METABO-OPEN 2021

metabo-open-2021

Statistics & Testimonials

4 - 6 October 2021

Open for Day 1 Introductory Part I only

OVERVIEW

DATE: October 4th – 6th 2021

PLACE: Online: ZOOM platform

BRIEF 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.

FINAL PROGRAM

DAY 1: 4th October 2021

Introductory part I (3+1 hours). This part is open to a wider public. Register here

Morning section 9:00 to 12:00 (Central European Time – Italy, France, Spain, Germany, etc)

  • Introduction to F.A.I.R. data management in metabolomics and actual situations in viticulture and wine science. Fulvio Mattivi (15 min) SLIDES
  • Introduction to MetaboLights. Thomas Payne (15 min) SLIDES
  • Introduction to Integrape data management guidelines. Stefania Savoi (10 min) SLIDES
  • How to describe a grapevine experiment and sample metadata. Éric Duchêne (25 min) SLIDES
  • Quality Control and Randomization in Metabolomics. Untargeted Metabolomic Workflow: From sample preparation to mass spectrometry analysis. Marynka Ulaszewska  (30 min)  SLIDES
  • Data transformation, Data analysis, and Metabolite IDs and annotation. Mar Garcia Aloy (20 min) SLIDES
  • Morning Q&A session
Afternoon section 15:00-16:00 (Central European Time – Italy, France, Spain, Germany, etc)
  • Afternoon Q&A session

DAY 2: 5th October 2021

Practical Part II (Hands-on, 3+1 hours). This part is addressed only to the selected trainees.

Morning section 9:00 to 12:00 (Central European Time – Italy, France, Spain, Germany, etc)

  • How to use the data from the public repositories 

Organized by Pietro Franceschi (with Marynka Ulaszewska, Mar Garcia Aloy, Panagiotis 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.

Afternoon section 15:00-16:00 (Central European Time – Italy, France, Spain, Germany, etc)
  • Afternoon Q&A session

DAY 3: 6th October 2021

Practical Part III (Hands-on, about 3+1 hours). This part is addressed only to the selected trainees.

Morning section 9:00 to 12:00 (Central European Time – Italy, France, Spain, Germany, etc)

  • Discussion/presentation of the homework from the previous part. (1 hour)

Organized by Pietro Franceschi (with Marynka Ulaszewska, Mar Garcia Aloy, Panagiotis Arapitsas, and Stefania Savoi).

  • How to upload data to MetaboLights (2 hours)

Organized by Stefania Savoi (with Panagiotis Arapitsas and Giulia Chitarrini)

Afternoon section 15:00-16:00 (Central European Time – Italy, France, Spain, Germany, etc)
  • Afternoon Q&A session and Closing remarks

SPEAKERS & TRAINERS

Fulvio Mattivi  | fulvio.mattivi@unitn.it | University of Trento, Trento, IT

Éric Duchêne  | eric.duchene@inrae.fr | Food and Environment, INRAe Colmar, France

Thomas Payne  | payne@ebi.ac.uk | Scientific Database Curator Metabolights – O’Donovan team: Metabolomics

Stefania Savoi  | savoi.stefania@gmail.com | AGAP, Institut Agro-Montpellier, France

Panagiotis Arapitsas  | panagiotis.arapitsas@fmach.it | Fondazione Edmund Mach, San Michele All’Adige, IT 

Marynka Ulaszewska  | maria.ulaszewska@gmail.com | Center for Omics Sciences, Proteomics and Metabolomics Facility, San Raffaele Scientific Institute, Milano, IT

Mar Garcia-Aloy  | mar.garcia@fmach.it | Fondazione Edmund Mach, San Michele All’Adige, IT

Pietro Franceschi  | pietro.franceschi@fmach.it | Fondazione Edmund Mach, San Michele All’Adige, IT

Giulia Chitarrini  | giulia.chitarrini@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.  Register here

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 (https://www.cost.eu/uploads/2021/04/Vademecum-V9-28-April-20212-1.pdf)

– 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

Panagiotis Arapitsas  | panagiotis.arapitsas@fmach.it

Stefania Savoi  | savoi.stefania@gmail.com