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.

Registration is now closed. Results were announced by email, on the 7th of October

Requirements

A fundamental understanding of Molecular Biology and basic knowledge of Statistics, Unix command line, R and/or Python are assumed. Suggested resources:

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