METHADA 2020 - Training school on Transcriptomic Metadata Handling and Data Analysis
29th November 2019
METHADA 2020 - Transcriptomic Metadata Handling and Data Analysis
5-7 February 2020
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.
|Computational Biology Unit, Fondazione Edmund Mach - Istituto Agrario San Michele All'Adige||Computational Biology Unit, Fondazione Edmund Mach - Istituto Agrario San Michele All'Adige|
José Tomás Matus
|INP-ENSAT Toulouse||I2SysBio, Valencia|
SELECTION CRITERIA FOR TRAVEL GRANTS
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 https://www.cost.eu/wp-content/uploads/2019/07/Vademecum_June2019.pdf).
Evaluation 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)
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)
-Oh my loft (approx. 100 euros/ night)
+34 683 67 20 97
-Colegio San Juan de Ribera (only two rooms available now)
Student Housing, 10min walk to the Institute. 30€/night including dinner.
Close to Turia station in Valencia
-Expo Hotel Valencia (approx 100 euros/ night)
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)
|9:00||Welcome from I2SysBio Director/Vice-director and COST Action MC Chair (Mario Pezzotti). Presentation of the Training School (Jerome Grimplet, Tomás Matus).|
|9:30||Introduction and setting up of the Jupyter Notebook working environment (Marco Moretto).|
|11:00||Metadata handling (Marco Moretto).
-Background. General standards: ISA tab tools, MIAMI protocol.
-Recurrent pitfalls in metadata submission. The NCBI-SRA case.
|14:30||Metadata 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.
|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)
|9:00||Transcriptomics 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).
|11:00||Transcriptomics data analysis (Continue)|
|12:00||Tools available at Galaxy for transcriptomic analysis (Jerome Grimplet).|
|14:30||Resources: The TomExpress RNA-Seq platform, what can we learn from the tomato community regarding public RNA-Seq data handling, visualization and mining? (Mohamed Zouine)|
|16:45||Grape-specific platforms (first part):
-GREAT (video-remote lecture: Camille Rustenholz, Amandine Velt, INRAE COLMAR).
-VitisNet/eFP-Browser Corvina (Jerome Grimplet).
Day 3 (7th Feb, 9:00-16:00)
|9:00||Grape-specific platforms Marco Moretto)
-Tutorial and Outputs from the VESPUCCI platform.
|11:00||Access to Phyton/R packages in Jupyter to see how VESPUCCI is built.|
|12:00||Metadata annotation in VESPUCCI as a case of study.|
|15:30||Discussion and roundup of Training school (Mario Pezzotti).|