Training school on Transcriptomic Metadata Handling and Data Analysis

29th November 2019

Now Closed 

See Presentations and Report Below






Presented at the The Second Annual Meeting of COST Action CA17111 (Ljubljana, SLOVENIA).


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TITLE: METHADA 2020 – Transcriptomic Metadata Handling and Data Analysis

DATE: 5-7 February 2020

VENUE: Institute for Integrative Systems Biology (I2SysBio). Valencia, Spain


The rise of the latest technologies combining physics, optics, chemistry and its application to molecular biology has led to high-throughput experiments, yielding an explosion of publicly available data. This data ranges from Next Generation Sequencing (NGS) to transcriptomics, phenomics, metabolomics to large scale single cell data. In the case of transcriptomics, which generates to date the biggest amount of data compared to other omics, protocols for data submission are not fully standardized for grapevine data and not controlled by the research community. Public available gene expression datasets have a hidden true potential in the light of data reanalysis and integration. In line with the FAIR (Findable Accessible Interoperable Reusable) principles our next challenge as a community relies on correct sample and experiment annotations, using controlled vocabularies to ensure both human readability and computational tractability. This training school addresses transcriptomics data handling and analysis, and it is organized in two modules. On the first unit, trainees will work to learn how to correctly annotate experiments and handle metadata in order to exploit standards and bio-ontologies for data annotation. Secondly, attendees will be trained in a reduced set of foundational skills to analyze and explore transcriptomic datasets, including resources freely available for the grapevine community. All trainees will learn on how to use Jupyter Notebook, an open-source language-agnostic web application (it supports over 40 programming languages including Python and R) that allows a wide range of workflows in data science and scientific computing without burdening the users with installation and maintenance tasks


Marco Moretto

Marco Moretto

Computational Biology Unit, Fondazione Edmund Mach - Istituto Agrario San Michele All'Adige

Paolo Sonego

Paolo Sonego

Computational Biology Unit, Fondazione Edmund Mach - Istituto Agrario San Michele All'Adige

Elie Maza

Elie Maza

INP-ENSAT Toulouse

José Tomás Matus

José Tomás Matus

I2SysBio, Valencia

Jérôme Grimplet

Jérôme Grimplet


COST gives each eligible trainee 700 euros as a financial contribution towards overall travel, accommodation and meal expenses of the Grantee.

Priority will be given to early career researchers and eligible candidates must be from COST member countries or MC Observers from Near-neighbouring countries (eligibility details available on pages 30/31 of the COST Vademecum of applicants will be based on the following criteria:

Postdocs, PhD students and early career PIs working in transcriptomics, genomics, and computational biology-related aspects of grapevine, with high motivation in spreading good metadata handling practices learned during the training school.

The training school is directed to computational biologists or biologists/biotechnologists with the following bioinformatics skills:

  • Basic knowledge of bioinformatics and computational biology theory
  • Basic programming in R and/or Python.

Selection of participants will be made by COST Integrape local organisers on the basis of all submitted data:

  • Reason for participating
  • Curriculum vitae
  • Recommendation letter (in case of PhD students and Postdocs)

Travel/Accommodation info

Valencia, Spain’s third-largest city, is very well communicated by planes with a major airport and high-speed trains from/to Madrid and Barcelona.
Valencia disposes of a large set of hotels fitting any budget. In addition, it offers flats and apartments, university dorms, studios and rooms for rent.


I2SysBio (Parc Cientific UV, Tram station ‘Santa Gemma’) is located in the town of Burjassot, just 12min from the city center of Valencia (by taxi) or 30min from the metro Station ‘Turia’ or ‘Pius XII’ (needs a transfer to a tram line at ‘Empalme’ or ‘Campus’ station). There is a diverse variety of hotel options inside the city (close to the city center or towards the Institute), or also inside the town of Burjassot. Here are some options:

Close to the Venue (Burjassot)

Close to Turia station in Valencia

If you rent through Airbnb make sure to be close to any metro/tram station
Any doubts you can contact the local organizers


The school counts with catering for the three days (coffee breaks and lunch will be offered free of charge to the attendees). The gala dinner will cost around 45-50 euros and will take place in a restaurant inside the city of Valencia.


Dr José Tomás Matus

Institute for Integrative Systems Biology
Carrer del Catedràtic Agustín Escardino Benlloch,
46980 Paterna, València

Dr Jérôme Grimplet

Centro de Investigación y Tecnología Agroalimentaria de Aragón
Avda. Montañana 930
50059 – Zaragoza
Phone: +34 976 71 3635


Day 1 (5th Feb, 9:00-18:00)

9:00Welcome from I2SysBio Director/Vice-director and COST Action MC Chair (Mario Pezzotti). Presentation of the Training School (Jerome Grimplet, Tomás Matus).
9:30Introduction and setting up of the Jupyter Notebook working environment (Marco Moretto).
11:00Metadata handling (Marco Moretto).
-Background. General standards: ISA tab tools, MIAMI protocol.
-Recurrent pitfalls in metadata submission. The NCBI-SRA case.
14:30Metadata handling (Continue, Marco Moretto and Tomas Matus).
-European metadata cases: upload from excel using ABI (Application Binary Interface).
-Relation between experimental designs and metadata annotation. Complex versus complicated designs.
 15:45 Coffee
 16:00 Best practices and useful tips for the analysis of gene expression data (Paolo Sonego).
-How to take decisions regarding: type of sequencing, number of replicates, depth, where to map reads (genome vs transcriptome, genome accessions) and annotations.


Day 2 (6th Feb, 9:00-18:00)

9:00Transcriptomics data analysis (Paolo Sonego)
-Practical session with a typical workflow on grapevine real data downloaded from GEO/SRA. DE Analysis, EDA and visualization of transcriptomics data using R/Bioconductor (Paolo Sonego).
11:00Transcriptomics data analysis (Continue)
12:00Tools available at Galaxy for transcriptomic analysis (Jerome Grimplet). SLIDES
14:30Resources: The TomExpress RNA-Seq platform, what can we learn from the tomato community regarding public RNA-Seq data handling, visualization and mining? (Mohamed Zouine) SLIDES
16:45Grape-specific platforms (first part):
-GREAT (video-remote lecture: Camille Rustenholz, Amandine Velt, INRAE COLMAR) SLIDES
-VitisNet/eFP-Browser Corvina (Jerome Grimplet).
21:00Gala Dinner

Day 3 (7th Feb, 9:00-16:00)

9:00Grape-specific platforms Marco Moretto)
-Tutorial and Outputs from the VESPUCCI platform.
11:00Access to Phyton/R packages in Jupyter to see how VESPUCCI is built.
12:00Metadata annotation in VESPUCCI as a case of study.
15:30Discussion and roundup of Training school (Mario Pezzotti).