Bioinformatics is growing in popularity rapidly over the past years due to lots of reasons, such as availability of high-throughput sequencing techniques, high-quality (open access) databases, as well as the availability of ready-to-use machine learning frameworks and libraries. The extent of applicability of the bioinformatics algorithms and programs is, however, often limited by computer resources that researchers have at hand. The goal of the Seasonal School is to evangelize HPC (High-Performance Computing) as the tool they can use to overcome this barrier limiting their research
There are a lot of tools available, that researcher working in this field can use, but most of them were developed for desktop applications. In this workshop, we will present tools / frameworks that are designed towards parallel computer architectures, thus suitable for running them on computer clusters or supercomputers. Participants will not only learn about dedicated bioinformatics software, such as BLAST (Basic Local Alignment Search Tool), but also on generally applicable tools, such as the R programming language or the Apache Spark framework, suitable for parallel (pre)processing of Big Data.
The workshop is composed of introductory sessions on bioinformatics and NGS (Next-Generation Sequencing), lectures and hands-on sessions on using R in parallel, a short course on analysis of large data sets with Apache Spark (primarily using Python) and finally the lecture on BLAST and how to convert BLAST tasks in parallel jobs.
The school is organized by the Computing Centre of Slovak Academy of Sciences (CC SAS). The venue is located directly in the campus of SAS close to Bratislava city centre, at the Plant Science and Biodiversity Centre. Bratislava is a beautiful historical city with international airport, not far from Vienna, Budapest and Prague, with a lots of opportunities for sightseeing and social life.
- Prof. Erik Bongcam Rudloff (Swedish University of Agricultural Science)
- Dr. Seija Sirkiä (Centre fo Scientific Computing - CSC, Finland)
- Mr. Apurva Nandan (CSC)
- Dr. Kimmo Mattila (CSC)