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.
Organisations
- University of Edinburgh (Lead Research Organisation)
- State University of Campinas (Collaboration)
- Oswaldo Cruz Foundation (Fiocruz) (Collaboration)
- Catholic University of Brasília (Collaboration)
- UNIVERSITY OF EDINBURGH (Collaboration)
- Universidade Federal de Minas Gerais (Project Partner)
- Universidade Católica de Brasília (Project Partner)
- University (State) of Campinas (Unicamp) (Project Partner)
Publications
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 | One of the partners on this award, Guilherme Oliveira, has since moved from academia to the Vale Institute of Technology (ITV) where he is currently interim director. ITV is owned by a large multinational mining company. His work on metabarcoding of species in the Carajas region is having an impact on the way that mining sites are selected, and is informing bioremediation strategies. It has been reported in mining journals. Another partner, Benilton Carvalho, is involved in a major project at the University of Campinas which, through exome sequencing of patients with early-onset epilepsy is making accurate predictions about individuals' responsiveness to specific anti-epileptic drugs. Both partners continue to collaborate with us through the GCRF-funded CABANA project and, as CABANA is a pan-Latin-American collaboration, their experience is being disseminated to other partners. |
| First Year Of Impact | 2019 |
| Sector | Agriculture, Food and Drink,Education,Environment,Healthcare |
| Impact Types | Societal |
| Description | Capacity building for bioinformatics in Latin America |
| Amount | £3,862,824 (GBP) |
| Funding ID | BB/P027849/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 10/2017 |
| End | 12/2021 |
| 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 | Guilherme Oliviera - Brazil Partnering Award |
| Organisation | Oswaldo Cruz Foundation (Fiocruz) |
| Department | Centro de Pesquisas René Rachou |
| Country | Brazil |
| Sector | Public |
| PI Contribution | Co-development and co-delivery of two workshops in Brazil: Genomics for working with pathogens and Bioinformatics for industry. |
| Collaborator Contribution | Co-development and co-delivery of two workshops in Brazil: Genomics for working with pathogens and Bioinformatics for industry. |
| Impact | Two workshops successfully delivered - see 'other outcomes' section |
| 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-... |