a non-profit association

PhD course: Metabarcoding Data Management and Open Data (Tartu, Estonia)

Course description
The focus of this course is on metabarcoding data management, using PlutoF platform services and annotating UNITE data sets. Course participants will learn how PlutoF platform can be used to 1) manage their own research data (incl. projects, traits and taxon interactions, 2) curate and annotate UNITE and INSD rDNA ITS data sets and 3) identify their unknown DNA sequences using UNITE reference data. Lectures and hands on sessions will be accompanied by scientific lectures on metabarcoding and -genomics. The culmination of the course is 1-day UNITE jamboree (see below) where participants will work with preparing published High Throughput Sequencing (HTS) data sets for specific UNITE SH release.

This course is organised by the University of Tartu, Natural History Museum and Doctoral School of Earth Sciences and Ecology, supported by the European Union, European Regional Development Fund (University of Tartu’s ASTRA project PER ASPERA).

Program at a glance
Venue: Chemicum, Ravila 14A, 50411 Tartu, Estonia (view location on the map)
Teachers: Urmas Kõljalg, Kessy Abarenkov, Martin Ryberg, Priscila Chaverri, Leho Tedersoo

29.05 Day I
08:30 - 12:00 Lecture and hands on (Open Data and data management in PlutoF, Specimen-based & Barcoding projects, Taxon Interactions, Traits)
12:00 - 13:00 Lunch
13:00 - 13:45 Scientific Lecture, Martin Ryberg
13:45 - 17:00 Hands on continues
19:00 Dinner & Scientific Discussions

30.05 Day II
08:30 - 12:00 Lecture and hands on (Metabarcoding projects)
12:00 - 13:00 Lunch
13:00 - 13:45 Scientific Lecture, Leho Tedersoo
13:45 - 17:00 Hands on continues
19:00 Dinner & Scientific Discussions

31.05 Day III
08:30 - 11:00 Lecture and hands on (Curating UNITE data sets, PlutoF analysis module, PipeCraft)
11:00 - 12:00 Scientific Lecture, Gareth W. Griffith "NextGen Sequence data and conservation biology: assessing the distribution of rare fungi"
12:00 - 13:00 Lunch
13:00 - 13:45 Scientific Lecture, Priscila Chaverri
13:45 - 17:00 Hands on continues
19:00 Dinner & Scientific Discussions

01.06 Day IV
UNITE jamboree where mycologists from NEFOM network (www.nefom.dk) labs will join the course. The aim of the common jamboree is to work with published HTS data sets by connecting associated traits with ITS sequences through samples, and preparing them for the specific UNITE SH release. We are looking forward to have a common paper including students and researchers taking part of the jamboree.

08:30 - 12:00 Lecture and hands on (UNITE HTS module, HTS annotations, Traits)
12:00 - 13:00 Lunch
13:00 - 17:00 Hands on continues
19:00 Dinner & Summing up the course

Travel info
Plane - There are direct flights on Helsinki-Tartu route once per day (see the flight schedule here). Alternatively, more frequent flights to Tallinn (Tallinn Airport) are available.
Ferry - You can take a ferry from Helsinki to Tallinn (check the schedule here).
Bus Tallinn-Tartu - If you arrive to Tallinn airport there is a bus stop on the 0 floor, where the bus to Tartu leaves every hour and it takes around 2.5 hours to arrive. NB! Only Tallinn-Tartu busses leaving at full hour (12:00; 13:00 etc.) stop in airport. Bus ticket could be bought from bus in cash or from a ticket machine in the airport (0 floor) by bankcard. In advance you can buy bus ticket via online system at http://www.tpilet.ee/en, choosing "Tallinna lennujaam" in the "From" field and "Tartu bussijaam" in the "To" field and pay by credit card. One-way ticket costs ca EUR 11. From Tallinn port you should take a taxi or a public transport of Tallinn to the bus station and then express bus. In case you take the express bus at full hour (12:00; 13:00 etc.), you have a free Wi-Fi connection in the bus during the whole journey. When you travel from Tartu to Tallinn, bus will make a stop in the airport but for the port you again have to take a taxi or public transport of Tallinn.

From Tartu airport you can take an airport shuttle to Tartu – look from the airport’s homepage under the transport.

Accommodation
Costs for accommodation (Dorpat Hotel), lunches and tea&coffee breaks will be covered.

Registration
Maximum of 15 participants will be accepted for the course. For registration and further information please contact us at info@plutof.ut.ee