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

10 25 50
publication icon
Alejandro Sánchez-Flores (2021) Essentials in Genomics

publication icon
Amann RI (2019) Toward unrestricted use of public genomic data. in Science (New York, N.Y.)

publication icon
Angela Peña-González (2020) Essentials in Metagenomics (Part II)

publication icon
Angela Peña-González (2020) Essentials in metagenomics (Part I)

publication icon
Camarillo-Guerrero LF (2021) Massive expansion of human gut bacteriophage diversity. in Cell

publication icon
Castillo-Vilcahuaman C (2021) Data mining of DNA sequences submitted by Peruvian institutions to public genetic databases in Revista Peruana de Biología

publication icon
Darnet S (2019) Deep evolutionary origin of limb and fin regeneration. in Proceedings of the National Academy of Sciences of the United States of America

 
Description Advocacy in Brazil to include Whole Exome Sequencing in the clinical practice for the etiological investigation of intellectual disabilities, for unknown causes, in children
Geographic Reach National 
Policy Influence Type Membership of a guideline committee
Impact In 2015 our CABANA partner at The University of Campinas, Brazil (UNICAMP) founded a Brazilian Initiative on Precision Medicine (BIPMed: www.bipmed.org). Since then, they have been making efforts to characterize the genomic landscape of Brazilian individuals, focusing on (the improvement) health care delivery through the Brazilian Health System (called SUS). In 2019: They coordinated cost-effectiveness analyses that led the Federal Government to include Whole Exome Sequencing in the clinical practice within SUS for the etiological investigation of intellectual disabilities (of unknown causes) in children (Portaria 18, 27 de março de 2019 - Secretaria de Ciência, Tecnologia e Insumos Estratégicos). Our Ci-Investigator Benilton de Sa Carvalho was invited by the Ministry of Health in Brazil as a member of the advising committee that led discussions and a draft proposal of a National Initiative (funded by the Federal Government) to enable the implementation of Genomics in SUS (Brazilian Health System). He also assessed research projects that are set up to be pilot studies for such National Initiative. At UNICAMP, they are participating in discussions to create a biotechnology undergraduate course (4-5 years long).
URL http://www.bipmed.org/
 
Description Braziian Ministry of Industry, Ministry of Environment Brazil-EU Dialogue on in silico Genetic Heritage in Brazilian ABS Legislation. 10-12 Dec 2019.
Geographic Reach South America 
Policy Influence Type Participation in a national consultation
 
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 Meeting with the Embassy of Mexico to discuss Bioinformatics and the CABANA project. As part of our on-going engagement activities the project partners at CINVESTAV Mexico engaged with the Embassy to advise on sequencing protocols in the country and region. The partners also raise the issue of the cost of important reagents into Mexico which is having a detrimental effect on the cost of sequencing and research.
Geographic Reach South America 
Policy Influence Type Gave evidence to a government review
 
Description Peruvian national funding agencies Inovate and Concytec
Geographic Reach South America 
Policy Influence Type Gave evidence to a government review
 
Description ARGENT: ARgentinian GEnomics for Tuberculosis
Amount £946,669 (GBP)
Funding ID EP/T015446/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 09/2019 
End 03/2021
 
Description Joint program Comparative genomics of Clostridium difficile from Costa Rican hospitals
Amount € 150,000 (EUR)
Funding ID FI-0228B-17 
Organisation Government of Germany 
Department Federal Ministry of Education and Research
Sector Public
Country Germany
Start 11/2018 
End 10/2021
 
Description Meeting policy challenges for a responsible biodiversity based bio-economy in Colombia
Amount £126,874 (GBP)
Funding ID EP/T025026/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 06/2020 
End 05/2021
 
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 Datasets made publicly available by CABANA Partner 
Description Datasets per CABANA publication Lynggaard, C., Nielsen, M., Santos-Bay, L., Gastauer, M., Oliveira, G., Bohmann, K. Vertebrate diversity revealed by metabarcoding of bulk arthropod samples from tropical forests. 2019. Environmental DNA. 1:329-341. https://doi.org/10.1002/edn3.34. DNA metabarcode data and PROTAX model available http://www.doi.org/10.17894/ucph.263de3a8-9d79-46c9-9b5e-8adca7e6a716 Lemos, L.N., Medeiros, J.D., Dini-Andreote, F., Fernandes, G.R., Varani, A.M., Oliveira, G., Pylro, V.S. Genomic signatures and co-occurrence patterns of the ultra-small Saccharimonadia (CPR/Patescibacteria phylum) suggest a symbiotic lifestyle. 2019. Molecular Ecology. 28(18):4259-4271. https://doi.org/10.1111/mec.15208 Metagenomic data available in GenBank accession SRR5161795 and SRR5161805 16S bacterial sequence data available in GenBank accession SRR5161796, SRR5161790, SRR5161799 and SRR5161803 Assembled genomes Candidatus "Saccharibacter sossegus" and Candidatus "Chaer renensis" are available in IMG under IMG genome IDs 2767802000 and 2767802001, and in the DDBJ/EMBL/GenBank under accession numbers SCKX00000000 and SCKW00000000. Ferreira, N.R., Araújo., J.A., Silva, S.H.M., Oliveira, G. Monteiro, R.C., Alves, Y.F.M., Lopes, A.S. Filamentous Fungal Diversity from Natural Fermentation of the Amazonian Cocoa Beans and Microbial Enzymes Activities. 2019. Annals of Microbiology. 1-13. Fungi ITS sequence data available at GenbAnk accessions MF039221, MF039205 -18, MF039220-24. Holguín, A.V., Cárdenas, P., Rabelo, L., Prada-Peñaranda, C., Buitrago, C., Clavijo, V., Oliveira, G., Leekitcharoenphon, P., Møller, F., Vives, M. Host resistance, genomics and population dynamics in a Salmonella enteriditis and Phage system. 2019. Viruses. 11(2), 188. https://doi.org/10.3390/v11020188 DNA Data Bank of Japan DDBJ/ European Nucleotide Archive ENA/GenBank under the accession MUNA00000000 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
Impact The stated activity meets the CABANA project objective of making bioinformatics datasets available for the broader scientific community and promotes Latin American researchers as equal collaborative partners, 
 
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
 
Title Leishmania-Host Interaction with Reactome, a Database of Biological Pathways and Processes. 
Description Julieth Murillo Silva contributed her research to the Reactome database. The pathways curated on the Reactome summarize the major steps of parasite internalization by the macrophage, the defence mechanisms that are turned on and the mechanisms of evasion of the parasite to counteract them 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
Impact Julieth Murillo Silva was a secondee on the CABANA project her research contributed to the information shared on Reactome and is publicly available for future researchers. 
URL https://reactome.org/content/detail/R-HSA-9658195.
 
Title Modelling and annotation of proteases bound to peptides. 
Description These scripts provide tools for modelling natural substrates bound to proteases with structural information available. The first script is focused on the modelling, which includes protocols for the modification of non-natural amino acids by natural counterparts, and the modelling of missing regions within the 8-mer peptide region that binds the protease binding site. In addition, a second script allows the modelling of any peptide based on the templates obtained from the first script, and the run of dynamic analysis and calculation of structural observables averages reported in the paper, including the accessible surface area (ASA) and the interface interaction energy. 
Type Of Material Data analysis technique 
Year Produced 2020 
Provided To Others? Yes  
Impact Uploaded by Rodrigo Ochoa, one of the CABANA secondees. Open and shared knowledge of bioinformatics tools 
URL https://github.com/rochoa85/Modelling-Protease-Substrates
 
Title PARCE: peptide design protocol 
Description As defined in the listed publication PARCE: Protocol for Amino acid Refinement through Computational Evolution. Ochoa, R., Soler, M., Laio., A., Cossio, P. (2020). Computer Physics Communications, 260, 107716 
Type Of Material Data analysis technique 
Year Produced 2020 
Provided To Others? Yes  
Impact Added by Rodrigo Ochoa a member of the CABANA secondment program. An open source Protocol for Amino acid Refinement through Computational Evolution that implements an advanced and promising method for the design of peptides and proteins. The protocol performs a random mutation in the binder sequence, then samples the bound conformations using molecular dynamics simulations, and evaluates the protein-protein interactions from multiple scoring. Finally, it accepts or rejects the mutation by applying a consensus criterion based on binding scores. The procedure is iterated with the aim to explore efficiently novel sequences with potential better affinities toward their targets. We also provide a tutorial for running and reproducing the methodology. 
URL https://github.com/PARCE-project/PARCE-1
 
Title RNASeq data 
Description Integrated phenotypic analysis of cocoa (Theobroma cacao L.) response to water deficit. 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
Impact Mayra Osorio used complementary approaches to characterise cocoa's (T. cacao L.) response to water deficit. She studied this phenotypic response in 6 different genotypes with commercial importance for cocoa producers in Colombia, combining both a physiological and molecular characterization of this complex response to abiotic stress. The data was uploaded onto EMBL-EBi's ArrayExpress at Expression Atlas 
URL https://www.ebi.ac.uk/gxa/home
 
Title Sunflower ~11K SNP matrix - available at Ensembl Plants 
Description Sunflower ~11K SNP matrix - available at Ensembl Plants 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
Impact The data was uploaded by Dr Carla Filippi who visited EMBL-EBI from INTA Argentina as a seconded in 2019. Her research in the Sunflower Genomics Group seeks to apply and integrate the concepts and technologies of genomics to assist crop breeding, identification of strains, diversity description and susceptibility characteristics where shared at EMBL-EBI. 
URL http://ftp://ftp.ensemblgenomes.org/pub/plants/release-49/variation/vcf/helianthus_annuus/
 
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 Alfredo Herrera-Estrella - CABANA 
Organisation Centre for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV)
Country Mexico 
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 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 Cei Abreu Goodger 
Organisation National Laboratory of Genomics for Biodiversity
Country Mexico 
Sector Public 
PI Contribution Project Management Responsibilities and representation on behalf of the partner organisation. 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 annual review of project activities and monitoring tools: Theory of Change, Logical Framework, Activity Plan, Baseline Questionnaire, Anecdotal Evidence Questionnaire. Support with the following project activities: Advisory Board presentations, preparation of policy symposia fostering continuing research links between Langebio and EMBL-EBI. Volunteered as a research secondments host.
Impact Research Secondment Host, Continuing research collaboration on genome and properties of indigenous yeast. Support and planning for a policy symposium in Mexico. Assisting in training workshops.
Start Year 2018
 
Description Guilherme Oliviera- CABANA 
Organisation Instituto Tecnológico Vale
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 Project Lead for the Research Secondment Project 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 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 Maximo Rivarola-CABANA 
Organisation Government of Argentina
Department National Institute of Agricultural Technology
Country Argentina 
Sector Public 
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 Worshop for 2018 planned, Bioinformatics Workshops in Latin America for 2018 planned,
Start Year 2017
 
Description Rebeca Campos 
Organisation University of Costa Rica
Country Costa Rica 
Sector Academic/University 
PI Contribution Supervised Rebeca as a CABANA secondee and supported her to take over leadership of CABANA's eLearning activities. Supervised web developer at EMBL-EBI and guided him on the development of the CABANA eLearning portal. Prakash developed the portal; major developments included creating the portal in Drupal 8, based on one previously developed for the BBSRC-funded 'Bioinformatics for Discovery' project; amending the authoring tool used to make it more user-friendly for course authors; providing support for multiple languages (primarily English and Spanish); writing a quiz module.
Collaborator Contribution Generated training content for the new portal; led a project to recruit and supervise secondees to develop new courses; developed a process to test new courses and have them reviewed by subject-matter experts; managed a secondee; recruited a web developer.
Impact Yes - it involves bioinformaticians, web developers, training experts and students
Start Year 2018
 
Description Ricardo Fujita - CABANA 
Organisation University of San Martín de Porres
Country Peru 
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 DNA barcoding and genomics tools to unravel the Amazonian biodiversity 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The talk was held at the Department of Evolutionary Genomics at the University of Copenhagen and advocated the use of genetic barcoding for rapid and accurate taxonomy
Year(s) Of Engagement Activity 2019
 
Description Developing a strategy and recommendations to characterize, valorize and utilize Peruvian biodiversity with help of bio-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 One of the CABANA Co-Investigators participated in a workshop in Arequipa Peru workshop on "developing a strategy and recommendations to characterize, valorize and utilize Peruvian biodiversity with the help of bioinformatics. The Peruvian authorities have participated in multiple CABANA events where the project has showcased the cost-effectiveness of Bioinformatics for decision making.
Year(s) Of Engagement Activity 2019
 
Description 1st Brazilian Symposium on access of genetic resources and traditional knowledge. 
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 was the first symposium of its kind in Brazil which looked at the issues of conservation and indigenous knowledge in the Amazonian rainforest and how bioinformatics could be of use. It was held on 6 Nov 2019. UFRJ Law School, Rio de Janeiro
Year(s) Of Engagement Activity 2019
 
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 A policy symposium on "Data driven biology for conservation and utilization of biodiversity, food security and health" 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact On 15th October 2019 at Richard Sawyer Auditorium, International Potato Center (CIP), Avenida la Molina 1895, La Molina, Lima, Peru, the CABANA project delivered a onbe day symposium on the use of Bioinformatics for decision making. The symposium was intended for policymakers and comprised of four sections of presentations covering, food security, biodiversity and infectious diseases and a round table discussion on the next steps of academic institutions and policy. The Symposium had 16 speakers and was opened by the UK Ambassador to Peru and was closed by Henry Harman Guerra, Director de Políticas y Programas de CTeI del CONCYTEC.
The symposium was the first attempt by many partners to engage in policy and the model will be used again.
Year(s) Of Engagement Activity 2019
 
Description Biodiversity Genomics 2020 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Cath Brooksbank participated in an expert panel discussion for the launch of the African Earth Biogenome Project, speaking specifically on capacity building and training. Guilherme Oliviera spoke in the session on biogenomes in Latin America.
Year(s) Of Engagement Activity 2020
URL https://www.sanger.ac.uk/science/biodiversity-genomics-2020/
 
Description Bioinformatics Education Summit 2020 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact CABANA partners and secondees (Alejandro Reyes, Pati Carvajal, Maria Trinidad Bernardi) participated for the first time in a global annual initiative to bring together the bioinformatics training community and work together on standards and guidelines. As a result, CABANA is now the co-organiser of the 2021 global bioinformatics summit, taking place in May 2021. Several papers and reports are also in progress.
Year(s) Of Engagement Activity 2020
 
Description Engagement and presentation with the Cambridge Festival of Plants 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact This event took place at Cambridge University Botanic Garden (CUBG) the EMBL-EBI Ensembl Plants team participated Lead by Bruno Contreras with the support of the CABANA secondee Carla Fillipi This is the current list of species considered: http://tiny.cc/5ch99y
Part of the engagement was an explanation of sequencing and genetics and a nature trail through the Botanic garden looking at particular plant species and their properties.
Year(s) Of Engagement Activity 2019
 
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 ISCB-LatAm 2020 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Participated in the the virtual ISCB-Latin America SoIBio BioNetMX Symposium on Bioinformatics 2020: Cath Brooksbank gave a career talk at the ISCB Student Council LatAm meeting; Alejandro Reyes gave a keynote talk, and CABANA seconded Rodrigo Ochoa gave a talk. CABANA also supported registration fee waivers for truly needy participants.
Year(s) Of Engagement Activity 2020
URL https://www.iscb.org/iscb-latinamerica2020
 
Description Imperial College, Latin American Society Symposium on Sustainability 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact A two day symposium was held at Imperial College 20-21 May 2019. The aim of the symposium was to explore the challenges of sustainability in Latin America. The Symposium was organized by the Imperial College Latin American Society with whom CABANA has a good working relationship. The CABANA project had a 2 hour afternoon slot where 3 CCABANA secondees showcased their research in Microbialites, Sunflower production and Soil Microbiome for crop health. Our keynote Speaker marco Cristancho presented on the challenges of coffee production in Latin America and the role of Bioinformatics. The afternoon session ended with a question and answer session highlighting the challenges and opportunities for the use of Bioinformatics for decission making.
Year(s) Of Engagement Activity 2019
URL https://www.imperial.ac.uk/news/191276/students-lead-debate-latin-american-sustainable/
 
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 Informing the Embassy of Mexico of Project Activities in their Country. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact At a conference call meeting with representatives of the Embassy of Mexico, the CABANA partners CINVESTAV and one CABANA seconded briefed the Embassy staff representatives on the CABANA project objectives and the work carried out in Mexico. We discussed the Covid related work and the challenges of importing reagents for sequencing in Mexico. The Embassy staff agreed to share the information with the Ministry of the Interior to see if import costs for scientific research could be reduced.
Year(s) Of Engagement Activity 2020
 
Description International SARS-CoV-2 Symposium 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact 123 people attended the 2-day virtual symposium entitled, "CABANA International Symposium: The Genome of SARS-CoV-2, its evolution and epidemiology in Latin America" hosted online by CGIAR's International Potato Center (CIP). Speakers from across Latin America presented research and surveillance efforts across the regions, inviting questions and comments from the audience and making recommendations for clinicians, researchers and policymakers. The symposium was generated by the CABANA partners who were interested in coordinating surveillance and sequence efforts in Latin America. The partners benefitted from CABANA innovation award funding to sequence Covid in five Latin American Countries, coordinate and share their findings, and look for Covid variants.
Year(s) Of Engagement Activity 2020
URL https://cipotato.org/event/international-symposium-genome-sars-cov-2-evolution-epidemiology-latin-am...
 
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 Meeting between Brazilian Scientists and the EU group to discuss Digital Sequence Information and ABS 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact The meeting reviewed the status of the Brazilian legislation (the relevance here is that is basically the country that has firmly made a position to have DSI as part of biodiversity) and the EU and international views on it. Participants presented their respective information regarding the issue, from the points of view of academics, industry, the CGEN (Brazil) and EU. Technical aspects were discussed by Brazilians (including myself) and EU (Guy Cochran and a representative from DMZ, Germany). We discussed the role of global resources and how they could participate in this discussion and implementation

We studied and discussed various complicated scenarios.

This was the opportunity to expand networks for the future of genomics/bioinformatics in Brazil and with Europe.
Attendees were:
Representative of the Ministry of Industry Science Communications and Innovation
Representative of the Ministry of Environment including CGEN
Representative of the Ministry of External Relations (diplomat types that are involved in the biodiversity dialogue)
Representative of the National Laboratory of Biology (this can be of interest for metabolic profiling and drug screening)
Year(s) Of Engagement Activity 2019
 
Description Natal Brazil Bioinformatics Symposium 
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 The symposium highlighted Bioinformatics presentations from Brazil and notably the use of genomics to unravel the Amazonian biodiversity.
Year(s) Of Engagement Activity 2019
 
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 Presentation in 4th North and North-east Brazil Bioinformatics Symposium in Braganca, Para, Brazil. Title: EMBL-EBI Resources and tools 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Postgraduate students
Results and Impact Over 200 researchers across North and North-east Brazil attended the 4th symposium in Bioinformatics, hosted at the Federal university of Para in Braganca. The 25 minute talk described EMBL-EBI, its mission and the available resources online for people to access. Special note was given to EuropePMC for literature searches, and BioStudies for linking all data from a study in one place. The CABANA project was also described, as well as where to find all previous training workshop materials. Dissemination of a biodiversity workshop to take place in May 2020 took place. After the presentation a few questions from the audience were focused on the accessibility of biodiversity data and its linkages to other databases.
Year(s) Of Engagement Activity 2019
URL https://doity.com.br/ivsnnb
 
Description Presentation on Virome analysis 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Dr Segundo Fuentes of The International Potato Centre, Lima Peru shared his work on virome analysis for better potato production. Segundo has been a participant in train the trainer activities and the CABANA Lima symposium in bioinformatics for discovery (2019)
Year(s) Of Engagement Activity 2020
URL https://www.youtube.com/watch?v=iRNIZJqzCyA
 
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
 
Description Support for the 2019 Latin American SoiBio confererance 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact The CABANA project supported travel fellowships from CABANA Countries to the X International Conference on Bioinformatics - SoIBio+10 that will take place in Montevideo (Uruguay) from the 28th October to the 1st November this year 2019 (https://sites.google.com/view/soibio19/home). The conference meets the CABANA objective of supporting sustainable Bioinformatics networks in Latin America.
Year(s) Of Engagement Activity 2019
URL https://www.cabana.online/news/travel-fellowship-soibio-2019
 
Description Symposium Presentation 
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 was the 4th North Northeast Brazil Symposium on Bioinformatics. 5-6 Dec 2019. The talk related to the CABANA objective of training of personnel in bioinformatics in academia and private companies.
Year(s) Of Engagement Activity 2019
 
Description Talk Using genomics for biodiversity conservation in the Amazon. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact EMBRAPA Genetic Resources 12 Dec 2019 Using genomics for biodiversity conservation in the Amazon. The talk promoted the use of Bar Coding as a more rapid and alternative method of conducting taxonomy in conservation of endagered ecosystems.
Year(s) Of Engagement Activity 2019
 
Description Travel Fellowships to the Latin America SoiBio Conference 2019 
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 The CABANA project offered 10 travel fellowships to CABANA partner countries to participate in the bi-annual X International Conference on Bioinformatics - SoIBio+10 that took place in Montevideo (Uruguay) from the 28th October to the 1st November this year 2019 (https://sites.google.com/view/soibio19/home). The activity is in line with the CABANA projects aim of supporting sustainable bioinformatics networks in Latin America.
Year(s) Of Engagement Activity 2019
URL https://www.cabana.online/news/travel-fellowship-soibio-2019
 
Description X-meeting 2021 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact Participated in the X-meeting Education Panel: challenges and opportunities in training a new generation of bioinformaticians
Year(s) Of Engagement Activity 2020
URL https://x-meeting.com/events/xmxp2020
 
Description Zoom and YouTube presentation on virus discovery 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact One of the CABANA CoIs presented his work on Virus discovery and Virome Analysis to an international audience in Latin America. This kind of presentation helps to create key informants among the CABANA partners who contribute to advising policymakers. Dr Jan Kreuze continues to be involved with Covid policy and sequencing in Peru.
Year(s) Of Engagement Activity 2020
URL https://www.youtube.com/watch?v=iQj8ZCwJ4nw