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)
- Number of eligible participants is limited. Participants from PRACE countries are accepted preferably.
- This event is free of charge. Participants should cover only expenses related to travelling and accommodation.
- Foreign participants will receive partial refundation of their travel/accommodation cost. The exact amount will depend on the total number of registered foreign participants (it is expected to be around 100-150 EUR)
- Participants are expected to bring their own laptop
How to reach the venue: show on Google maps
From the (main) train station:
- Take the bus number 21 from the bus stop "SAV" (direction "Devínska Nová Ves"). Exit bus on stop „Mokrohájska“ (the first stop after „Patrónka“). Cross the road from the stop, walk past a grove and enter the SAV campus throuhg a small gate. The venue (with a large sign "Botanický ústav") is close behind the entrance to your right.
From the bus station (Mlynské nivy):
- Take the bus number 21 and follow the instructions above.
From other parts of Bratislava:
- Take bus number 21, 22, 30, 34, 38 or 83. Follow the instructions above
- Take bus number 25, 37, 63, 92 or 192, or trolley bus number 211 or 212. Exit on the stop „Patrónka“. Change to bus number 21, 22, 30, 34, 38 or 83. Follow the instructions above.
- Take bus number 36. Exit on stop "Dúbravská cesta", that is right next to the venue.
Slovak Academy of Sciences provides following accommodation facility for foreign visitors:
Recently renovated dormitory/hotel "Kramáre" (30 minutes walk, 2.5 km / 5-8 minutes by public transportation, lines 204, 212, from bus stop "Bárdošova" + 5 minutes walk from bus stop "Patrónka". Address: Royova 10, 831 01 Bratislava). 10 single rooms for 40 EUR/night with wifi, bathroom and small kitchen are available or 3 aparments with one double bed and one extendable bed for 50 EUR/night (no limitation of number of persons). Wifi, bathroom and small kitchen is available. Breakfast is not included, nor served.
For any visitor (including Slovaks):
Dormitory/Hotel "Devínska Nová Ves" (15 minutes by public transportation, line 21, from bus stop "Štefana Králika" + 5 minutes walk from bus stop "Patrónka". Address: Ivana Bukovčana 9, 841 07 Bratislava). 6 single rooms for 10 EUR/night and 4 double rooms for 6 EUR/person/night are available. No wifi, no breakfast and 3 rooms share a bathroom.
We made a reservation of the aforementioned lodging until 12:00 of 6th of April. Please let us know is you are interested, after the deadline we can't guarantee the availability.