Next-Generation Sequencing Data Analysis
When?
Where?
Registration
Schedule
Speakers
Organising Committee
Sponsors
Contact
Conclusions
Beer and science event
When?
15-16 November 2018
Where?
West University, Timișoara, Romania
Organisers
RSBI (@RoBioinfo), Politehnica University of Timișoara, and West University Timișoara
Registration
A registration fee of 40 euros is required from academia participants to cover meals and dinner. Bursaries are available (up to 10 places; with 50% reduction or full fee exemption), and are awarded on merit and motivation. Mention in the registration form if you intend to apply for it.
Industry participants registration fee is 140 euros.
Requirements
A fundamental understanding of Molecular Biology and basic knowledge of Statistics, Unix command line, R and/or Python are assumed. Suggested resources:
- Unix: http://www.ee.surrey.ac.uk/Teaching/Unix/
- Perl: https://learn.perl.org/books/beginning-perl/
- Python: https://thepythonguru.com/
Speakers
The list of confirmed speakers and trainers is:
- Viorica Chelban (University College London, Institute of Neurology, UK)
- Hugues Richard (Pierre and Marie Curie University, Paris, France)
- Petr Daněček (University of Cambridge, Cambridge, UK)
- Valeriu Ohan (Wellcome Sanger Institute, Cambridge, UK)
- Aleksandra Świercz (University of Technology, Poznan, Poland)
- Bogdan Mirăuță (European Bioinformatics Institute, Cambridge, UK)
Schedule
Day 1 (DNA Sequencing)
| Time | Subject | Trainer/Speaker |
| 9:00 – 9:30 | Introduction to NGS | Hugues Richard |
| 9:30 – 10:00 | (Theory) File formats, QC | Petr Daněček |
| 10:00 – 10:30 | (Hands-on) File formats, QC | Petr Daněček, Valeriu Ohan |
| 10:30 – 11:00 | Coffee Break | |
| 11:00 – 11:30 | (Theory) Alignment |
Petr Daněček |
| 11:30 – 12:00 | (Hand-on) Alignment | Petr Daněček, Valeriu Ohan |
| 12:00 – 13:00 | Lunch | |
| 13:00 – 14:30 | (Theory + Hand-on) Variant Calling | Petr Daněček, Valeriu Ohan |
| 14:30 – 15:00 | Coffee Break | |
| 15:00 – 17:00 | (Theory + Hand-on) Genome Assembly | Aleksandra Świercz |
| 17:00 | Dinner at Cramele Recas |
Day 2: RNA Sequencing
| Time | Subject | Trainer/Speaker |
| 9:00 – 10:30 | RNA-Seq: QC, Mapping and Differential Expression Analysis. (I) | Hugues Richard |
| 10:30 – 11:00 | Coffee Break | |
| 11:00 – 12:00 | RNA-Seq: QC, Mapping and Differential Expression Analysis. (II) | |
| 12:00 – 13:00 | Lunch | |
| 13:00 – 13:25 | Talk: RNA-Seq, CLIP-Seq and Alternative splicing | Hugues Richard |
| 13:25 – 13:50 | Talk: Single-cell RNA sequencing | Bogdan Mirăuță |
| 13:50 – 14:10 | Talk: Sequencing with long read technologies (Oxford Nanopore and Pacific Biosciences) | Aleksandra Świerc |
| 14:10 – 14:30 | Talk: New kids on the block: 10x Genomics, Dovetail Genomics, Optical maps | Petr Daněček |
| 14:30 – 15:00 | Coffee break | |
| 15:00 – 15:45 | Talk: Gene discovery and clinical validation of NGS results in neurological disorders |
Viorica Chelban |
| 15:45 – 16:15 | Talk: Samtools and the pros and cons of writing code for academic research | Valeriu Ohan |
| 16:15 – 16:45 | Panel Discussion | All speakers and trainers |
| 16:45 – 17:00 | Farewell |
Organising committee
- Monica Abrudan (Wellcome Sanger Institute, Cambridge, UK)
- Irina Armean (European Bioinformatics Institute, Cambridge, UK)
- Bogdan Mirauță (European Bioinformatics Institute, Cambridge, UK)
- Daniela Zaharie (West University, Timișoara, Romania)
- Cristian Zimbru (Politehnica University, Timișoara, Romania)
Satellite event -Beer and Science – organising committee
- Catalina Barbarosie (Bucharest, Romania)
- Iona Hapsa (Cluj, Romania)
- Mihai Ionita (Bucharest, Romania)
Sponsors
EURO Working Group on the Operational Research in Computational Biology, Bioinformatics and Medicine (EWG CBBM)
Research Institute e-Austria, Timisoara, Romania
Contact
For any queries, please contact us.
Conclusions
20 out of 29 course participants filled in the feedback form and rated the event on average as 4.3/5.
All of the trainers’ names were found among trainees’ favourites!
Suggestions from participants:
“Congratulations for the event! I have learned a lot during these 2 days. I have also met a lot of nice people.”
“Keep doing what you’re doing. You’re a gold mine for the science community in Romania.”
“If you’ll ever expand the Workshop to be longer, a training on how to use coding programs on a basic level would be great. Even though links to tutorials were sent prior to training, due to our everyday work, it’s hard to find time to go through tutorials, so a hands-on basic training at the venue would probably be more useful.”
“Extend practical part of the courses. If possible try to extend course to 4-5 days because just 2 days makes lessons too condensed and little rushed. Maybe provide handouts at least for practical part – list of commands that will be used – it would help participants with weaker command line knowledge and would avoid trying to copy long code form for projection.”
“Yes, it is very cool meeting and it should be definitely longer (4-6 days). I am so thankful to be invited here, good time!”
On the downside, there were some significant problems with internet connection, due to a fault in a network. We will ensure this will not happen at future events.
Beer and Science
Enthusiastic trainees organised a satellite event, called Beer & Science, on the 16th of November in a public house.
The public listened to 7 short talks, which were followed by discussions, over beer and burgers.
- Hughes Richard – Alternative splicing and its impact on protein structure
- Marin Rodovcic -CRISPRcas immunity in Ecoli
- Eugen Ursu – Cancer immunology
- Alice Bîlc – Antibiotic Resistance caused by efflux pumps in Acinetobacter baumani
- Anna Lesniewska – Packages for genomics data <- SeQuiLa
- Adela Chiriță – Rare genetic diseases
- Mihai Ioniță – GMO friend or foe
We do hope that Beer and Science will be repeated at future RSBI events!
Beer photo by I.H.
Cover photo by: padurariu adrian 1, CC BY 3.0
