TY - JOUR A1 - Ahmed, Zeeshan A1 - Zeeshan, Saman A1 - Huber, Claudia A1 - Hensel, Michael A1 - Schomburg, Dietmar A1 - Münch, Richard A1 - Eylert, Eva A1 - Eisenreich, Wolfgang A1 - Dandekar, Thomas T1 - ‘Isotopo’ a database application for facile analysis and management of mass isotopomer data JF - Database N2 - The composition of stable-isotope labelled isotopologues/isotopomers in metabolic products can be measured by mass spectrometry and supports the analysis of pathways and fluxes. As a prerequisite, the original mass spectra have to be processed, managed and stored to rapidly calculate, analyse and compare isotopomer enrichments to study, for instance, bacterial metabolism in infection. For such applications, we provide here the database application ‘Isotopo’. This software package includes (i) a database to store and process isotopomer data, (ii) a parser to upload and translate different data formats for such data and (iii) an improved application to process and convert signal intensities from mass spectra of \(^{13}C\)-labelled metabolites such as tertbutyldimethylsilyl-derivatives of amino acids. Relative mass intensities and isotopomer distributions are calculated applying a partial least square method with iterative refinement for high precision data. The data output includes formats such as graphs for overall enrichments in amino acids. The package is user-friendly for easy and robust data management of multiple experiments. KW - stable-isotope Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-120102 VL - 2014 IS - bau077 ER - TY - JOUR A1 - Dandekar, Thomas A1 - Ahmed, Zeeshan A1 - Saman, Zeeshan A1 - Huber, Claudia A1 - Hensel, Michael A1 - Schomburg, Dietmar A1 - Münch, Richard A1 - Eisenreich, Wolfgang T1 - Software LS-MIDA for efficient mass isotopomer distribution analysis in metabolic modelling JF - BMC Bioinformatics N2 - Background The knowledge of metabolic pathways and fluxes is important to understand the adaptation of organisms to their biotic and abiotic environment. The specific distribution of stable isotope labelled precursors into metabolic products can be taken as fingerprints of the metabolic events and dynamics through the metabolic networks. An open-source software is required that easily and rapidly calculates from mass spectra of labelled metabolites, derivatives and their fragments global isotope excess and isotopomer distribution. Results The open-source software “Least Square Mass Isotopomer Analyzer” (LS-MIDA) is presented that processes experimental mass spectrometry (MS) data on the basis of metabolite information such as the number of atoms in the compound, mass to charge ratio (m/e or m/z) values of the compounds and fragments under study, and the experimental relative MS intensities reflecting the enrichments of isotopomers in 13C- or 15 N-labelled compounds, in comparison to the natural abundances in the unlabelled molecules. The software uses Brauman’s least square method of linear regression. As a result, global isotope enrichments of the metabolite or fragment under study and the molar abundances of each isotopomer are obtained and displayed. Conclusions The new software provides an open-source platform that easily and rapidly converts experimental MS patterns of labelled metabolites into isotopomer enrichments that are the basis for subsequent observation-driven analysis of pathways and fluxes, as well as for model-driven metabolic flux calculations. KW - LS-MIDA Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-95882 UR - http://www.biomedcentral.com/1471-2105/14/218 ER - TY - JOUR A1 - Ahmed, Zeeshan A1 - Zeeshan, Saman A1 - Dandekar, Thomas T1 - Mining biomedical images towards valuable information retrieval in biomedical and life sciences JF - Database - The Journal of Biological Databases and Curation N2 - Biomedical images are helpful sources for the scientists and practitioners in drawing significant hypotheses, exemplifying approaches and describing experimental results in published biomedical literature. In last decades, there has been an enormous increase in the amount of heterogeneous biomedical image production and publication, which results in a need for bioimaging platforms for feature extraction and analysis of text and content in biomedical images to take advantage in implementing effective information retrieval systems. In this review, we summarize technologies related to data mining of figures. We describe and compare the potential of different approaches in terms of their developmental aspects, used methodologies, produced results, achieved accuracies and limitations. Our comparative conclusions include current challenges for bioimaging software with selective image mining, embedded text extraction and processing of complex natural language queries. KW - humans KW - software KW - image processing KW - animals KW - computer-assisted KW - data mining/methods KW - natural language processing Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-162697 VL - 2016 ER - TY - THES A1 - Zeeshan, Ahmed T1 - Bioinformatics Software for Metabolic and Health Care Data Management T1 - Metabolische Flux-Analyse N2 - Computer Science approaches (software, database, management systems) are powerful tools to boost research. Here they are applied to metabolic modelling in infections as well as health care management. Starting from a comparative analysis this thesis shows own steps and examples towards improvement in metabolic modelling software and health data management. In section 2, new experimental data on metabolites and enzymes induce high interest in metabolic modelling including metabolic flux calculations. Data analysis of metabolites, calculation of metabolic fluxes, pathways and their condition-specific strengths is now possible by an advantageous combination of specific software. How can available software for metabolic modelling be improved from a computational point of view? A number of available and well established software solutions are first discussed individually. This includes information on software origin, capabilities, development and used methodology. Performance information is obtained for the compared software using provided example data sets. A feature based comparison shows limitations and advantages of the compared software for specific tasks in metabolic modeling. Often found limitations include third party software dependence, no comprehensive database management and no standard format for data input and output. Graphical visualization can be improved for complex data visualization and at the web based graphical interface. Other areas for development are platform independency, product line architecture, data standardization, open source movement and new methodologies. The comparison shows clearly space for further software application development including steps towards an optimal user friendly graphical user interface, platform independence, database management system and third party independence especially in the case of desktop applications. The found limitations are not limited to the software compared and are of course also actively tackled in some of the most recent developments. Other improvements should aim at generality and standard data input formats, improved visualization of not only the input data set but also analyzed results. We hope, with the implementation of these suggestions, metabolic software applications will become more professional, cheap, reliable and attractive for the user. Nevertheless, keeping these inherent limitations in mind, we are confident that the tools compared can be recommended for metabolic modeling for instance to model metabolic fluxes in bacteria or metabolic data analysis and studies in infection biology. ... N2 - Informatik Ansätze (Software, Datenbank, Management-Systeme) sind wichtige Werkzeuge für die Forschung in der Biologie. Ausgehend von einer vergleichenden Analyse zeigt diese Arbeit eigene Schritte und Beispiele zur Verbesserung von metabolischer Modellierungs-Software und Gesundheit Datenmanagementsystemen auf. Neue experimentelle Daten über Metaboliten und Enzyme führen zu hohem Interesse an metabolischen Modellierungen einschließlich Stoffwechselflusses Berechnungen. In Kapitel 2 zeigen wir, das die Datenanalyse von Metaboliten, die Berechnung der Stoffflüsse und Wege sowie die spezifischen Softwarestärken nur durch eine vorteilhafte Kombination voll ausgeschöpft werden. Wie kann Software zur metabolischen Modellierung von einer informatischen Sicht her verbessert werden? Eine Anzahl von verfügbaren und gut etablierten Softwareansätzen wird zunächst einzeln diskutiert. Dazu gehören Informationen über Software-Herkunft, Fähigkeiten, Entwicklung und verwendeten Methodik einschließlich Testdatensätzen und Modellen. Ein Vergleich zeigt, merkmalsbasierte Einschränkungen und Vorteile der verglichenen Software für spezifische Aufgaben in der metabolischen Modellierung. Häufige Einschränkungen der verglichenen Software sind ihre Abhängigkeit von Drittanbietern, kein umfassendes Datenbank-Management und kein Standard-Format für Dateneingabe und -ausgabe. Die grafische Visualisierung für komplexe Visualisierungen von Daten und die Web-basierte grafische Benutzeroberfläche kann oft noch verbessert werden. Andere Bereiche für weitere Entwicklung sind Plattformunabhängigkeit, Produktlinien-Architektur, Daten-Standardisierung, die Open-Source-Bewegung und neue Algorithmen und Methoden. Der Vergleich zeigt deutlich Möglichkeiten für weitere Entwicklung von Softwareanwendungen auf, einschließlich Schritten in Richtung einer optimalen, benutzerfreundlichen grafischen Benutzeroberfläche, Plattform-Unabhängigkeit, Datenbank-Management-System und Unabhängigkeit von weiterer software, vor allem im Falle von Desktop-Anwendungen. Die gefundenen Einschränkungen sind von allgemeiner Bedeutung für bioinformatische Modellierungssoftware einschließlich jüngster Entwicklungen. Weitere Verbesserungen betreffen standardisierte Formate und eine, verbesserte Visualisierung von Eingabedatensatz und analysierten Ergebnissen. Wir hoffen, dass mit der Umsetzung dieser Vorschläge metabolische Software-Anwendungen professioneller werden, billiger, zuverlässiger und attraktiver für den Anwender. Trotz dieser inhärenten Einschränkungen im Hinterkopf sind wir zuversichtlich und ... KW - Stoffwechsel KW - Modell KW - Software KW - Gesundheitswesen KW - Datenbanksystem KW - Metabolische Flux-Analyse KW - Massen-Isotopomer Verteilungs-Analyse KW - Datenbank KW - Management-Systeme KW - Metabolic Flux Analysis KW - Mass Isotopomers Distribution Analysis KW - Software KW - Database KW - Management System Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-73926 ER - TY - JOUR A1 - Zeeshan, Ahmed T1 - Towards Performance Measurement and Metrics Based Analysis of PLA Applications N2 - This article is about a measurement analysis based approach to help software practitioners in managing the additional level complexities and variabilities in software product line applications. The architecture of the proposed approach i.e. ZAC is designed and implemented to perform preprocessesed source code analysis, calculate traditional and product line metrics and visualize results in two and three dimensional diagrams. Experiments using real time data sets are performed which concluded with the results that the ZAC can be very helpful for the software practitioners in understanding the overall structure and complexity of product line applications. Moreover the obtained results prove strong positive correlation between calculated traditional and product line measures. KW - Programmierbare logische Anordnung KW - Analysis KW - Measurement KW - Software product lines KW - Variability Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-68188 ER -