Brazil Partnering Award: data acquisition and training for -omics in food, fuels and fisheries research

Lead Research Organisation: University of Edinburgh
Department Name: The Roslin Institute

Abstract

Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.

Publications

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Rocca-Serra P (2016) Data standards can boost metabolomics research, and if there is a will, there is a way. in Metabolomics : Official journal of the Metabolomic Society

 
Description Extension of EMBL-EBI's Train-the-trainer programme.
As of 2019, EMBL-EBI's Train-the-trainer activities have shaped ELIXIR's Train the trainer programme, led to new train-the-trainer activities for Latin American Researchers through the CABANA project, and contributed to discussions on a global scale, primarily through the ISCB and GOBLET.

Additionally we developed two new courses, one of which has now become a staple part of the EMBL-EBI training programme - Integrative Omics (renamed Introduction to Multiomics Data Integration in 2019). The Livestock Genomics course, together with its train-the-trainer activity, has been updated as part of CABANA's train-the-trainer offering, and has also generated interest from the US NSF-funded FAANG network. EMBL-EBI and the Roslin Institute continue to collaborate on delivery of this course.
Exploitation Route The training courses developed with support from this award form part of the suite of training courses and resources delivered by EMBL-EBI and thus continue to be used by others.

Using the training they gained at EMBL-EBI to further their own teaching and change some of their practices - this has been indicated through personal discussion with some of the trainers.

We also continued to evolve our links, including bringing one of the Brazilian trainers over to join a workshop focused on metagenomics training material collation and curation as part of an ELIXIR funded workshop.
Sectors Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software)

URL https://www.embl.de/training/index.php
 
Description Alan Archibald - Brazil Partnering Award 
Organisation University of Edinburgh
Department The Roslin Institute
Country United Kingdom 
Sector Academic/University 
PI Contribution Design and delivery of a series of bioinformatics training workshops in collaboration with the Roslin Institute and our partners in Brazil
Collaborator Contribution Co-design and co-delivery of a series of bioinformatics training workshops in collaboration with the Roslin Institute and our partners in Brazil
Impact To date, we have delivered 5 training workshops in Brazil: RNAseq and ChIPseq data analysis http://www.ebi.ac.uk/training/course/rna-seq-and-chip-seq-data-analysis-course-campinas-brazil-07-10-april-2014 Genomics for working with pathogens http://www.ebi.ac.uk/training/course/genomics-working-pathogens-brazil Metagenomics bioinformatics: http://www.ebi.ac.uk/training/course/metagenomics-bioinformatics-brazil-2014 Exploring variation in animal genomes: http://www.ebi.ac.uk/training/course/exploring-variation-animal-genomes-brazil-2014 Bioinformatics for industry: http://www.ebi.ac.uk/training/course/embl-ebi-workshop-bioinformatics-industry We have also delivered workshop in the UK, back to back with a 'train the trainer' workshop in which four 'apprentice' trainers from Brazil developed their training skills and put them immediately into practice at a workshop on animal genomics (see http://www.ebi.ac.uk/training/course/AnimalGenome2014)
Start Year 2013
 
Description Benilton Carvalho - Brazil Partnering Award 
Organisation State University of Campinas
Country Brazil 
Sector Academic/University 
PI Contribution We co-developed and co-delivered two workshops at UNICAMP, one on RNAseq and ChIPseq data analysis; the other on exploring variation in animal genomes
Collaborator Contribution Benilton co-developed and co-delivered the two above-mentioned workshops and hosted them. More importantly, he successfully applied to CNPq for matching funds for our BBSRC Brazil Partnering Award. Without this, it would not have been possible to deliver this project at all.
Impact Two successful workshops - see other outcomes.
Start Year 2013
 
Description Gabriel da Rocha Fernandes - Brazil Partnering Award 
Organisation Catholic University of Brasília
Country Brazil 
Sector Academic/University 
PI Contribution Co-development and delivery of a workshop
Collaborator Contribution Co-development and delivery of a workshop
Impact Successful delivery of a workshop - see 'other outcomes' section; Gabriel also attended our first train-the-trainer workshop and contributed to delivery of the subsequent animal genomics workshop.
Start Year 2013
 
Description Animal Genome Informatics 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This course provided an overview of key issues in animal informatics, bioinformatics tools, and procedures for the analysis and annotation of the genomes sequences of animals, with an emphasis on the analysis of NGS data. It was delivered using a mixture of lectures, computer-based practical sessions and interactive discussions. The course provided a platform for discussion of the key questions and challenges in the field. It was preceded by a one-week 'train-the-trainer' event in which we supported visitors from our Brazil Partnering Award to develop and deliver training on the course.
Year(s) Of Engagement Activity 2014
URL http://www.ebi.ac.uk/training/events/2014/animal-genome-informatics
 
Description Bioinformatics Workshop, Campinas, Brazil, 2015 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This course provided participants with an introduction to EMBL-EBI and its data tools and resources, covering the whole spectrum of biological / life sciences. Hands-on sessions focused on providing skills in sequence searching and alignment and making use of resources focused on functional genomics, protein identification and protein interactions.
Year(s) Of Engagement Activity 2015
URL http://wwwdev.ebi.ac.uk/training/events/2015/bioinformatics-workshop-campinas-brazil-2015
 
Description Bioinformatics Workshop, University of São Paulo, Brazil, 2015 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This course provided participants with an introduction to EMBL-EBI and its data tools and resources, covering the whole spectrum of biological / life sciences. Hands-on sessions focused on providing skills in sequence searching and alignment and making use of resources focused on functional genomics, protein identification and protein interactions.
Year(s) Of Engagement Activity 2015
URL http://www.ebi.ac.uk/training/events/2015/bioinformatics-workshop-university-sao-paulo-brazil-2015
 
Description EMBL-EBI workshop on Bioinformatics for Industry, Brazil 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact This one-day workshop, held in association with the ISCB Latin America Conference, provided an overview of the molecular information tools and resources that are available in the public domain through the EMBL-EBI. The day
began with some broad overviews of the kinds of information that can be accessed in a straightforward and cost-effective manner from via the internet. This will include descriptions of the types of data, how it is curated from the scientific literature or gathered from large-scale scientific projects, how the data quality is maintained, how it is shared globally with other resource providers and how it can be accessed and used effectively in scientific applications. We presented clear examples of how this information can be used in industry, specifically in health research and agriculture.
Year(s) Of Engagement Activity 2014
URL http://wwwdev.ebi.ac.uk/training/events/2014/embl-ebi-workshop-bioinformatics-industry-brazil
 
Description Exploring variation in animal genomes (Brazil, 2014) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This course provided an overview of key issues in animal informatics, bioinformatics tools, and procedures for the analysis and annotation of the genomes sequences of animals, with an emphasis on the analysis of NGS data. It was delivered using a mixture of lectures and computer-based practical sessions.
Year(s) Of Engagement Activity 2014
URL http://wwwdev.ebi.ac.uk/training/events/2014/exploring-variation-animal-genomes-brazil-2014
 
Description Genomics for working with pathogens (Brazil) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This course provided delegates with hands-on training in annotation genomes and accessing genomic information via the Ensembl Genomes browser, for those working in the area of pathogen genomes. An overview of high throughput sequencing workflows and analysis (mainly using RNA-seq) was presented, including introductions to the use of R and Bioconductor.
Year(s) Of Engagement Activity 2014
URL http://www.ebi.ac.uk/training/events/2014/genomics-working-pathogens-brazil
 
Description Introduction to integrative omics 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This course will provided participants with an overview of working with a number of 'omics' data types in an integrated manner, considering both the potential and the caveats of this approach. The course focused on the use of public data resources and open access tools for enabling integrated working, with an emphasis on data visualisation. It was preceded by a one-week 'train-the-trainer' event in which we supported visitors from our Brazil Partnering Award to develop and deliver training on the course.
Year(s) Of Engagement Activity 2015
URL http://www.ebi.ac.uk/training/events/2015/introduction-integrative-omics
 
Description Metagenomics Bioinformatics (Brazil 2014) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This course provided an introduction to the use of publicly available resources for the management, sharing, analysis and interpretation of metagenomics data, including both marker gene and whole gene shotgun (WGS) approaches. Delegates gained hands-on experience of a range of data resources and tools, interspersed with lectures.
Year(s) Of Engagement Activity 2014
URL http://www.ebi.ac.uk/training/events/2014/metagenomics-bioinformatics-brazil-2014
 
Description RNA-Seq and ChiP-Seq Data Analysis Course - Campinas, Brazil - 07-10 April 2014 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This course familiarised the participants with advanced data analysis methodologies and provided hands-on training on the latest analytical approaches. Lectures gave insight into how biological knowledge can be generated from RNA-seq and ChIP-seq experiments, and illustrated different ways of analysing such data. Practicals consisted of computer exercises that enabled the participants to apply statistical methods to the analysis of RNA-seq and ChIP-seq data under the guidance of the lecturers and teaching assistants.
Year(s) Of Engagement Activity 2014
URL http://www.ebi.ac.uk/training/events/2014/rna-seq-and-chip-seq-data-analysis-course-campinas-brazil-...