ForBio talk:
What I do in GBIF and in the University of Helsinki
Why bother teaching
Education networks: managing time and money
Teaching experiences 2013-2015
Teaching plans & invitations 2016
Species, habitats and skills: teaching boreal biodiversity and data across borders
1. Dmitry Schigel
University of Helsinki
Species, habitats and skills:
teaching boreal biodiversity
and data across borders
2. Outline
• What I do in GBIF and in the University of Helsinki
• Why bother teaching
• Education networks: managing time and money
• Teaching experiences 2013-2015
• Teaching plans & invitations 2016
5. GBIF BY THE NUMBERS
652,948,064
species occurrence
records
15,882
datasets
804
data-publishing
institutions
• http://www.gbif.org | 01 APR 2016
6. Dmitry Schigel: 2012-2015
Academy of Finland
Colonization gates and establishment
of wood-decaying fungi in European Spruce
X =
2014 -> GBIF
7. Approaches and outlook:
e.g. Population Biology in Fragmented
Landscapes, Biodiversity in Dead Wood
Skills: Sample preps for NGS,
Microscopy, Bioinformatics, Databases
Facts: Species diversity &
identification, morphology
8. University of Helsinki
Finland
Moscow State University
Russia
Swedish University
of Agricultural Sciences
2016: Nordic – Russian Boreal Biodiversity
and Data Education Network
9. Education and outreach
• Polypores of the Białowieża forest Oct 2013
• Biodiversity in dead wood, Helsinki Nov 2013
• Next-gen seq sample prep course, Uppsala Jun 2014
• Biodiversity informatics and data management Jul 2014
• Polypore course, Russia Aug 2014
• Polypore course, Finland: ForBio Sep 2014
• Dead wood meeting, Lammi: SIU May 2015
* * *
• Dead wood meeting & course Lammi Aug 2016
• Polypores as tools in forest conservation Lammi Sep 2016
• Biodiversity data skills Tartu Nov 2016
14. Biodiversity in Dead Wood
2013 course
• An introductory course for graduate and advanced
undergraduate students, 1 week
• Cover various aspects of the habitat, organism groups and
ecological processes connected with dead wood
• Guest experts on dead wood provide deeper coverage of
research field
• Present dead wood research
1. 15 h lectures (5 days x 3 h), learning diaries = 2 ECTS
2. optional 5 h journal club, essays = 2 ECTS
3. optional book exam = 3 ECTS
7 ECTS =
17. Kilpisjärvi
• Subarctic ecology and
biogeography
• Accomodation for 66
• Lecture and meeting
rooms
• Vans and boats
• Lake-side sauna
University of Helsinki
www.helsinki.fi/kilpis
ForBio:
Data management
course
2014
20. published record (existence approved by
scientific community, a bibliographic
reference in peer-reviewed paper exists)
collected (at least one reliably identified specimen in
a clearly designated private or public collection)
recorded, not collected (e.g.with the identifiable photo, video, sound
recording) ?Anax imperator
observed
21.
22.
23. Education and outreach
• Polypores of the Białowieża forest Oct 2013
• Biodiversity in dead wood, Helsinki Nov 2013
• Next-gen seq sample prep course, Uppsala Jun 2014
• Biodiversity informatics and data management Jul 2014
• Polypore course, Russia Aug 2014
• Polypore course, Finland: ForBio Sep 2014
• Dead wood meeting, Lammi: SIU May 2015
* * *
• Dead wood meeting & course Lammi Aug 2016
• Polypores as tools in forest conservation Lammi Sep 2016
• Biodiversity data skills Tartu Nov 2016
24. Polypores as tools in forest conservation:
species ID course
• Teachers: O. Miettinen, O. Manninen, T.
Niemelä
• Target group: MSc students, biology /
forestry
Time: 19-23 September 2016
• Place: Lammi biological station, Finland
• Quota: ~ 15 people
• Test: identification exam
• Reading in advance required: Wikipedia
page, kelo tree paper, Finnish, Swedish and
Russian indicator species guides.
2016
25. Biodiversity data management and open data:
data skills course
• Teachers: U. Kõljalg, K. Abarenkov, H. Koivula, (D. Schigel)
• Target group: MSc students, biology
• Time: 1-5 November 2016
• Place: Tartu, Estonia
• Quota: ~ 15 people LUCY (2014)
2016
27. Lammi
• Forests and lakes
• 120 km from Helsinki
• Accomodation for 100
• Large and small rooms
and labs
• One e-mail booking
• Lake-side sauna
University of Helsinki
www.helsinki.fi/lammi
ForBio:
Dead Wood
Course 2016,
Polypores as tools
Other events include species identification and sample preparetion skills, data management skills and finally, dead wood symposium
2013 course
Note! Mere undocumented observtions are temporary subcases of Not Finnish until some evidence is provided. Observed, not recorded (= line in a note book or undocumented record in Hatikka) are waiting approval before some proof is provided. This, e.g. means that Hatikka observations of a species with at least one record or collection are all valid observation of a Finnish species (subject to identification accuracy).
In the most simple system, we need to decide if a certain species belongs to Finnish biota or not. We need to have a set of criteria that allows any species in any checklist to be called Finnish or not.
This is a draft of tagging guidelines for LUOMUS teams to manage the existing (uploaded and online) cheklists and to prepare the new checklists, preferably using the template provided by the ICT team (link). The non-scientific division of species into Finnish and non-Finnish is, however essential for smooth functioning of the e-systems of LUOMUS, for separating national and external collections, for conservation-related issues and many other preactical reason.
Screenshots from 2015
Group photo, programme
Archive slides!
Dead wood meeting 2015
Gallery photos
Other events include species identification and sample preparetion skills, data management skills and finally, dead wood symposium
Polypores as indicators 2016
Images from Finnish wiki
Image of Lammi station
Summary: Hands on course from data collection to the data management and publishing data as Open Data. Students will learn how to: 1) collect taxon occurrence or sample based data; 2) handle their data by keeping standards and quality aspects in mind (creating personal data management plans) 3) create integrated databases for the different data types (observations, specimens, sampling areas, samples, DNA sequences, traits, interactions, references); 4) manage and share datasets; 5) publish datasets with DataCite (DOIs), in GBIF, or in online journals (Pensoft).
DS: From SIU application, what was promised, and on what I will need to report to SIU:
Young researchers in natural sciences are educated to collect, analyze, publish and disseminate the scientific information, but handling and managing data is often overlooked aspect of researcher's life. There has been little to no university teaching of this important set of skills in the Nordic - Russian region. The key principles of biodiversity data management and the most important tools will be covered by the course given by the leading experts in this growing field.
POSter
Almost a society, beetles, fungi,
Almost have a journal
Almost have a website and social media groups
Almost have a conferences
Almost have a study programme.