and make more or less use of the information in these databases to aid the layout process. However, visualisation becomes also more and more important in modelling and simulation tools which mostly do not offer additional connections to databases. Therefore, layout algorithms used in these tools have to work independently of any databases. In addition, all of the existing algorithms face some limitations with respect to the number of edge crossings when it comes to larger biochemical systems due to the interconnectivity of these. Last but not least, in some cases, biochemical conventions are not met properly. RESULTS: Out of these reasons we have developed a new algorithm which tackles these problems by reducing the number of edge crossings in complex systems, taking further biological conventions into account to identify and visualise cycles. Furthermore the algorithm is independent from database information in order to be easily adopted in any application. It can also be tested as part of the SimWiz package (free to download for academic users at [1]). CONCLUSION: The new algorithm reduces the complexity of pathways, as well as edge crossings and edge length in the resulting graphical representation. It also considers existing and further biological conventions to create a drawing most biochemists are familiar with. A lot of examples can be found on [2]

    PathMAPA: a tool for displaying gene expression and performing statistical tests on metabolic pathways at multiple levels for Arabidopsis

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    BACKGROUND: To date, many genomic and pathway-related tools and databases have been developed to analyze microarray data. In published web-based applications to date, however, complex pathways have been displayed with static image files that may not be up-to-date or are time-consuming to rebuild. In addition, gene expression analyses focus on individual probes and genes with little or no consideration of pathways. These approaches reveal little information about pathways that are key to a full understanding of the building blocks of biological systems. Therefore, there is a need to provide useful tools that can generate pathways without manually building images and allow gene expression data to be integrated and analyzed at pathway levels for such experimental organisms as Arabidopsis. RESULTS: We have developed PathMAPA, a web-based application written in Java that can be easily accessed over the Internet. An Oracle database is used to store, query, and manipulate the large amounts of data that are involved. PathMAPA allows its users to (i) upload and populate microarray data into a database; (ii) integrate gene expression with enzymes of the pathways; (iii) generate pathway diagrams without building image files manually; (iv) visualize gene expressions for each pathway at enzyme, locus, and probe levels; and (v) perform statistical tests at pathway, enzyme and gene levels. PathMAPA can be used to examine Arabidopsis thaliana gene expression patterns associated with metabolic pathways. CONCLUSION: PathMAPA provides two unique features for the gene expression analysis of Arabidopsis thaliana: (i) automatic generation of pathways associated with gene expression and (ii) statistical tests at pathway level. The first feature allows for the periodical updating of genomic data for pathways, while the second feature can provide insight into how treatments affect relevant pathways for the selected experiment(s)

    Visualisierung biochemischer Reaktionsnetze

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    In dieser Arbeit werden Anforderungen an die Darstellung biochemischer Reaktionsnetze untersucht und die Netze unter dem Gesichtspunkt der Visualisierung modelliert. Anschliessend wird ein Algorithmus zum Zeichnen biochemischer Reaktionsnetze entwickelt und analysiert.In this dissertation we investigate the requirements for the visualisation of biochemical reaction networks. We compose a model for these networks that lends itself to visualisation and develop and analyse an algorithm to create drawings of the networks

    Kreuzungen in Cluster-Level-Graphen

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    Clustered graphs are an enhanced graph model with a recursive clustering of the vertices according to a given nesting relation. This prime technique for expressing coherence of certain parts of the graph is used in many applications, such as biochemical pathways and UML class diagrams. For directed clustered graphs usually level drawings are used, leading to clustered level graphs. In this thesis we analyze the interrelation of clusters and levels and their influence on edge crossings and cluster/edge crossings.Cluster-Graphen sind ein erweitertes Graph-Modell mit einem rekursiven Clustering der Knoten entsprechend einer gegebenen Inklusionsrelation. Diese bedeutende Technik um Zusammengehörigkeit bestimmter Teile des Graphen auszudrücken wird in vielen Anwendungen benutzt, etwa biochemischen Reaktionsnetzen oder UML Klassendiagrammen. Für gerichtete Cluster-Graphen werden üblicherweise Level-Zeichnungen verwendet, was zu Cluster-Level-Graphen führt. Diese Arbeit analysiert den Zusammenhang zwischen Clustern und Level und deren Auswirkungen auf Kantenkreuzungen und Cluster/Kanten-Kreuzungen

    SEMEDA (Semantic Meta-Database) : ontology based semantic integration of biological databases

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    Köhler J. SEMEDA (Semantic Meta-Database) : ontology based semantic integration of biological databases. Bielefeld (Germany): Bielefeld University; 2003.The work presented in this thesis is outlined in the following. The state of the art in the relevant disciplines is introduced and reviewed in chapter 2. This includes on the one hand the current state of molecular biological databases, their heterogeneity and the integration of molecular biological databases. On the other hand the current usage of ontologies in general and with special regard to database integration is described. The principles of semantic database integration as introduced in this thesis are new and suitable to be used also in other database integration systems, which have to deal with a high number of semantically heterogeneous databases. Therefore in Chapter 3 the newly introduced principles for ontology based semantic database integration are presented independent of their implementation. Chapter 4 introduces the requirements for the implementation of a semantic database integration system (SEMEDA). Several general requirements for the integration of molecular biological systems from the scientific literature are discussed with regard to the feasibility of their implementation in general and in SEMEDA. In addition, the requirements specific to semantic database integration are introduced. In addition how the BioDataServer is used to overcome "technical" heterogeneity, so that SEMEDA only has to deal with semantic heterogeneity is analysed. In chapter 5, an appropriate data structure for storing ontologies, database metadata and the semantic definitions as described in Chapter 3 is developed. Subsequently, it is discussed how this data structure can be edited and queried. In Chapter 6, SEMEDAs software design, implementation and system architecture is given. Chapter 7 describes the use of SEMEDA and its interfaces. The user interface SEMEDA-edit is used to collaboratively edit ontologies and to semantically define databases using ontologies. SEMEDA-query is the query interface that provides uniform access to heterogeneous databases. In addition, a set of procedures exists which can be used by external applications. In order to use SEMEDA to semantically define databases, an appropriate ontology is needed. Although SEMEDA allows building ontologies from the scratch, due to the fact that generating ontologies is a labour intensive time-consuming task, it would be preferable to use an existing ontology. Therefore, in chapter 8 several ontologies were evaluated for their usability in SEMEDA. The intention was to find out if a suitable ontology can be found and imported or whether it is more appropriate to build a custom ontology for SEMEDA. It turned out that the existing ontologies were not well suited for semantic database integration. In chapter 9 general and SEMEDA specific ontology design principles are introduced which were then followed to build a custom ontology for database integration. The structure of this custom ontology and some issues concerning its use for semantic database integration are explained. In chapter 10, the practical use of SEMEDA is described by two examples. The first section of this chapter shows how SEMEDA supports the building of user schemata for the BioDataServer. The second section describes how the clone database of the RZPD Berlin (Deutsches Ressourcenzentrum für Genomforschung GmbH) is connected to SEMEDA and thus linked to the other databases. In the discussion (chapter 11) SEMEDA is compared to existing database integration systems, especially other ontology based integration systems. It is further discussed how principles for semantic database integration apply to other database integration systems and how they might be implemented there. A database mirror is proposed to improve the overall performance of SEMEDA and the BioDataServer

    Forschungsbericht 2000 : Berichtszeitraum 1997-1998

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    Eine junge Einrichtung mit 100jähriger Tradition: Das ist die Fachhochschule - Dortmund. Der scheinbare Widerspruch ist schnell aufzulösen. Die Fachhochschule Dortmund wurde zwar offiziell 1971 gegründet, ihre älteste Vorgängereinrichtung, die "Königliche Werkmeisterschule für Maschinenbauer" eröffnete jedoch ihre Pforten bereits im Jahre 1890. Am Grundgedanken hat sich in der langen Zeit jedoch nichts geändert: Studium und Lehre sind an der Lösung von anwendungsnahen Problemen und Aufgaben orientiert, erfahrene Professoren garantieren die Verbindung zur Praxis und ermöglichen heute ein perspektivenreiches Studium in neun Fachbereichen mit insgesamt 20 Studiengängen: Vom Design über Informatik und Ingenieurwissenschaften bis hin zu Sozialwesen und Wirtschaft sind heute rund 8500 Studenten an der Fachhochschule Dortmund eingeschrieben. Dortmund mit seinen rund 600 000 Einwohnern hat nicht nur eine leistungsfähige Industrie, günstige Einkaufsmöglichkeiten, ein reichhaltiges Kulturangebot und ein begeisterungsfähiges Fußballpublikum: Umgeben von 50 Prozent Grünflächen wachsen hier zunehmend zukunftsorientierte Betriebe der Hochtechnologie und kompetente Dienstleistungsunternehmen mit Schwerpunkten zum Beispiel in der Medien-, Software- und der Versicherungswirtschaft heran. Gemeinsam mit der Universität und anderen Forschungseinrichtungen unterstützt die Fachhochschule diese Entwicklung mit einem wichtigen "Betriebskapital": Gut ausgebildeten Fachkräften. Zum Beispiel in der modernen Informations- und Kommunikationstechnik - Stichwort: Multimedia-, der Konstruktion von Komponenten für die Fabrik von morgen oder der Entwicklung von Systemen für den Umweltschutz. Neu im Angebot der FH sind die Studiengänge "Fahrzeug- und Verkehrstechnik", "Gebäudesystemtechnik" sowie zwei Verbundstudiengänge (Fernstudiengänge mit Präsenzphasen für Berufstätige) für Wirtschaftsinformatik und Verwaltungsbetriebswirtschaft. Doch nicht nur Technik und Wirtschaft bestimmen das Angebot: Die Fachhochschule trägt ihre Verantwortung für die Zukunft auch durch Ausbildung auf dem sozialen Sektor und in gestalterischkünstlerischen Bereichen Rechnung

    Personen- und Vorlesungsverzeichnis : Wintersemester 2007/08

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    Retrodigitalisierte Vorlesungsverzeichnisse der Johannes-Gutenberg-Universität. Teilweise auch enthaltend: - Vorlesungsverzeichnis - Personenverzeichnis - Studienverzeichnis - Personalverzeichni
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