Research groups High Performance Computing Applications for Science and Engineering - Bioinformatics (HPCA4SE-Bioinformatics)

High Performance Computing Applications for Science and Engineering - Bioinformatics (HPCA4SE-Bioinformatics)

Research interests focus on performance engineering problems applied to tools, programming environments and applications commonly used in the field of bioinformatics. In many join collaborations with researchers from other groups/institutions, we have developed high-performance solutions for various advanced computing environments, such as: multicore systems (servers, supercomputers, ...), distributed systems and cloud environments, manycore systems / accelerators (GPUs, Xeon Phi MIC) and environments Big Data (Hadoop, HDFS, ...).

The group has experience on several problems, including: simple and multiple sequence alignment, massive sequence data processing, workflow management, medical image processing, coalescence models in population studies, analysis of polymorphims,...Results have been applied to environments and tools such as T-Coffee, GEM,  BWA, msPar, Galaxy, FreeSurfer, MamPol, by using parallelization techniques based on the most common models: MPI, OpenMP, CUDA, OpenCL, MapReduce,...

Main projects

  • 1.

    Computational thinking and performance engineering for life sciences and environmental applications

    The project aims to improve the solutions provided by different fields of life sciences and environment science through the application of computational thinking and performance engineering to fit to the current computation systems. In particular, several bioinformatic applications and tools are going to be to analyzed over current computing systems (multi core processors, GPUS, accelerators, cloud computing,…) and will be adapted to improve their performance. From this experience, a general methodology for adapting applications to new emerging computer systems will be created together with a comprehensive body of knowledge that can be used by other applications or application fields. Ref. MINECO TIN2014-53234-C2-1-R. Period 2015 - 2017.

    http://grupsderecerca.uab.cat/hpca4se/en/content/computational-thinking-and-performance-engineering-life-sciences-and-environmental

  • 2.

    MyCore

    The project develops research on ideas, techniques, policies, and mechanisms for the efficient execution of multidisciplinary applications with high computing and data requirements on systems in the multi/many core era, including clusters, peta/exascale supercomputers, peer-to-peer systems, and cloud computing systems. The project is organized in four related layers: applications; programming models and execution environments; performance modeling, evaluation and tuning; and resource management mechanisms. Several bioinformatic applications were studied as part of the first layer. Ref. MINECO TIN2011-28689-C02-01. Period 2012 - 2014.

    http://grupsderecerca.uab.cat/hpca4se/en/content/mycore-project

  • 3.

    Supercomputing and eScience

    Project’s main goal is to advance in the field of applied supercomputing through several areas of science. In particular, the main goal in the life science workpackage was the creation of a multiscale simulation platform for the study of RNA-mediated regulatory processes in eukaryotic organisms. Our group collaborated with genomic scientists in the development of high-throughput methods for massive genome. Ref. MICINN CSD2007-00050. Period 2007 - 2013.

    http://www.syec.es/programa-supercomputación-y-eciencia

Website

Institutions

Bioinformatics expertise:

Group Leader:

Ana Ripoll

Bioinformatics services offered