Parallel and Distributed Architectures
News and Events
- Master- & Bachelorarbeiten und HiWi Position im aktiven und kooperativem Lernen in HPC
- Die AG von Professor Bertil Schmidt (http://hpc.informatik.uni-mainz.de) bietet einige interessante Master- und Bachelorarbeiten sowie eine HiWi Position im Projekt „Aktives und kooperatives Lernen in der Informatik am Beispiel High Performance Computing und paralleler Programmierung“ an.
- Master- & Bachelorarbeiten in HPC auf dem Intel Xeon Phi Co-Processor
- Die AG von Professor Bertil Schmidt (http://hpc.informatik.uni-mainz.de) bietet einige interessante Bachelor- und Masterarbeiten im Bereich der parallelisierten Sequenzanalyse auf dem neuen Intel Xeon Phi Prozessor an.
- Master- & Bachelorarbeiten und HiWi-Stelle in Informatik im All-Food-Seq Projekt
- Die AG von Professor Bertil Schmidt (http://hpc.informatik.uni-mainz.de) bietet einige interessante Bachelor- und Masterarbeiten sowie eine HiWi Stelle im „All-Food-Seq“ Projekt in Kollaboration mit dem Institut für Molekulargenetik (Prof. Thomas Hankeln) an.
- Research Associate in GPU Computing
- The Institute of Computer Science at the Johannes-Gutenberg University (JGU) Mainz invites applications for a Research Associate position in the group of Professor Bertil Schmidt (http://hpc.informatik.uni-mainz.de)
- Successful CUDA Practical at Institute of Computer Science
- The Parallel and Distributed Architectures group headed by Professor Bertil Schmidt offered its first CUDA Praktikum in September 2012 using state-of-the-art CUDA-enabled GPUs.
- University of Mainz is now a Cuda Research Center
Introduction
Our group focuses on the design, implementation and evaluation of scalable tools for genomic sequence analysis (Bioinformatics) and computational science applications. Our approach is based on using modern high performance computing (HPC) technologies, such as
- Manycore architectures (such as CUDA-enabled GPUs)
- Multicore architectures
- Heterogeneous clusters
- FPGAs
Using these platforms we design efficient parallel algorithms that can serve as a foundation for a wide variety of tools, such as
- short/long-read aligners (e.g. CUSHAW)
- de-novo short/long-read genome assemblers (e.g. PASHA, Taipan)
- short/long-read clustering (e.g. CRiSPy-CUDA, DySC)
- multiple sequence aligners (e.g. MSA-Probs, MSA-CUDA)
- sequence database searching (e.g. CUDA-BLASTP, CUDASW++ (Smith-Waterman))
- short/long-read error correction (e.g. SHREC, DecGPU)
- motif finding (e.g. CUDA-MEME)
- solving linear equations by iterative sparse matrix-vector multiplication (e.g. Integer factorization for RSA cryptography with the Block-Wiedemann algorithm)
Our methods and tools are often developed in collaboration with interdisciplinary partners at JGU Mainz, such as the Department of Biology, Medical School, and the Institute of Molecular Biology.
For the pioneering work in the area of CUDA-enabled bioinformatics, we have been awarded the status of a CUDA Research Center and a CUDA Teaching Center.
Computergrafik und Animation (Vorlesung/Übung)
