Mayra Osorio has joined the EMBL-EBI Gene Expression Team for her CABANA secondment. Hosted by Dr Irene Papatheodorou, Mayra’s project is to characterise and compare the phenotypic response to water deficit stress of two cocoa genotypes with contrasting physiological behaviour to this kind of stress. Using a transcriptomic approach (RNAseq), she expects to develop analysis pipelines for differential expression analysis of transcriptomic data, coexpression and regulatory network modelling, and comparative transcriptomics. This knowledge should benefit breeding programs and contribute to enhance yield, sustainability and welfare around cocoa cropping.
Mayra is on secondment from the Pontificia Universidad Javeriana, Colombia, where she is a PhD student in the Plant and Crop Biology lab of the Department of Biology.

The CABANA workshop Genomic Analysis of Crop Biodiversity using R, took place 25-28 June 2019, at LANGEBIO, CINVESTAV in Mexico. Eighteen delegates from five countries were trained in molecular markers, R programming, hierarchical clustering, various diversity metrics from DNA markers, core subset selection, association phenotype-genome and design of biodiversity studies. As requested by the trainees, concepts and analysis on GWAS (Genome-Wide Association Studies) were also covered. Data for the hands-on activities came from maize microsatellites, chilli pepper transcriptome and a large data set of wheat SNPs. CABANA provided fellowships to nine delegates from Latin America. Our thanks go to instructors Octavio Martínez and and Jose Manuel Villalobos-Escobedo (Langebio, Cinvestav, Mexico) and M. Humberto Reyes-Valdés (Universidad Autónoma Agraria Antonio Narro, Mexico).

Learn more about the CABANA project in our video! Meet the partners and hear about the crucial role bioinformatics plays in supporting research across Latin America in the three challenge areas of communicable disease, sustainable food production & protection of biodiversity https://youtu.be/tUJ-Q4ODGbs. Video by Jeff Dowling, EMBL-EBI @jeffdowling

CABANA was pleased to join the 3rd Latin American symposium on Sustainable development at Imperial College, London in May. Cath Brooksbank, Marco Cristancho, Ian Willis and Piv Gopalasingam had the opportunity to share the project’s goals and progress. CABANA secondees Valeria Faggioli, Federico Vignale and Carla Valeria Filippi presented their research on bioinformatics in agriculture sustainability, conservation and biodiversity, and sunflower breeding. ‘The experience of attending and presenting results in the symposium was impressive for many reasons’ said Valeria Faggioli. ‘First of all, I could meet colleagues from Latin America who are working in the UK on many topics regarding key issues about the sustainability of food production in Latin America. Moreover, as a member of the National Institute of Agriculture Technology in Argentina, the meeting represented the opportunity of generating international networks for future collaborations regarding the use of bioinformatics in different situations.’

Hannele Lindqvist-Kreuze, a Molecular Breeder at the International Potato Center (CIP) in Lima, Peru recently undertook a CABANA secondment with Jose De Vega and his team at Earlham Institute in the UK. Hannele proposed the secondment project with the aim to increase the capacity of Latin American breeder of autopolyploid crops in using modern genomics tools in their breeding programs. The project started with existing real-life data generated in the CIP breeding program of tetraploid potato that was used to develop a bioinformatics workflow starting from marker identification and ending in the identification of genomic regions responsible for the trait of interest. Eventually, the workflow will be validated using other data. The workflow and the tools have already been used as an example during the CABANA workshop “Exploring Biodiversity through Bioinformatics” that took place at CIP April 9-12, 2019, where Hannele was one of the Trainers. Hannele reports that she is now much more fluent in using linux and R. Additionally, the newly created network between CIP and Earlham has prompted the exploration of a shared research project.
Read more about Hannele and other CABANA secondees: https://www.cabana.online/secondees

The deadline to receive applications for CABANA secondments is 15th February. Scientists from Latin America will spend 6 months to pursue a bioinformatics research topic in the challenge areas of the CABANA project. Secondments can be with CABANA partner research institutions in Latin America or in the UK. We encourage you to contact a potential host in advance of an application to discuss and shape your project proposal. See the research interests of the hosts here: http://www.cabana.online/research-secondment.

The second call for secondments is open! CABANA’s research secondments are aimed at catalysing lasting collaborations between researchers in Latin America and bioinformatics groups in the UK. Secondments can be with CABANA partner research institutions in Latin America or at EMBL-European Bioinformatics Institute in the UK. Scientists from Latin America will spend 6 months to pursue a bioinformatics research topic in the challenge areas of the CABANA project.
The deadline for applications is 15th February 22:00 GMT.
Full details can be obtained here: http://www.cabana.online/research-secondment

The GCRF-funded CABANA project is delighted to offer travel fellowships of up to US $1000 for researchers to attend the ISCB-LA-SoIBio-EMBNet Conference. The fellowships are open to scientists at any stage of their career. Early-stage researchers and researchers from minority groups are especially encouraged to apply. Read more

In this free interactive webinar, Cath Brooksbank will explain how CABANA will support bioinformatics research and training in Latin America through a combination of research secondments, train-the-trainer workshops, short courses and eLearning. Come and find out how your organisation can get involved.

Watch the webinar on youtube

CABANA's kick-off meeting was hosted by Benilton Carvalho in Campinas, Brazil. All our partner institututions participated in two days of discussions, presentations and interactive activities. The goals of the meeting were to... (1) provide an opportunity for the members of the CABANA consortium to get to know each other – vital to the success of the project; (2) learn about each other’s scientific interests, challenges and successes related to bioinformatics capacity building; (3) agree on how we will capture data on our current capacity so that we can monitor our achievements throughout the project; and (4) define a selection process for our activities, to ensure that we have broad scientific, demographic and geographical reach. Some of the outcomes of our discussions will be summarised in our upcoming webinar. Thank you to all our participants for a great start to the project, and especially to Benilton for being a wonderful host.