📅 February 1 — 8, 2023
📍 Comenius University Bratislava, Bratislava, Slovakia

❯ Visit the event website for more details

The ALPACA Winter School will take place in February at Comenius University Bratislava. It give participants hands-on laboratory experience, allowing them to better understand wet-lab possibilities and limitations and become more effective collaborators with wet-lab biologists. No previous experience with wet lab is required.

Preliminary topics include:

  • (i) Basic laboratory techniques, DNA extraction (UK BA, 0.5 ECTS);
  • (ii) Sequencing with Oxford Nanopore devices: from DNA sample to sequences (J.Nosek UKBA, 1 ECTS),
  • (iii) Illumina sequencing for clinical diagnostics (J.Budiš GENETON, 1 ECTS),
  • (iv) Data analysis challenges (T.Vinař UK BA, 0.5 ECTS),
  • (v) Soft-skills: Efficient interdisciplinary communication (Z.Iqbal EMBL, 0.5 ECTS),
  • (vi) Soft-skills: Intellectual Property: Management and issues (W.Pirovano BC, 0.5 ECTS).
Table of Contents
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Schedule

❯ See the Programme on the event website

Part I: Wet lab workshop (Wednesday–Saturday)

Participants working in small groups under supervision of experts will prepare samples and sequencing libraries from several strains of Lodderomyces elongisporus using ONT MinION. In addition, some short lectures complement the lab experience explaining the process. The goal is to get familiar with basic laboratory skills and necessary background.

Social outing (Sunday morning)

likely a trip to a castle near Bratislava

Part II: Analysis workshop (Sunday evening–Wednesday)

The focus of the analysis part will be on analysis of the data produced during the wet lab part of the school, augmented with additional data sets produced ahead of the school, with both traditional and pangenomic methods. The plan is to produce a joint paper at the end of the analysis workshop (most likely Microbiology Resource Announcements, G3, DNA Research or similar). 

Registration and important information

The event is open to the public, space permitting. Register your interest by September 23, 2022 (closed).

  • There is limited space in the wet lab, priority is given to ALPACA students/affiliates and PANGAIA participants.
  • All are very welcome to the analysis workshop (would like PIs involved in analysis).
  • There will be a discussion on limitations with ALPACA / PANGAIA coordinators, which registered participants will get to know by mid-October.

We need leaders for the analysis workshop:

  • Genome/haplotype assembly
  • Variant calling
  • Pan-genome construction
  • Pan-genome analysis
  • Will have some data ahead of time

Venue

Wet lab school (Feb 1-Feb 4)

The wet lab school will be held at the seminar room and in the laboratories of the Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava.

Address: Ilkovičova 6, Bratislava
Main room: CH1-222

Analysis workshop (Feb 5-Feb 8)

The analysis workshop will be held at the Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava.

Address: Mlynská dolina, Bratislava, building M
Main room: Lecture hall C



Winter School (wet lab): “Collaborating with wet-lab biologists”