Summer School in Bioinformatics & NGS Data Analysis (NGSchool2016) will be held on August 14-21, 2016 in Dolný Smokovec, Slovakia. In the course of one week, the participants will attend the series of lectures and workshops, covering various aspects of Computational Biology, focusing on state-of-the-art techniques related to Next-Generation Sequencing (NGS) and its application in research, health-care and industry. It is mainly addressed to students and researchers in early stage of their careers. Nevertheless, we invite also more advanced researchers to apply.
The course will cover wide range of topics:
- introduction to Linux and Bioinformatics focusing on NGS-related analyses
- general handling of NGS data
- data formats (FastQ, SAM, BAM, VCF)
- Quality Control
- de novo genome & transcriptome assembly
- gene prediction and functional annotation
- detection of SNPs & SVs (deletions, duplications, inversions, translocations)
- prediction of functional effects of detected variants
- RNA-Seq & differential expression analyses
- bisulphite sequencing, ChIP-Seq & Hi-C data analysis
- GWAS & integration of molecular data
- applications of NGS in biomedicine
You will learn both, command-line (Linux) and online (Galaxy) tools. People having no prior experience with Bioinformatics are welcome, but strong motivation is desired!
Participants should bring their own laptops with Ubuntu installed! We will provide some toy examples, but we encourage you to bring your own datasets.
The course will be held in English.
You can find detailed programme draft below. We will have morning (9-13) and afternoon (14-18) sessions, with coffee breaks ~11:00 and ~16:00. Breakfast will be served from 8:00, lunch at 13:00 and dinner around 19:00.
|Day 0: Sunday|
|18:00||Welcome & Shot talks #1||Leszek Pryszcz|
|Day 1: Monday|
|9:00||Introduction to Linux||Roman Cheplyaka|
|14:00||Introduction to Bioinformatics & NGS||Tomáš Vinař / Broňa Brejová|
|Day 2: Tuesday|
|9:00||Genome & transcriptome assembly||Leszek Pryszcz / German Demidov|
|14:00||Functional genome annotation||Marina Marcet-Houben|
|18:00||Introduction to Statistics & R||German Demidov|
|Day 3: Wednesday|
|9:00||CNV detection||German Demidov|
|14:00||Differential expression||Leszek Pryszcz|
|18:00||Library construction for NGS||Paulina Stachula|
|Day 4: Thursday|
|12:00||From ChIP-seq to Hi-C||Bartek Wilczyński|
|14:00||Bisulphite sequencing||Russell Hamilton|
|20:00||Shot talks #2||Leszek Pryszcz|
|Day 5: Friday|
|9:00||Molecular data integration||Jacek Marzec|
|Day 6: Saturday|
|9:00||NGS & Biomedicine||Sophia Derdak|
|Day 7: Sunday|
|9:00||Recap & farewell||Leszek Pryszcz|
You can find all #NGSchool2016 materials here.
- Broňa Brejová, Univerzita Komenského, Bratislava, SK
- Roman Cheplyaka, Software engineer, Odessa, UKR
- German Demidov, CRG, Barcelona, ES
- Sophia Derdak, CNAG, Barcelona, ES
- Russell Hamilton, University of Cambridge, UK
- Matej Lexa, Masaryk University, Brno, CZ
- Maciej Łapiński, IIMCB, Warsaw, PL
- Marina Marcet-Houben, CRG, Barcelona, ES
- Jacek Marzec, BCI, London, UK
- Leszek Pryszcz, IIMCB, Warsaw, PL
- Paulina Stachula, IIMCB, Warsaw, PL
- Tomáš Vinař, Univerzita Komenského, Bratislava, SK
- Bartek Wilczyński, MIM, University of Warsaw, PL
We'll organise set of social events, including BBQ nights, movie night, hiking in High Tatras and sightseeing (ie. Łomnica, Strbske Pleso). We'll make sure, there is plenty of fun, beside hard working during workshops ;)
Registration is now closed. We will repeat the course in 2017. You can express you interest in the next edition here.
Registration will be opened between 1 May and 1 July 2016 (12:00 CET). The registration fee is €50. This will cover all expenses (materials, accommodation, meals and travel grant), thanks to generous support from International Visegrad Fund.
We will offer ~25 places. Successful applicants will be notified three weeks after registration deadline.
To register follow this link.
#NGSchool2016 in numbers
We have received over 80 applications from 15 countries (52 from V4), from these 30 applicants from 11 countries were selected by our Scientific committee. Selected participants represented several fields of Science (including biology, biochemistry, medicine, computer science and related disciplines) and stages of career (undergrad, master and PhD students, as well as, postdocs).