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rDNA ITS based identification of Eukaryotes and their communication via DOIs
NEFOM workshop "Back to the roots" and linked PhD course

NEFOM workshop "Back to the roots"

Dates: April 19-20, 2021
Format: Online using Zoom
Description: At the NEFOM workshop "Back to the roots" all network labs and invited researchers will meet to discuss how forest biodiversity open data and associated digital services should be built and brought together in a FAIR way. An overview of the best practices in data management, analysis, service development and publishing will be given by invited speakers. Workshop will be followed by 2-days practical PhD course on full data lifecycle and best data management practices.
Registration: Closed

Program
19.04 Day 1 (for project partners only)
11.00 - 13.00 EEST (10.00 - 12.00 CEST) session 1 (presentations)
13 - 14 EEST (12 - 13 CEST) Lunch Break
14.00 - 16.00 EEST (13.00 - 15.00 CEST) session 2 (presentations and discussion)

20.04 Day 2 (open to public)
Session 1 (scientific presentations)
11:00 - 11:30 EEST (10:00 - 10:30 CEST) "Data management in Genomic observatories networks – examples from the marine ARMS-MBON" by Matthias Obst (University of Gothenburg, Sweden) (PDF)
11:30 - 12:00 EEST (10:30 - 11:00 CEST) "Global Biodiversity Information Facility" by Dmitry Schigel (GBIF)
12:00 - 12:30 EEST (11:00 - 11:30 CEST) "Assessment of biases using different sequencing technologies for fungal ITS metabarcoding" by Carles Castaño (Swedish University of Agricultural Sciences, Sweden) (PDF)
12:30 - 13:00 EEST (11:30 - 12:00 CEST) "Using UNITE to augment species data for investigating biogeographic patterns" by Tom W. May (Royal Botanic Gardens Victoria, Australia) (PDF)

13 - 14 EEST (12 - 13 CEST) Lunch Break

Session 2 (scientific presentations and taxonomy flash talks)
14:00 - 14:30 EEST (13:00 - 13:30 CEST) "Is there such thing as the "best" metabarcoding workflow?" by Sten Anslan (Technische Universität Braunschweig, Germany; University of Tartu, Estonia) (PDF)
14:30 - 15:30 EEST (13:30 - 14:30 CEST) - Taxonomy flash talks:
            "Flaviporus citrinellus" by Reda Iršėnaitė (Nature Research Centre, Lithuania) (PDF)
            "Cortinarius osloensis - IUCN global redlist species from the relict calcareous Tilia forest" by Tor Erik Brandrud (Norwegian Institute for Nature Research, Norway) (PDF)
            "An introduction to European species of Calocera" by Anton Savchenko (University of Tartu, Estonia)
            "Nivicolous myxomycetes in lowlands: undescribed species diversity?" by Iryna Yatsiuk (University of Tartu, Estonia)
            "Pseudotryblidium neesii, a fungus associating lichens" by Ave Suija (University of Tartu, Estonia) (PDF)
15:30 - 16:00 EEST (14:30 - 15:00 CEST) - "UNITE and analytical services" by Urmas Kõljalg and Kessy Abarenkov (University of Tartu, Estonia)
16:00 - 17:00 EEST (15:00 - 16:00 CEST) - Discussion

The workshop and linked PhD course are organised by the NEFOM network in cooperation with the ECOLCHANGE Centre of Excellence and funded by the SNS and ForBioeconomy.

    



PhD course "Metabarcoding Data Management and Analysis"

Dates: April 21-22, 2021
Format: Online
Description: PhD students and young researches will be trained on full data life cycle and best data management practices for biodiversity and metabarcoding data. Course participants will learn about 1) High Throughput Sequencing (HTS) data life cycle in general and on PlutoF platform, 2) data analysis for species discovery from environmental (eDNA) samples through UNITE analysis as EOSC-Nordic services, 3) data publishing to GBIF, 4) communicating species in research papers.
Registration: see the registration for NEFOM workshop above.

Preliminary program
21.04 Day 1
10:00 - 12:00 (EEST) Session 1
10:00 – 10.10 Welcoming words (Kessy Abarenkov)
10:10 – 11:00 “HTS data life cycle” (Mohammad Bahram & Sten Anslan)
11:00 – 12:00 Raw sequence data processing and analysis workflows:
      “PipeCraft” (Sten Anslan)
      “SCATA” (Karina Clemmensen)
12:00 - 12:45 Break
12:45 - 14:45 Session 2
12:45 – 14:45 Hands-on: “Metabarcoding projects in PlutoF” (Kessy Abarenkov)
14:45 - 15:30 Break
15:30 - 17:30 Session 3
15:30 – 16:00 “Introduction to SH&TH paradigms” (Urmas Kõljalg)
16:00 – 17:30 Hands-on: “Data analysis in UNITE/PlutoF” (Kessy Abarenkov)

22.04 Day 2
10:00 - 12:00 (EEST) Session 1
10:00 – 11:00 Hands-on “Data analysis in UNITE/PlutoF“ continues (Kessy Abarenkov)
11:00 – 12:00 PlutoF publishing (Kessy Abarenkov)
12:00 - 12:45 Break
12:45 - 14:45 Session 2
12:45 – 14:45 Hands-on “Publishing to GBIF” (Kessy Abarenkov)
14:45 - 15:30 Break
15:30 - 17:30 Session 3
15:30 – 17:30 “Curating UNITE datasets via third-party annotations” (R. Henrik Nilsson)

Teachers:
Urmas Kõljalg (University of Tartu, Estonia)
Kessy Abarenkov (University of Tartu, Estonia)
Karina Clemmensen (Swedish University of Agricultural Sciences, Sweden)
Mohammad Bahram (University of Tartu, Estonia)
Sten Anslan (Technische Universität Braunschweig, Germany; University of Tartu, Estonia)
R. Henrik Nilsson (University of Gothenburg, Sweden)