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APPLICATION DEADLINE: 15th SEPTEMBER 2021 

Overview

DATE:

October 4th – 6th 2021

PLACE:

Online: ZOOM platform

PROGRAM:

To manage the exponential rise in biological data and their relative metadata information, it has become necessary to submit raw data to ad-hoc public repositories. Publicly-available metabolomic datasets have hidden, true potential in the light of data reanalysis and integration. Therefore, there is an urgent need to make this biological data and information available to the entire plant scientific community.

The aim of this training school is to provide knowledge and tools on experimental design, metabolomics data and metadata management, as well as their upload to public repositories according to FAIR  (Findable, Accessible, Interoperable, Reusable) principles, and demonstrate how to reuse data already present in public repositories. 

This online training school is divided into three modules.

The first module, open to the wider public, will be an introduction to the experimental design description, metabolomics data and metadata management. More information can be found on the Integrape Data Management web page.

The second module will address reusing the dataset previously presented to the public repositories by various informatic tools.

Finally, the third module will be focused on the step-by-step upload of a metabolomic study to the public repository of MetaboLights.

Trainers

Prof. Fulvio Mattivi  | fulvio.mattivi@unitn.it

University of Trento, Trento, IT

Prof. Éric Duchêne  | eric.duchene@inrae.fr

Food and Environment, INRAE Colmar, France

Dr Stefania Savoi  | savoi.stefania@gmail.com

Dr Panagiotis Arapitsas  | panagiotis.arapitsas@fmach.it

Fondazione Edmund Mach, San Michele All’Adige, IT 

Dr Marynka Ulaszewska  | maria.ulaszewska@gmail.com

Center for Omics Sciences, Proteomics and Metabolomics Facility, San Raffaele Scientific Institute, Milano, IT

Dr Mar Garcia-Aloy  | mar.garcia@fmach.it

Fondazione Edmund Mach, San Michele All’Adige, IT

Dr Pietro Franceschi  pietro.franceschi@fmach.it

Fondazione Edmund Mach, San Michele All’Adige, IT 

SELECTION CRITERIA OF TRAINEES

Participation in the introductory part I is open to a wider public. All are invited to register.

Evaluation of applications for the practical parts II and III will be based on the following criteria:

Priority will be given to those with the correct criteria among PhD students, early career researchers and others from COST member countries as well as MC Observers from Near-Neighbouring countries. Those with correct criteria from non-COST countries are also encouraged to apply. COST eligibility details are available on pages 27/28 of the COST Vademecum (LINK)

 Postdocs, PhD students, PIs and bioinformaticians working in metabolomics related to grapevine with a high motivation to spread these good practices learned during the training school.

 A maximum of 20 trainees will be selected for the practical parts II and III. 

Selection of participants to the practical parts II and III will be made by COST Integrape local organisers on the basis of all submitted data:

  • Motivation letter (pdf)
  • Curriculum vitae (pdf)

The training school is free to attend, but as the training school will be online, travel expenses will not be reimbursed.

CONTACTS   

Dr Panagiotis Arapitsas  | panagiotis.arapitsas@fmach.it

Dr Stefania Savoi  | savoi.stefania@gmail.com

PRELIMINARY PROGRAM

Introductory part I (2-3 hours). This part is open to a wider public.

  • Introduction to F.A.I.R. data management in metabolomics and actual situations in viticulture and wine science. Fulvio Mattivi (10-15 min)
  • Introduction to MetaboLights. TBD (10-15 min)
  • Introduction to Integrape: How to submit metabolomic data to MetaboLights. Stefania Savoi (10 min)
  • How to describe a grapevine experiment and sample metadata. Éric Duchêne (20-25 min)
  • Sample preparation, Separation and Mass Spectrometry protocols description. Marynka Ulaszewska  (20 min)
  • Data transformation, Data analysis, and Metabolite IDs and annotation. Mar Garcia Aloy (20 min)
  • Final Q&A session

Practical Part II (Hands-on, about 2-3 hours). This part is addressed only to the selected students.

  • How to use the data from the public repositories 

Organized by Pietro Franceschi (with Marynka UlaszewskaMar Garcia AloyPanagiotis Arapitsas, and Stefania Savoi). At the end of this part, students will get homework (as a group or alone) to do and discuss the day after.

Practical Part III (Hands-on, about 2-3 hours). This part is addressed only to the selected students.

  • Discussion/presentation of the homework from the previous part. (30-60 min)

Organized by Pietro Franceschi (with Marynka UlaszewskaMar Garcia AloyPanagiotis Arapitsas, and Stefania Savoi).

  • How to upload data to MetaboLights (1-2 hours)

Organized by Stefania Savoi (with Panagiotis Arapitsas)

  • Closing remarks

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