Summer School in Bioinformatics & NGS Data Analysis (#NGSchool2017) will be held on 10-17 September 2017 in CBiES, Jachranka 81 k/Warszawy. 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.
In 2017, we'll focus on data analysis from single-cell technologies. As before, the course will cover wide range of topics, selected by popularity among attendees. Example topics include:
- introduction to Linux and Bioinformatics focusing on NGS-related analyses
- programming in R / Bioconductor, Python
- data visualisation
- general handling of NGS data
- data formats (FastQ, SAM, BAM, VCF)
- Quality Control
- de novo genome & transcriptome assembly
- dealing with heterozygous/polymorphic genomes
- 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
- Epigenomics: bisulphite sequencing, ChIP-seq, ChIA-PET, ATAC-seq, Hi-C data analysis
- applications of NGS in biomedicine
- GWAS & integration of molecular data
- personalised medicine
- microbial genomics
- low input & single-cell: sample preparation & data analysis
You will learn both, command-line (Linux) and online 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.
Workshops (in italic) last typically 4 hours and consists of theoretical introduction and practical exercises. In the evenings, we'll have lecture-only sessions (marked with underline), shot-talks, discussions and some more relaxed activities (optional).
|Day 0: Sunday|
|15:00||Introduction to Linux, Bioinformatics & NGS||Broňa Brejová & Tomáš Vinař|
|18:00||Welcome & Shot talks #1||Leszek Pryszcz|
|Day 1: Monday|
|9:00||Data visualisation||Przemysław Biecek|
|14:00||Molecular data integration||Jacek Marzec|
|20:00||Shot talks #2||Leszek Pryszcz|
|Day 2: Tuesday|
|9:00||Workflows & pipelines||Alina Frolova|
|14:00||Genome & transcriptome assembly from single-cell data||Andrey Prjibelski|
|20:00||Beta & Bit games||Przemysław Biecek|
|Day 3: Wednesday|
|9:00||Detection of SNPs & structural variations (CNVs)||Tomasz Gambin|
|14:00||Introduction to Statistics / RNA structure probing||German Demidov / Łukasz Kiełpiński|
|18:00||Team-working: Moving forward and enjoying science together / Open science - discussion||Panagiotis Theodorakis /
|20:00||Chilling evening BBQ #1 & #OpenScience contest|
|Day 4: Thursday|
|9:00||Functional genome annotation||Marina Marcet-Houben|
RNase H sequence preferences influence antisense oligonucleotide efficiency and have shaped the HIV-1 genome
|Day 5: Friday|
|9:00||Single-cell RNA-seq analysis||Davis McCarthy|
|14:00||Differential expression analysis||Davis McCarthy|
|18:00||Genome structure & function [keynote]||Noam Kaplan|
|Day 6: Saturday|
|9:00||Single-cell Hi-C data analysis||Aleksandra Galitsyna|
|14:00||ATAC-seq / Microbial genomics||Katarzyna Kędzierska / Adam Witney|
|18:00||Problem-oriented sessions||Check FB group for details|
|20:00||Chilling evening BBQ #2|
|Day 7: Sunday|
|10:00||Recap & farewell||Leszek Pryszcz|
- Noam Kaplan, Technion, Haifa, Il
- Davis McCarthy, EBI, Hinxton, UK
- Przemysław Biecek, Warsaw University of Technology, PL
- Broňa Brejová & Tomáš Vinař, Univerzita Komenského, Bratislava, SK
- German Demidov, CRG, Barcelona, ES
- Alina Frolova, IMBG, Kyiv, UA
- Aleksandra Galitsyna, MSU, Moscow, RU
- Tomasz Gambin, Warsaw University of Technology, Warsaw, PL
- Aliaksei Holik, CRG, Barcelona, ES
- Katarzyna Kędzierska, University of Virginia, Charlottesville, USA
- Łukasz Kiełpinski, Hoffmann-La Roche, Frederiksberg, DK
- Maciej Łapiński, IIMCB, Warsaw, PL
- Marina Marcet-Houben, CRG, Barcelona, ES
- Jacek Marzec, BCI, London, UK
- Andrey Prjibelski, SPSU, St. Petersburg, RU
- Leszek Pryszcz, IIMCB, Warsaw, PL
- Paweł Szczęsny, IBB, Warsaw, PL
- Panagiotis Theodorakis, Institute of Physics PAN, Warsaw, PL
- Adam Witney, SGUL, London, UK
You can find all #NGSchool2017 materials here.
We'll organise set of social events, including BBQ nights, movie night, volleyball games and kayaking. We'll make sure, there is plenty of fun, beside hard working during workshops ;)
Registration will be opened between 1 May and 30 June 2017 (11:59 CET).
To register, follow this link: http://bit.ly/ngschoool2017_registration
We will offer ~30 places. Successful applicants will be notified two weeks after registration deadline.
The expenses related to the course, including full boarding oscillate around €550.
The registration will be free of charge given we get sufficient funding. We'll post more details in the end of May 2017. In addition, we are planning to accept limited number of participants that will be able to cover all the expenses by themselves. This year, we have received the grant from International Visegrad Fund, so the registration for #NGSchool2017 covering accommodation and full boarding will be free of charge.