Software Transactional Memory, OpenMP and Pthread implementations of the Conjugate Gradients Method - a Preliminary Evaluation

This paper shows the runtime and cache-efficiency of parallel implementations of the Conjugate Gradients Method based on the three paradigms Software Transactional Memory (STM), OpenMP and Pthreads. While the two last named concepts are used to manage parallelization as well as synchronization, STM was designed to handle only the latter. In our work we disclose that an improved cache efficiency does not necessarily lead to a better execution time because the execution time is dominated by the thread wait time at the barriers

Performance Optimization Strategies for Transactional Memory Applications

This thesis presents tools for Transactional Memory (TM) applications that cover multiple TM systems (Software, Hardware, and hybrid TM) and use information of all different layers of the TM software stack. Therefore, this thesis addresses a number of challenges to extract static information, information about the run time behavior, and expert-level knowledge to develop these new methods and strategies for the optimization of TM applications

Integrative bioinformatics applications for complex human disease contexts

This thesis presents new methods for the analysis of high-throughput data from modern sources in the context of complex human diseases, at the example of a bioinformatics analysis workflow. New measurement techniques improve the resolution with which cellular and molecular processes can be monitored. While RNA sequencing (RNA-seq) measures mRNA expression, single-cell RNA-seq (scRNA-seq) resolves this on a per-cell basis. Long-read sequencing is increasingly used in genomics. With imaging mass spectrometry (IMS) the protein level in tissues is measured spatially resolved. All these techniques induce specific challenges, which need to be addressed with new computational methods. Collecting knowledge with contextual annotations is important for integrative data analyses. Such knowledge is available through large literature repositories, from which information, such as miRNA-gene interactions, can be extracted using text mining methods. After aggregating this information in new databases, specific questions can be answered with traceable evidence. The combination of experimental data with these databases offers new possibilities for data integrative methods and for answering questions relevant for complex human diseases. Several data sources are made available, such as literature for text mining miRNA-gene interactions (Chapter 2), next- and third-generation sequencing data for genomics and transcriptomics (Chapters 4.1, 5), and IMS for spatially resolved proteomics (Chapter 4.4). For these data sources new methods for information extraction and pre-processing are developed. For instance, third-generation sequencing runs can be monitored and evaluated using the poreSTAT and sequ-into methods. The integrative (down-stream) analyses make use of these (heterogeneous) data sources. The cPred method (Chapter 4.2) for cell type prediction from scRNA-seq data was successfully applied in the context of the SARS-CoV-2 pandemic. The robust differential expression (DE) analysis pipeline RoDE (Chapter 6.1) contains a large set of methods for (differential) data analysis, reporting and visualization of RNA-seq data. Topics of accessibility of bioinformatics software are discussed along practical applications (Chapter 3). The developed miRNA-gene interaction database gives valuable insights into atherosclerosis-relevant processes and serves as regulatory network for the prediction of active miRNA regulators in RoDE (Chapter 6.1). The cPred predictions, RoDE results, scRNA-seq and IMS data are unified as input for the 3D-index Aorta3D (Chapter 6.2), which makes atherosclerosis related datasets browsable. Finally, the scRNA-seq analysis with subsequent cPred cell type prediction, and the robust analysis of bulk-RNA-seq datasets, led to novel insights into COVID-19. Taken all discussed methods together, the integrative analysis methods for complex human disease contexts have been improved at essential positions.Die Dissertation beschreibt Methoden zur Prozessierung von aktuellen Hochdurchsatzdaten, sowie Verfahren zu deren weiterer integrativen Analyse. Diese findet Anwendung vor allem im Kontext von komplexen menschlichen Krankheiten. Neue Messtechniken erlauben eine detailliertere Beobachtung biomedizinischer Prozesse. Mit RNA-Sequenzierung (RNA-seq) wird mRNA-Expression gemessen, mit Hilfe von moderner single-cell-RNA-seq (scRNA-seq) sogar für (sehr viele) einzelne Zellen. Long-Read-Sequenzierung wird zunehmend zur Sequenzierung ganzer Genome eingesetzt. Mittels bildgebender Massenspektrometrie (IMS) können Proteine in Geweben räumlich aufgelöst quantifiziert werden. Diese Techniken bringen spezifische Herausforderungen mit sich, die mit neuen bioinformatischen Methoden angegangen werden müssen. Für die integrative Datenanalyse ist auch die Gewinnung von geeignetem Kontextwissen wichtig. Wissenschaftliche Erkenntnisse werden in Artikeln veröffentlicht, die über große Literaturdatenbanken zugänglich sind. Mittels Textmining können daraus Informationen extrahiert werden, z.B. miRNA-Gen-Interaktionen, die in eigenen Datenbank aggregiert werden um spezifische Fragen mit nachvollziehbaren Belegen zu beantworten. In Kombination mit experimentellen Daten bieten sich so neue Möglichkeiten für integrative Methoden. Durch die Extraktion von Rohdaten und deren Vorprozessierung werden mehrere Datenquellen erschlossen, wie z.B. Literatur für Textmining von miRNA-Gen-Interaktionen (Kapitel 2), Long-Read- und RNA-seq-Daten für Genomics und Transcriptomics (Kapitel 4.2, 5) und IMS für Protein-Messungen (Kapitel 4.4). So dienen z.B. die poreSTAT und sequ-into Methoden der Vorprozessierung und Auswertung von Long-Read-Sequenzierungen. In der integrativen (down-stream) Analyse werden diese (heterogenen) Datenquellen verwendet. Für die Bestimmung von Zelltypen in scRNA-seq-Experimenten wurde die cPred-Methode (Kapitel 4.2) erfolgreich im Kontext der SARS-CoV-2-Pandemie eingesetzt. Auch die robuste Pipeline RoDE fand dort Anwendung, die viele Methoden zur (differentiellen) Datenanalyse, zum Reporting und zur Visualisierung bereitstellt (Kapitel 6.1). Themen der Benutzbarkeit von (bioinformatischer) Software werden an Hand von praktischen Anwendungen diskutiert (Kapitel 3). Die entwickelte miRNA-Gen-Interaktionsdatenbank gibt wertvolle Einblicke in Atherosklerose-relevante Prozesse und dient als regulatorisches Netzwerk für die Vorhersage von aktiven miRNA-Regulatoren in RoDE (Kapitel 6.1). Die cPred-Methode, RoDE-Ergebnisse, scRNA-seq- und IMS-Daten werden im 3D-Index Aorta3D (Kapitel 6.2) zusammengeführt, der relevante Datensätze durchsuchbar macht. Die diskutierten Methoden führen zu erheblichen Verbesserungen für die integrative Datenanalyse in komplexen menschlichen Krankheitskontexten

Electrokinetic optimization of a micromixer for lab-on-chip applications

This paper is concerned with the optimization of an electrokinetic micromixer suitable for Lab-on-Chip and other microfluidic applications. The mixing concept is based on the combination of an alternating electrical excitation applied to a pressure-driven base flow in a meandering microchannel geometry. The electrical excitation induces a secondary electrokinetic velocity component which results in a complex flow field within the meander bends. A mathematical model describing the physicochemical phenomena present within the micromixer is implemented in an in-house Finite-Element-Method code. We first perform simulations comparable to experiments concerned with the investigation of the flow field in the bends. The comparison of simulation and experiment reveals excellent agreement. Hence, the validated model and numerical schemes are employed for a numerical optimization of the micromixer performance. In detail, we optimize the secondary electrokinetic flow by finding the best electrical excitation parameters, i.e. frequency and amplitude, for a given waveform. The simulation results of two optimized electrical excitations featuring a discrete and a continuous waveform are compared and discussed. The results demonstrate that the micromixer is able to achieve high mixing degrees very rapidly

Fast algorithm for real-time rings reconstruction

The GAP project is dedicated to study the application of GPU in several contexts in which real-time response is important to take decisions. The definition of real-time depends on the application under study, ranging from answer time of μs up to several hours in case of very computing intensive task. During this conference we presented our work in low level triggers [1] [2] and high level triggers [3] in high energy physics experiments, and specific application for nuclear magnetic resonance (NMR) [4] [5] and cone-beam CT [6]. Apart from the study of dedicated solution to decrease the latency due to data transport and preparation, the computing algorithms play an essential role in any GPU application. In this contribution, we show an original algorithm developed for triggers application, to accelerate the ring reconstruction in RICH detector when it is not possible to have seeds for reconstruction from external trackers