Capacity building for bioinformatics in Latin America

Lead Research Organisation: EMBL - European Bioinformatics Institute
Department Name: Outreach and Training

Abstract

Data-driven biology promises to have a major impact on health, agriculture and environmental management. However, in Latin America uptake of data-driven biology has lagged behind despite a clear need. For example, Analysis of human genome data submitted to public databases shows that populations of African and Latin American descent, Hispanics, and indigenous people are barely represented in genomics studies[1]. Given the need to have genome data from those populations for the development of precision medicine in clinical practice, it is necessary to boost the collection of genomics data in Latin American populations. A similar scenario is found for biodiversity in the region, where there is a gap in the knowledge of the majority of the living organisms, which represents over 60% of the total number of terrestrial species on the biosphere[2]. Only by understanding the impact on biodiversity of human-driven activities such as intensive farming and urbanisation can we find a balance between economic development and the preservation and sustainable use of natural resources.
We propose a capacity-building programme, led by EMBL-EBI in close collaboration with new and existing collaborators in Latin American countries, including Argentina, Brazil, Colombia, Costa Rica, Mexico, Peru and Venezuela - all countries on the ODA development list. Through a combination of secondments, training workshops, eLearning resources and 'train-the-trainer' activities, we will sustainably build expertise in the fundamental skills required to generate, store, visualise, analyse and interpret biomolecular data. We will focus on three use cases: (1) Food security; (2) Data-driven monitoring and management of communicable disease; and (3) monitoring biodiversity.
Biological data can be used to track pandemics in humans and livestock (the recent Zikavirus outbreak, for example), understand and mitigate the causes of crop failure, and monitor biodiversity. Our top priority area in the ODA development strategy is therefore strengthening resilience and response to crises.
Latin America is a major producer and exporter of meat, fruit, vegetables and coffee. Biofuel production is also growing. These industries are crucial for the development of the region, and yet put huge pressure on Latin America's unparalleled biodiversity, which is not only of enormous importance in its own right but also contributes to economic prosperity through ecotourism. Data-driven biology can facilitate the production of crops and livestock that are more resilient to environmental challenges and enables sophisticated monitoring of an area's biodiversity. Our second priority area in the ODA development strategy is therefore promoting global prosperity.
By incorporating training on how to manage bioinformatics research infrastructure, and by involving local funders and policymakers in these workshops, we hope to contribute to the professionalisation of bioinformatics services throughout the region. This will enhance Latin America's ability to provide a significant contribution to international research projects such as the Global Alliance for Genomics and Health.
Expected outcomes of the project include:
Increased use of bioinformatics tools and resources to solve research problems of direct relevance to the ODA development strategy
Increased use of bioinformatics to solve applied research problems
A sustainable network of skilled bioinformaticians who are also motivated and talented trainers of other researchers
Enduring collaborations and mentorships that encourage women and other underrepresented groups in the research community to develop successful careers in bioinformatics and related subjects.
[1] Popejoy, A.B., & Fullerton, S.M. (2016) Genomics is failing on diversity. Nature, 538(7624), 161
[2] UNEP-WCMC (2016) The State of Biodiversity in Latin America and the Caribbean: A mid-term review of progress towards the Aichi Biodiversity Targets. UNEP-WCMC, UK

Planned Impact

Building links and contacts: We have developed innovative instruments to reach a large number of scientists in the region. Our proposal includes leading scientists in 6 Latin American countries on the ODA list and a mechanism for reaching out to more. Each partner has committed to nucleating a bioinformatics community of practice in their country, hosting workshops for scientists throughout the region, identifying candidates for secondments, and locating potential hosts for secondments in Latin America. This will accelerate implementation of state of the art -omics and bioinformatics to solve problems of direct relevance to economic growth and crisis mitigation.
We will improve accessibility and scalability of our programme with elearning courses in a 'responsive' format appropriate for mobile devices. We will use this platform to reach out to those who might not have the opportunity to participate in face-to-face courses.
Co-production of knowledge: Our training model emphasises collaboration with scientists in the UK, throughout Latin America, and in major international initiatives. This will build a sustainable community of bioinformatics experts in the region, well placed to contribute significantly to science on a global scale. It is essential that our project respects cultural diversity and the knowledge of Latin America's indigenous peoples; we will seek input from our partners on how best to share this knowledge (e.g. medicinal use of native species) whilst allowing intellectual property to remain with its originators. Key to the entire programme will be our inclusivity policy: travel funds for 30% of the places on our workshops will be used to incentivise participation by women and minority ethnic groups. The inclusion of women and minority groups as trainers, trainees, visitors and supervisors will similarly be incentivised, and a mentorship programme will underpin this.
Impact on economic development and wellbeing in Latin America: Our project will close the gap between developed and developing countries in genomics and bioinformatics, stimulating critical and creative thinking for development based on local needs. Participants in the programme will be trained to develop innovative solutions to major local problems such as those concerned with tropical and subtropical human diseases, monitoring the under-studied magnificent biodiversity in the region, and investigating vulnerability of crops and environments to climate change.
Legacy of the project: Our project focuses primarily on capacity building for data-driven biological research through a network of experts throughout the region, with lasting international collaborations anchored in the UK and outcomes that will be made use of by the research community at large (see objectives section). However, we cannot ignore the potential of our consortium to inspire the next generation of Latin American life scientists. Providing support and training materials suitable for tertiary education is the first step in this direction: our train the trainer courses will provide guidance and content suitable for tertiary educators, and we have established links with universities in the region. Some of our partners have also delivered successful outreach projects to schools (The Ondas programme in Colombia, for example). We will organise a summit meeting towards the end of the project to bring together scientists, teachers and other stakeholders to share expertise on how to inspire the next generation. Our programme fits the requirement of strong global and regional collaborations that are aligned with the Education 2030 goals. We will strengthen mobility of staff and learners, and the flow of students moving abroad to enhance academic credentials, students' competencies, and global competitiveness.

Publications

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Description CoI Benliton Carvalho: Membership of Grupo de Trabalho em Gestão de Dados de Pesquisa and organisation of a workshop on challenges and best practices in scientific data management (http://www.fapesp.br/eventos/opendata)
Geographic Reach National 
Policy Influence Type Influenced training of practitioners or researchers
URL http://www.fapesp.br/eventos/opendata
 
Description Crick Africa Network Independent Advisory Committee
Geographic Reach Africa 
Policy Influence Type Membership of a guideline committee
URL https://www.crick.ac.uk/partnerships/crick-african-network
 
Description Mexican Ministry of Agriculture and the National Council of Science and Technology (SAGARPA-CONACYT)
Amount $1,200,000 (USD)
Funding ID Project 292546. 
Organisation National Council on Science and Technology (CONACYT) 
Sector Public
Country Mexico
Start 09/2018 
End 08/2020
 
Title Anecdotal Evidence Questionnaire 
Description The anecdotal evidence questionnaire is a tool to track the perception of progress during the lifetime of the project. It is asking the Project Co-Investigators to reflect year on year whether the situation regarding access to funding and a critical mass of bioinformatics/computational biology services and researchers in the local context is improving or diminishing. The perceptions captured in this qualitative survey can be triangulated with more quantitative data from the baseline questionnaire and subsequent quantitative questionnaires to get a more well-rounded picture of bioinformatics research and its application to CABANA's challenge areas throughout and beyond the lifetime of the project. 
Type Of Material Improvements to research infrastructure 
Year Produced 2018 
Provided To Others? No  
Impact It is too early to say. The anecdotal evidence questionnaire was circulated to our Latin American partners in April 2018, with the goal of capturing impressions from the previous calendar year. We will need results from more than one iteration of the survey to track trends. 
 
Title CABANA Baseline Questionnaire 
Description The CABANA project focuses on capacity strengthening for bioinformatics and computational biology in Latin America. The CABANA baseline questionnaire conducted in April 2018 provides a snapshot of the state of affairs in 2017 in bioinformatics and computational biology in nine Latin American academic research institutions in Mexico, Costa Rica, Colombia, Peru, Argentina and Brazil. It is one of several tools developed to track progress towards CABANA's two higher-level objectives: (1) Partner institutions (have developed a critical mass of bioinformaticians and scientists able to) conduct collaborative Pan-Latin American bioinformatics research at the highest international level in infectious diseases, food security and biodiversity. (2) "A pan-Latin American and sustainable capacity-building programme for bioinformatics research operates with at least 6 partner institutions. The baseline questionnaire confirms the need for additional resources for bioinformatics and computational biology in Latin America and the need for additional capacity building. It identifies a shortage of local trainers and suggests a need for increased cross-border and international collaboration. CABANA's partner countries fall broadly into a relatively well-resourced group (Argentina, Brazil, Colombia, Mexico) and a more poorly resourced group (Peru, Costa Rica). However, the results of the baseline questionnaire suggest that all nine institutions have a unique constellation of strengths, weaknesses, stakeholders, and capacity-strengthening needs. CABANA must be receptive and responsive to these differing needs and remain a truly collaborative partnership for the best and most sustained impact. 
Type Of Material Improvements to research infrastructure 
Year Produced 2018 
Provided To Others? Yes  
Impact The project partners have developed an understanding of the current state of affairs in its 9 partner institutions. The partners can track progress and set priorities and project objectives accordingly. The project will be able to compare its impact in December 2022 to the baseline. Regular follow-up questionnaires will enable the project team to track progress. 
 
Title EMBL-EBI user tracking for Latin America 
Description The CABANA project has tracked the number of users of the EMBL-EBI website from Latin America for 2017. We will be able to compare user statistics year on year for the duration of the CABANA project (and beyond) to track whether there are any significant increases in users of EMBL-EBI services from the region. Whilst an increase in users may not necessarily be directly attributed to CABANA, 'bursts' of activity around workshops might be indicative of a short-term impact, and might influence longer-term usage of open access bioinformatics data in the region. 
Type Of Material Improvements to research infrastructure 
Year Produced 2018 
Provided To Others? No  
Impact Too early to say. We will be able to track changes when we have received the 2018 data and beyond. 
URL http://www.ebi.ac.uk
 
Title GenBank 
Description Coffee rust fungus sequences, transcriptone shotgun assembly 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact The data is Latin American data collected and curated in Colombia thereby promoting Colombia's science and research capacity for a world crop and shared internationally 
URL http://www.ncbi.nlm.nih.gov/nuccore/1377213572?log$=activity
 
Title Genbank 
Description Coffee Rust Fungus Sequences 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact The Biological information is of Colombian origin, was extracted and analysed and shared with the international research Community thereby showcasing Colombian research to global challenges, for an international crop. 
URL http://www.ncbi.nlm.nih.gov/nuccore/1379039250?log$=activity
 
Description Adrian Turjanski-CABANA 
Organisation University of Buenos Aires
Country Argentina 
Sector Academic/University 
PI Contribution Project Management Responsibilities for the start-up of the project, commencement of implementation activities, notably, Train the Trainer workshops, Research Secondments, Training Workshops in Latin America and preparation of E-learning Courses.
Collaborator Contribution Contribution to the project start up with the following documents: Theory of Change, Logical Framework, Activity Plan, Baseline Questionnaire, Anecdotal Evidence Questionnaire. Support with the following project activities: Research Secondments, hosting Training Workshops in Latin America in 2018/2019
Impact Research Secondments for 2018/2019 planned, Train the Trainer Workshop for 2018 planned, Bioinformatics Workshops in Latin America for 2018 planned,
Start Year 2017
 
Description Alejandro Reyes - CABANA 
Organisation University of the Andes
Country Colombia 
Sector Academic/University 
PI Contribution Project management responsibilities for the start-up of the project, commencement of implementation activities, notably, Train the Trainer workshops, Research Secondments, Training Workshops in Latin America and preparation of E-learning Ccurses.
Collaborator Contribution Project lead for the E-Learning Activities. Contribution to the project start up with the following documents: Theory of Change, Logical Framework, Activity Plan, Baseline Questionnaire, Anecdotal Evidence Questionnaire. Support with the following project activities: E-Learning bioinformnatics course implements at the University of the Andes in conjunction with EMBL-EBI. Research secondments, hosting training workshops in Latin America in 2018/2019
Impact Research Secondments for 2018/2019 planned, Train the Trainer Workshop for 2018 planned, Bioinformatics Workshops in Latin America for 2018 planned, E-Learning Bioinformatics Course implemented at University of the Andes.
Start Year 2017
 
Description Andres Gatica 
Organisation University of Costa Rica
Country Costa Rica 
Sector Academic/University 
PI Contribution Project Management Responsibilities for the start-up of the project, commencement of implementation activities, notably, Train the Trainer workshops, Research Secondments, Training Workshops in Latin America and preparation of E-learning Courses.
Collaborator Contribution Project lead Train-the-Trainer project activity. Contribution to the project start up with the following documents: Theory of Change, Logical Framework, Activity Plan, Baseline Questionnaire, Anecdotal Evidence Questionnaire. Support with the following project activities: Research Secondments, hosting Training Workshops in Latin America in 2018/2019
Impact Research Secondments for 2018/2019 planned, Train the Trainer Workshop for 2018 planned, Bioinformatics Workshops in Latin America for 2018 planned, E-Learning for 2018 planned.
Start Year 2017
 
Description Benilton Carvalho - CABANA 
Organisation State University of Campinas
Country Brazil 
Sector Academic/University 
PI Contribution Project Management Responsibilities for the start-up of the project, commencement of implementation activities, notably, Train the Trainer workshops, Research Secondments, Training Workshops in Latin America and preparation of E-learning Courses.
Collaborator Contribution Contribution to the project start up with the following documents: Theory of Change, Logical Framework, Activity Plan, Baseline Questionnaire, Anecdotal Evidence Questionnaire. Organisation of the 2017 Co-Principle Investigators' meeting. Support with the following project activities: Research Secondments, hosting Training Workshops in Latin America in 2018/2019
Impact Research Secondments for 2018/2019 planned, Train the Trainer Workshop for 2018 planned, Bioinformatics Workshops in Latin America for 2018 planned, First Annual meeting of the Co-Investigators completed.
Start Year 2017
 
Description Jan Kreuze - CABANA 
Organisation International Potato Center
Country Peru 
Sector Charity/Non Profit 
PI Contribution Project Management Responsibilities for the start-up of the project, commencement of implementation activities, notably, Train the Trainer workshops, Research Secondments, Training Workshops in Latin America and preparation of E-learning Courses.
Collaborator Contribution Leadership for Research Secondment activities. Contribution to the project start up with the following documents: Theory of Change, Logical Framework, Activity Plan, Baseline Questionnaire, Anecdotal Evidence Questionnaire. Support with the following project activities: Research Secondments, Hosting training workshops in Latin America in 2018/2019.
Impact Research Secondments for 2018/2019 planned, Train the Trainer Workshop for 2018 planned, Bioinformatics Workshops in Latin America for 2018 planned.
Start Year 2017
 
Description Marco Cristancho - CABANA 
Organisation University of the Andes
Country Colombia 
Sector Academic/University 
PI Contribution Project Management Responsibilities for the start-up of the project, commencement of implementation activities, notably, Train the Trainer workshops, Research Secondments, Training workshops in Latin America and preparation of E-learning Courses.
Collaborator Contribution Deputy Principal Investigator, project lead for Policy. Contribution to the project start up with the following documents: Theory of Change, Logical Framework, Activity Plan, Baseline Questionnaire, Anecdotal Evidence Questionnaire. Support with the following project activities: Research Secondments, hosting Training Workshops in Latin America in 2018/2019
Impact Research Secondments for 2018/2019 planned, Train the Trainer Workshop for 2018 planned, Bioinformatics Workshops in Latin America for 2018 planned,
Start Year 2017
 
Description Ricardo Fujita - CABANA 
Organisation University of San Martín de Porres
PI Contribution Project Management Responsibilities for the start-up of the project, commencement of implementation activities, notably, Train the Trainer workshops, Research Secondments, Training Workshops in Latin America and preparation of E-learning Courses.
Collaborator Contribution Contribution to the project start up with the following documents: Theory of Change, Logical Framework, Activity Plan, Baseline Questionnaire, Anecdotal Evidence Questionnaire. Support with the following project activities: Research Secondments, hosting Training Workshops in Latin America in 2018/2019
Impact Research Secondments for 2018/2019 planned, Train the Trainer Workshop for 2018 planned, Bioinformatics Workshops in Latin America for 2018 planned.
Start Year 2017
 
Description 20 Travel Fellowships for ISCB-LA SOIBIO EMBnet conference, 5-9 November 2018 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Postgraduate students
Results and Impact Twenty travel fellowships for postgraduates to attend the ISCB-LA SOIBIO EMBnet conference were offered by the CABANA project. CABANA is committed to supporting scientists from underrepresented groups and the fellowships are to identify and support those who would not otherwise have access to training and networking opportunities with the international research community owing to lack of funding. Preference is being given to minority ethnic groups and other underrepresented groups.
Year(s) Of Engagement Activity 2018
URL https://www.iscb.org/iscb-latinamerica2018-travel-fellowships
 
Description ISCB-LA SOIBIO EMBnet 2018 
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 ISCB-LA SOIBIO EMBnet 2018 attracts top regional and international scientists in the life sciences and offers a scientific programme on scientific discovery involving bioinformatics and computational biology. This is a key Latin American Bioinformatics conference where Dr Cath Brooksbank was a guest speaker, and also provided Train the Trainer with our Co-Investigators, Drs Guilherme Oliveira, Alejandro Reyes and Selene Fernandez. Also Dr Marco Cristancho delivered a two day workshop on Open Data Tools
Year(s) Of Engagement Activity 2018
URL http://www.iscb.org/iscb-latinamerica2018-preconference-workshops
 
Description Industry Workshop on "From Genomics and Bioinformatics to Personalized Medicine"Organized by the National Direction of Institutional Cooperation and Integration of the Ministry of Science, Technology and Productive Innovation (DNCII-MINCyT), the European Bioinformatics Institute of the European Molecular Biology Laboratory (EMBL-EBI) and the School of Exact and Natural Sciences (FCEyN) of the University of Buenos Aires (UBA) 
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 workshop aimed to share the latest advances in personalised medicine to industry partners and share market opportunities and joint collaborations in Latin America
Year(s) Of Engagement Activity 2018
 
Description Key Note Speaker, Dr. César Rodríguez Sánchez Facultad de Microbiología/CIET 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact This Keynote speech was to showcase the research conducted in Cost Rica with Clostridium difficile
Year(s) Of Engagement Activity 2018
 
Description Policy discussion to maintain National Parks and track biodiversity 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Meeting with IBAMA/ICMBio Brazil, which are federal Agencies that oversee environmental licensing, access to genetic resources, and maintain National Parks. Held at the Vale Institute, Belem, Brazil, the objective of the discussion was how to include genomics an computational tools as ways of accessing and monitoring biodiversity.
Year(s) Of Engagement Activity 2018
 
Description Special session on education at ISCB-LA-SoIBio-EMBNet conference 2018 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact CABANA partners Alejandro Reyes and Selene Fernandez were invited to participate in a special session on education at the ISCB-LA-SoIBio-EMBNet conference 2018. The session reached around 200 conference participants.
Year(s) Of Engagement Activity 2018
URL https://www.iscb.org/iscb-latinamerica2018