METABO-OPEN 2021

 

4 - 6 October 2021

APPLICATION DEADLINE: 15th SEPTEMBER 2021 

 


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.

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)
  • Introduction to MetaboLightsThomas Payne (15 min)
  • Introduction to Integrape data management guidelines. Stefania Savoi (10 min)
  • How to describe a grapevine experiment and sample metadataÉric Duchêne (25 min)
  • Sample preparation, Separation and Mass Spectrometry protocols description, Data Quality control. Marynka Ulaszewska  (30 min)
  • Data transformation, Data analysis, and Metabolite IDs and annotation. Mar Garcia Aloy (20 min)
  • 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 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.

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 UlaszewskaMar Garcia AloyPanagiotis Arapitsas, and Stefania Savoi).

  • How to upload data to MetaboLights (2 hours)

Organized by Stefania Savoi (with Panagiotis Arapitsas)

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

 


SPEAKERS &TRAINERS

Prof. Fulvio Mattivi  | This email address is being protected from spambots. You need JavaScript enabled to view it. | University of Trento, Trento, IT

Prof. Éric Duchêne  | This email address is being protected from spambots. You need JavaScript enabled to view it. | Food and Environment, INRAe Colmar, France

Dr Thomas Payne  | This email address is being protected from spambots. You need JavaScript enabled to view it. | Scientific Database Curator Metabolights - O'Donovan team: Metabolomics

Dr Stefania Savoi This email address is being protected from spambots. You need JavaScript enabled to view it. | AGAP, Institut Agro-Montpellier, France

Dr Panagiotis Arapitsas  | This email address is being protected from spambots. You need JavaScript enabled to view it. | Fondazione Edmund Mach, San Michele All’Adige, IT 

Dr Marynka Ulaszewska  | This email address is being protected from spambots. You need JavaScript enabled to view it. | Center for Omics Sciences, Proteomics and Metabolomics Facility, San Raffaele Scientific Institute, Milano, IT

Dr Mar Garcia-Aloy  | This email address is being protected from spambots. You need JavaScript enabled to view it. | Fondazione Edmund Mach, San Michele All’Adige, IT

Dr Pietro Franceschi  This email address is being protected from spambots. You need JavaScript enabled to view 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 (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   

Dr Panagiotis Arapitsas  | This email address is being protected from spambots. You need JavaScript enabled to view it.

Dr Stefania Savoi  | This email address is being protected from spambots. You need JavaScript enabled to view it.

 

Important Dates

An open call for the Short Term Scientific Missions  (STSM) of COST Action INTEGRAPE is now available using a 2-step evaluation procedure. With STSMs INTEGRAPE can fund your stay in another institution to undertake collaborative research.

STSMs for this grant period should be performed up until end of September 2021.
More information available at STSM GRANTS


An open call is now available for the Inclusiveness Target Countries (ITC) Grants of COST Action INTEGRAPE

If you come from an Inclusiveness Target Country, INTEGRAPE can fund your virtual attendance at the conference of your choice.

The proposed conference must take place before September 30th, 2021.

Application till 4 weeks before scheduled conference date and submission of a scientific report and fee invoice within 30 days after end of conference.
More information available at ITC GRANTS