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Faculty of Arts and HumanitiesDean's Office, Faculty of Arts and HumanitiesJakobi 2, r 116-121 51005 Tartu linn, Tartu linn, Tartumaa EST0Institute of History and ArchaeologyJakobi 2 51005 Tartu linn, Tartu linn, Tartumaa EST0Institute of Estonian and General LinguisticsJakobi 2, IV korrus 51005 Tartu linn, Tartu linn, Tartumaa ESTInstitute of Philosophy and SemioticsJakobi 2, III korrus, ruumid 302-337 51005 Tartu linn, Tartu linn, Tartumaa EST0Institute of Cultural ResearchÜlikooli 16 51003 Tartu linn, Tartu linn, Tartumaa EST0Institute of Foreign Languages and CulturesLossi 3 51003 Tartu linn, Tartu linn, Tartumaa EST0School of Theology and Religious StudiesÜlikooli 18 50090 Tartu linn, Tartu linn, Tartumaa EST0Viljandi Culture AcademyPosti 1 71004 Viljandi linn, Viljandimaa EST0Professors emeritus, Faculty of Arts and Humanities0Associate Professors emeritus, Faculty of Arts and Humanities0Faculty of Social SciencesDean's Office, Faculty of Social SciencesLossi 36 51003 Tartu linn, Tartu linn, Tartumaa EST0Institute of EducationJakobi 5 51005 Tartu linn, Tartu linn, Tartumaa EST0Johan Skytte Institute of Political StudiesLossi 36, ruum 301 51003 Tartu linn, Tartu linn, Tartumaa EST0School of Economics and Business AdministrationNarva mnt 18 51009 Tartu linn, Tartu linn, Tartumaa EST0Institute of PsychologyNäituse 2 50409 Tartu linn, Tartu linn, Tartumaa EST0School of LawNäituse 20 - 324 50409 Tartu linn, Tartu linn, Tartumaa EST0Institute of Social StudiesLossi 36 51003 Tartu linn, Tartu linn, Tartumaa EST0Narva CollegeRaekoja plats 2 20307 Narva linn, Ida-Virumaa EST0Pärnu CollegeRingi 35 80012 Pärnu linn, Pärnu linn, Pärnumaa EST0Professors emeritus, Faculty of Social Sciences0associate Professors emeritus, Faculty of Social Sciences0Faculty of MedicineDean's Office, Faculty of MedicineRavila 19 50411 Tartu linn, Tartu linn, Tartumaa ESTInstitute of Biomedicine and Translational MedicineBiomeedikum, Ravila 19 50411 Tartu linn, Tartu linn, Tartumaa ESTInstitute of PharmacyNooruse 1 50411 Tartu linn, Tartu linn, Tartumaa ESTInstitute of DentistryL. Puusepa 1a 50406 Tartu linn, Tartu linn, Tartumaa ESTInstitute of Clinical MedicineL. Puusepa 8 50406 Tartu linn, Tartu linn, Tartumaa ESTInstitute of Family Medicine and Public HealthRavila 19 50411 Tartu linn, Tartu linn, Tartumaa ESTInstitute of Sport Sciences and PhysiotherapyUjula 4 51008 Tartu linn, Tartu linn, Tartumaa ESTprofessors emeritus, Faculty of Medicine0associate Professors emeritus, Faculty of Medicine0Faculty of Science and TechnologyDean's Office, Faculty of Science and TechnologyVanemuise 46 - 208 51003 Tartu linn, Tartu linn, Tartumaa ESTInstitute of Computer ScienceNarva mnt 18 51009 Tartu linn, Tartu linn, Tartumaa ESTInstitute of GenomicsRiia 23b/2 51010 Tartu linn, Tartu linn, Tartumaa ESTEstonian Marine Institute0Institute of PhysicsInstitute of ChemistryRavila 14a 50411 Tartu linn, Tartu linn, Tartumaa ESTInstitute of Mathematics and StatisticsNarva mnt 18 51009 Tartu linn, Tartu linn, Tartumaa EST0Institute of Molecular and Cell BiologyRiia 23, 23b - 134 51010 Tartu linn, Tartu linn, Tartumaa ESTTartu ObservatoryObservatooriumi 1 61602 Tõravere alevik, Nõo vald, Tartumaa EST0Institute of TechnologyNooruse 1 50411 Tartu linn, Tartu linn, Tartumaa ESTInstitute of Ecology and Earth SciencesJ. Liivi tn 2 50409 Tartu linn, Tartu linn, Tartumaa ESTprofessors emeritus, Faculty of Science and Technology0associate Professors emeritus, Faculty of Science and Technology0Area of Academic SecretaryHuman Resources OfficeUppsala 6, Lossi 36 51003 Tartu linn, Tartu linn, Tartumaa EST0Area of Head of FinanceFinance Office0Area of Director of AdministrationInformation Technology Office0Administrative OfficeÜlikooli 17 (III korrus) 51005 Tartu linn, Tartu linn, Tartumaa EST0Estates Office0Marketing and Communication OfficeÜlikooli 18, ruumid 102, 104, 209, 210 50090 Tartu linn, Tartu linn, Tartumaa EST0Area of Vice Rector for Academic AffairsOffice of Academic AffairsUniversity of Tartu Youth AcademyUppsala 10 51003 Tartu linn, Tartu linn, Tartumaa ESTStudent Union OfficeÜlikooli 18b 51005 Tartu linn, Tartu linn, Tartumaa EST0Centre for Learning and TeachingArea of Vice Rector for ResearchUniversity of Tartu LibraryW. Struve 1 50091 Tartu linn, Tartu linn, Tartumaa ESTGrant OfficeArea of Vice Rector for DevelopmentCentre for Entrepreneurship and InnovationNarva mnt 18 51009 Tartu linn, Tartu linn, Tartumaa EST0University of Tartu Natural History Museum and Botanical GardenVanemuise 46 51003 Tartu linn, Tartu linn, Tartumaa EST0International Cooperation and Protocol Office0University of Tartu MuseumLossi 25 51003 Tartu linn, Tartu linn, Tartumaa EST0Area of RectorRector's Strategy OfficeInternal Audit Office
Metabarcoding: from Lab to Bioinformatics
On-site in Tartu 1-7 August 2022
High-throughput metabarcoding methods have become a routine analysis tool in biodiversity research and ecology in general. This course will cover the principles of metabarcoding workflow, from the laboratory analyses to bioinformatic analyses of the high-throughput sequencing data.
Laboratory work includes steps for sample preparation, DNA extraction, PCR and sequencing library preparation. The practical sessions are supplemented with theoretical lectures.
Hands-on metabarcoding data set analyses will mostly follow PipeCraft 2 pipeline (user-friendly graphical user interface software for non-bioinformaticians) but basics of command-line interface and usage of high-performance clusters will be also covered.
| Focus area: | Biology, Ecology, Mycology, and Microbiology | Coordinating unit at UT |
Chair of Mycology, Institute of Ecology and Earth Sciences |
| Study Field: | Biology, Mycology, Microbiology, and Ecology | Course Leader | Dr. Niloufar Hagh-Doust, Research fellow at University of Tartu |
| Format | Practical and theoretical sessions | Location | Tartu, Estonia |
| Course dates: | 1-7 August 2022 | Apply by: | 19 June 2022 |
| ECTS: | 4 (evaluation method: participants will be asked to prepare a 2 page report) | Fee: | 450 € |
| Study group | MSc/PhD and Post-doc | Language | English |
Lecturers:
- Prof. Leho Tedersoo, University of Tartu
- Prof. Urmas Kõljalg, University of Tartu
- Dr. Sten Anslan, University of Tartu
- Dr. Vladimir Mikryukov, University of Tartu
- Dr. Kessy Abarenkov, University of Tartu
- Dr. Niloufar Hagh-Doust, University of Tartu
- Dr. Heidi Tamm, University of Tartu
- Ali Hakimzadeh, University of Tartu
Monday
- Opening lecture
- Lectures on the basic concepts of DNA extraction, PCR and primer selection, metabarcoding and sequencing technologies and necessary steps to build up metabarcoding libraries. There will be an opportunity for software installation troubleshooting after the lecture.
Tuesday
- Practical sessions in the laboratory including DNA extraction and PCR.
Wednesday
- Practical lab sessions on preparing metabarcoding libraries.
- Bioinformatics sessions with a lecture by Sten Anslan plus software installation troubleshooting if necessary.
Thursday
- Practical sessions on bioinformatic data analysis.
Friday
- Bioinformatics practical sessions
- Lecture on Publishing to GBIF/UNITE/PlutoF
- Closing lecture.
The participants can take part in cultural group activities after the study sessions.
Participants will be expected to have a basic understanding about molecular biology.
The target audience are Master and PhD students, early career researchers (post-docs), or senior researchers, either from Industry or Academia, with no or little prior knowledge on metabarcoding techniques. This workshop is mainly aimed for students and researchers with a background in ecology, biodiversity research or community biology who wish to use molecular tools for their research.
Entry requirements:
- Online application form
- Motivation letter (up to 1 page) that demonstrates the applicant’s motivation to participate, his/her expectations about the programme, how participation in the summer programme relates to his/her studies and interests, and how the applicant plans to use the gained experience and knowledge in the future.
- Transcript of academic records
- Copy of passport
PS: Only complete applications including all annexes submitted by the deadline will be considered for selection.
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Understanding the main concepts, potentials and limitations of metabarcoding techniques.
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Knowledge of the laboratory procedures necessary for metabarcoding.
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Ability to set up the working environment for bioinformatic analysis.
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Knowledge of key bioinformatic procedures for metabarcoding sequence data analyses.
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Understanding of the full cycle of data management and publishing.
Two weeks prior to the start of the programme an information file will be sent to all participants. This file contains the daily schedule and relevant contact information of the programme managers.
Students are responsible for their travel, accommodation and travel insurance (visa arrangements if needed) from their home country to Tartu and back to their home country. It is recommended to visit the Tartu Welcome Centre website and arrival and housing section to find accommodation opportunities.
The University of Tartu will offer 20 tuition waivers (scholarships) altogether for citizens of Ukraine for all summer courses. It will cover the course fee and cultural programme. Accommodation and daily expenses are not included.
The selection process is going to be based on the motivation letter. In order to apply for the scholarship please submit your application to the summer course and upload a motivation letter (no longer than approx 1 A4 page).