Asadulina, Albina: A dictionary of chemical names and synonyms merged from different resources based on 2d graph representation for the purpose of recognition of chemical names in the text. Bonn, 2010 Bonn, Aachen, International Center for Information Technology (B-IT), Master Thesis, 2010 Schlagwörter: Master Thesis Institutsveroffentlichung: SCAI

Gu, Lei: Analyzing human complex diseases by applying genome-wide association study, candidate approach, pathway-based approach and endophenotype analysis. Bonn, 2010 Bonn, Aachen, International Center for Information Technology (B-IT), Master Thesis, 2010 Schlagwörter: Master Thesis Institutsveröffentlichung: SCAI: Abteilung: BIO

Tallam, Aravind: Extraction of numerical measures, statistical evidences and units, their relation extraction with the text. Bonn, Aachen, 2010 Bonn, Aachen, International Center for Information Technology (B-IT), Master Thesis, 2010 Schlagwörter: Master Thesis Institutsveröffentlichung: SCAI: Abteilung: BIO

Gurulingappa, Harsha: Concept-based semi-automatic extension of drug hierarchies. Bonn : B-it, 2009 Bonn-Aachen International Center for Information Technology, Master Thesis, 2009 Schlagwörter: Master Thesis Institutsveröffentlichung: SCAI: Abteilung: BIO Volltext

Haupt, Carina S.: Markush structure reconstruction : a prototype for their reconstruction from image and text into a searchable, context sensitive grammar based extension of SMILES. Sankt Augustin, 2009 Sankt Augustin, Hochschule Bonn-Rhein-Sieg, Master Thesis, 2009 Schlagwörter: chemoCR; Markush; extSMILES; context free grammar; patent search; structure reconstruction; Master Thesis Institutsveröffentlichung: SCAI: Abteilung: BIO
Abstract: Today publications are digitally available which enables researchers to search the text and often also the content of tables. On the contrary, images cannot be searched which is not a problem for most fields, but in chemistry most of the information are contained in images, especially structure diagrams. Next to the "normal" chemical structures, which represent exactly one molecule, there also exist generic structures, so called Markush structures. These contain variable parts and additional textual information which enable them to represent several molecules at once. This can vary between just a few and up to thousands or even millions. This ability lead to a spread of Markush structures in patents, because it enables patents to protect entire families of molecules at once. Next to the prevention of an enumeration of all structures it also has the advantage that, if a Markush structure is used in a patent, it is much harder to determine whether a specific structure is protected by it or not. To solve the question about the protection of a structure, it is necessary to search the patents. Appropriate databases for this task already do exist, but are filled manually. An automatic processing does not yet exist. In this project a Markush structure reconstruction prototype is developed which is able to reconstruct bitmaps including Markush structures (meaning a depiction of the structure and a text part describing the generic parts) into a digital format and save them in the newly developed context-free grammar based file format extSMILES. This format is searchable due to its context-free grammar based design. To be able to develop a Markush structure reconstruction prototype, an in depth analysis of the concept of Markush structures and their requirements for a reconstruction process was performed. Thereby it is stated, that the common connection table concept of the existing file formats is not able to store Markush structures. Especially challenging are conditions for most of the formats. Thus, a context-free grammar based file format is developed, which extends the SMILES format. This extSMILES called format assures the searchability of the results by its context-free grammar based concept, and is able to store all information contained in Markush structures. In addition it is generic, extendable and easily understandable. The developed prototype for the Markush structure reconstruction uses ext- SMILES as output format and is based on the chemical structure recognition tool chemoCR and the Unstructured Information Management Architecture UIMA. For chemoCR modules are developed which enable it to recognize and assemble Markush structures as well as to return the reconstruction result in extSMILES. For UIMA on the other hand, a pipeline is developed, which is able to analyse and translate the input text files to extSMILES. The results of both tools then are combined and presented in chemoCR. An evaluation of the prototype is performed on a representative set of twelve structures of interest and low image quality which contain all typical Markush elements. Trivial structures containing only one R-group are not evaluated. Due to the challenging nature of the images, no Markush structure could be correctly reconstructed. But by regarding the assumption, that R-group definitions which are described by natural language are excluded from the task, and under the condition that the core structure reconstruction is improved, the rate of success can be increased to 58.4%. Volltext

Müller, Bernd: Visualization and analysis of extracted information from full text and patent corpora. Bonn, Aachen, 2009 Bonn-Aachen International Center for Information Technology, Master Thesis, 2009 Schlagwörter: Master Thesis Institutsveröffentlichung: SCAI: Abteilung: BIO

Praveen, Paurush: Computational modeling of host-pathogen protein interactions. Bonn, Aachen, 2009 Bonn-Aachen International Center for Information Technology, Master Thesis, 2009 Schlagwörter: Master Thesis Institutsveröffentlichung: SCAI: Abteilung: BIO

Sahadevan, Sudeep: Adaptation of the mining environment SCAIView to the needs of animal scientists. Sankt Augustin, 2009 Bonn-Aachen International Center for Information Technology, Master Thesis, 2009 Schlagwörter: Master Thesis Institutsveröffentlichung: SCAI: Abteilung: BIO
Abstract: Researches in biological sciences are knowledge based, where any prior knowledge in a given research field is as important as the formulation of a hypothesis. Text mining and knowledge discovery methods have been utilized in human genomics and related fields for identifying genes, proteins, related networks and to enrich the identified entities with external database information, the important prior knowledge in the field. But, in livestock genomics however, the extraction of prior information is restricted to traditional keyword search and document retrieval. The aim of this thesis is the introduction of text mining applications to livestock genomics and associated field. ProMiner, a dictionary and rule based named entity recognition system and the associated knowledge dscovery platform SCAIView has been successfully used in human, mouse and plant genomics and related fields. Through this thesis the existing SCAIView and the associated system was adapted for the use in livestock genomics field and the present version works with cattle and pig data. Considering the importance given to the preimplantation period in cattle genomics, a terminology for cattle preimplantation period was developed and integrated into the adapted livestock genomics version of SCAIView to aid concept based search. The present version of livestock genomics SCAIView is intended as a prototype for demonstrating possibilities of text mining and knowledge discovery to the researchers
in livestock genomics. Volltext

Weuffel, Thomas; Kaul, Manfred (Betreuer); Berrendorf, Rudolf (Betreuer): Vorbelegung und lose Reservierung von Ressourcen in lokalen Cluster-Umgebungen : Evaluation, Modellierung und Implementierung eines objektorientierten Cluster-Schedulers unter Berücksichtigung von Advance Reservation und loser Reservierung. Sankt Augustin, 2009 Sankt Augustin, Hochschule Bonn-Rhein-Sieg, Master Thesis, 2009 Schlagwörter: scheduling; scheduler; local resource managment system; lose reservaitions; reservation; advance reservation; cluster; Master Thesis Institutsveröffentlichung: SCAI: Abteilung: BIO
Abstract: Heutige Cluster bestehen aus einzelnen Rechnersystemen, die über schnelle Netzwerkverbindungen untereinander kommunizieren und durch ein Local Resource Management System (LRMS) gesteuert werden, welches die Aufgaben plant und die Schnittstelle des Clusters darstellt. Ein Zusammenschluss mehrerer Cluster zu einem Grid ermöglicht die Ausführung von komplexen Workflows und die Lösung von Problemen, die auf Grund ihrer Komplexität auf einem einzelnen System nicht lösbar sind. Dabei müssen häufig Ressourcen im Grid co-allokiert werden, was Advance Reservation voraussetzt. Das von der Fraunhofer Gesellschaft bisher eingesetzte LRMS Extensive Argonne Scheduling sYstem (EASY) erlaubt die Erstellung neuer Jobs und Reservierungen. Der in einer Reservierung auszuführende Job muss jedoch bei derer Erstellung angegeben werden, was oftmals problematisch ist. Eine Anbindung einer Grid-Middleware ist wegen einer fehlenden Schnittstelle nur umständlich über einen zusätzlichen Adapter möglich. In dieser Arbeit wurde ein neues objektorientiertes LRMS konzipiert und implementiert. Es wurden offene und flexible Schnittstellen erstellt, die für die Anbindung externer Applikationen oder eigener Clients genutzt werden können. Die Anforderungen von Advance Reservation wurden bei der Konzeption berücksichtigt, so dass jede Reservierung nun eine eigene, verwaltbare Queue besitzt. Ein erstelltes, flexibles Modell zur Implementierung von Scheduling-Algorithmen erlaubt dem Cluster-Betreiber außerdem, das Scheduling auch im Betrieb an die aktuellen Anforderungen anzupassen. Weiterhin wird der durch Reservierungen bedingte Auslastungsverlust beim Scheduling betrachtet. Reservierungen fragmentieren den Schedulingplan und es können Zeiträume entstehen, in denen Ressourcen ungenutzt sind. Um Reservierungen bereits während dem Scheduling besser zu berücksichtigen, wurde eine Divide & Conquer- basierte Variante eines Algorithmus erstellt, der zu einem Zeitpunkt die optimale Belegung der freien Ressourcen berechnet. Ein neuer Typ von Reservierung - die lose Reservierung - wird eingeführt, welche durch einen frühesten Start-, einen spätesten Endzeitpunkt und eine Ausführungsdauer definiert ist. Es wird die Vermutung untersucht, ob der Einsatz von losen Reservierungen zu einer Erhöhung der Auslastung beziehungsweise der gleichzeitig planbaren Reservierungen führt. Durch Messungen konnte gezeigt werden, dass sowohl durch die losen Reservierungen als auch den modifizierten Algorithmus im Vergleich zu beispielsweise FCFS eine vergleichbare, in Teilbereichen sogar bessere Auslastung erzielt wird.

Thomas, Philippe: Automated extraction of variation mentions from literature sources and mapping to a unique database identifier. Tübingen, 2008 Tübingen, Univ., Master Thesis, 2008 Schlagwörter: Master Thesis Institutsveröffentlichung: SCAI: Abteilung: BIO Volltext

Younesi, Erfan: Analysis of molecular interaction networks associated with breast cancer tumour susceptibility. Bonn, 2008 Bonn, Univ., Master Thesis, 2008 Schlagwörter: disease model; network biology; breast cancer; susceptibility; Master Thesis Institutsveröffentlichung: SCAI: Abteilung: BIO
Abstract: Recent application of network theory to biological area has laid down the foundation of a model framework so-called "integrative functional informatics" or "integrative bioinformatics". Within the frame of this thesis project, such a model framework is proposed to tackle the complexity of tumor susceptibility in breast cancer. Incorporation of a priori but hidden knowledge in the literature using text-mining and knowledge discovery techniques proved to be of value in leveraging the ability of interpretation of current knowledge as well as identification of novel associations between biological entities.The proposed integrative approach and the resultant model in this research offer a network-based explanation for the emergence of complex phenotypes in a complex polygenic disorder such as breast cancer. Volltext

Faroughi, Arash: Integration von VO-Management Technologien in UNICORE. Gummersbach, 2007 Gummersbach, Fachhochschule, Master Thesis, 2007 Schlagwörter: Master Thesis Institutsveröffentlichung: SCAI: Abteilung: Bioinformatik
Abstract: Reliable authentication and authorisation are crucial for both service providers and their customers, where the former want to protect their resources from unauthorised access and fraudulent use while their customers want to be sure that unauthorised access to their data is prevented. In Grid environments Virtual Organisations (VO) have been adopted as a means to organise and control access to resources and data based on roles that are assigned to users. Moreover, attribute based authorisation has emerged providing a decentralised approach with better scalability. Up to now UNICORE authentication and authorisation is based on X.509-certificates only. In this master thesis we will present two implementational solutions to integrate both role or attribute based authorisation using VOMS and attribute based authorisation using Shibboleth into UNICORE. Volltext

Gattermayer, Tobias: SCAIView : Annotation and Visualization System for Knowledge Discovery. Bonn, Aachen, 2007 Bonn-Aachen International Center for Information Technology, Master Thesis, 2007 Schlagwörter: Master Thesis Institutsveröffentlichung: SCAI

Gündel, Michaela: ArrayProcess : Work Flow for Microarrays. Bonn, Aachen, 2007 Bonn-Aachen International Center for Information Technology, Master Thesis, 2007 Schlagwörter: Master Thesis Institutsveröffentlichung: SCAI

Ou, Chia-Hao: Extension of chemoCR : from reconstruction of chemical molecules to reconstruction of whole chemical reactions. Bonn, Aachen, 2007 Bonn-Aachen International Center for Information Technology, Master Thesis, 2007 Schlagwörter: Master Thesis Institutsveröffentlichung: SCAI

Shahid, Mohammad: Large Scale Virtual High Throughput Screening (vHTS) on an Optical High Speed Testbed. Bonn, 2007 Bonn, Bonn-Aachen International Center for Information Technology (B-IT), Master Thesis, 2007 Schlagwörter: Master Thesis Institutsveröffentlichung: SCAI: Abteilung: Bioinformatik
Abstract: The over growing burden of antimalarial drug resistance places much emphasis on the immediate development of new antimalarial drugs. Malaria is a dreadful disease and the risk continues to the global health as the resistance develops more quickly than the development of new drugs. To combat Malaria, a large scale virtual high throughput screening activity was conducted using new potential drug targets. Triosphosphate isomerase and Enoyl-acyl carrier protein reductase were selected as novel drug targets. These enzymes play a very significant role in the life cycle of the malarial parasite. Compound libraries containing hundreds of thousands of small molecules were designed using similarity measures for the in silico virtual screening by molecular docking using two different docking algorithms; FlexX and AutoDock. To meet the computational demands and to speed up the discovery process, large scale virtual screening was deployed on a Grid infrastructure using the UNICORE middleware. The relevance of the Grid services in the drug discovery program is demonstrated in this project. New candidate compounds for the selected malarial targets were identified and recommended for further optimization and biological analysis. Volltext

Galunic, Goran; Berrendorf, Rudolf (Betreuer); Kaul, Manfred (Betreuer); Clees, Tanja (Betreuer): Parallelisierung des Galerkin Produkts im AMG Verfahren mit OpenMP. Sankt Augustin, 2006 Sankt Augustin, Hochschule Bonn-Rhein-Sieg, Master Thesis, 2006 Schlagwörter: Master Thesis Institutsveröffentlichung: SCAI: Abteilung: NUSO.SAMG

Faisal, Ahmed: Analysis of data transfer methods between non-matching meshes in multiphysics simulations. Nürnberg, 2005 Nürnberg, Univ., Master Thesis, 2005 Schlagwörter: Master Thesis Institutsveröffentlichung: SCAI

Horn, Eva: Generierung einer Ontologie für die Klassifikation von Docking-Tools. Bingen, 2005 Bingen, Fachhochschule, Master Thesis, 2005 Schlagwörter: Master Thesis Institutsveröffentlichung: SCAI

Vemula, Rajendra: Fluid structure interaction and thermal coupling in automobile engine exhaust manifold using Mesh Based Parallel Code Coupling Interface (MpCCI). Bochum, 2005 Bochum, Univ., Master Thesis, 2005 Schlagwörter: Master Thesis Institutsveröffentlichung: SCAI

Wäldrich, Oliver: Meta-Scheduling-Architekturen in komplexen Grid-Umgebungen. Sankt Augustin, 2005 Sankt Augustin, Hochschule Bonn-Rhein-Sieg, Master Thesis, 2005 Schlagwörter: Master Thesis Institutsveröffentlichung: SCAI