Between February 24th - March 4th 2020 the University of Costa Rica hosted the CABANA workshop, “NGS analysis applied to virome sequencing in agricultural systems”.
This workshop was unique in that the first week was focused on nucleic acids extraction (small and large RNAs) and library preparation to sequence on the NextSeq Illumina instrument. For this we had a great team of trainers, Segundo Fuentes and Ana Pérez from CIP; Ivannia Atmetlla, Ricardo Chinchilla and Rebeca Campos from UCR. We wanted a small group (10) of trainees to use the protocols and evaluate whether this wet-lab training could improve their experimental design and understanding of data analysis later on. Though we had some drawbacks, as is natural from wet-lab trainings, some comments from the trainees show the importance of complementing, when possible, bioinformatics training and wet-lab experience:
“The trainers have a lot of experience in the topics covered during the course and they were able to clear all the doubts that emerged during the course of the workshop. It was very useful that one can participate in each step of the library preparation, because I consider that is the only way to really learn the protocol.”
“Everything was good. I learned new techniques, also some procedures I did before but not for NGS so I learned how to adapt it for NGS.”
“The hands-on part. I have the feeling that everyone learns better from doing experiments.
“After the workshop I have been thinking about some ideas for future projects using the knowledge aquired from the course”
“Great experience with well-known trainers and collaborators. I would definitely love to repeat this experience. Thanks CABANA and UCR”
The following week we had a full room (21) of participants from Argentina, Brasil, Colombia, Ecuador, Mexico, Peru, and Costa Rica, to learn the basic analysis to identify and reconstruct viral genomes from small RNAs using the software VirusDetectW, Geneious, RDP and R libraries for network analysis. The trainers Jan Kreuze, Ricardo Alcala and Segundo Fuentes did a great job.
Thank you to all the organizers, trainers and trainees for making this another successful CABANA workshop!
“Chemoinformatics in Drug Discovery” hosted at the National Laboratory in Genomics for Biodiversity (CINVESTAV UGA LANGEBIO) between October 15th and 18th, 2019 was a successful CABANA workshop. Twenty-four delegates from different regions of Latin America - Mexico, Colombia, Peru, Argentina and Cuba – attended the workshop and discovered Mexico’s heart. Our 5 speakers Dr. Jose Luis Medina Franco (from UNAM Mexico City), Dr. Fabien Plisson (from CINVESTAV UGA LANGEBIO, Irapuato), MSc. Rodrigo Ochoa (University of Antioquia, Colombia) as well as UNAM students MSc. Barbara Diaz and Edgar Lopez introduced the participants to theories and practices in computer-aided drug discovery – structure-based and ligand-based drug discovery. All classes were well received. The workshop opened new collaborations and possible projects between the represented institutions.
CABANA partner, Ricardo Fujita from Universidad de San Martín de Porres, Peru, gave a presentation to the Latin America Regional Conference to fight Illegal Wildlife Trade in Lima on 1st October.
Ricardo discussed how the identification of specimens, part of them or processed products, by a system using DNA Barcodes or DNA metabarcodes is a must to help the protection against smuggling and extinction of endangered species.
It raised interest and willingness to collaborate from Peru National Prosecutor for the Environment, the Prosecutor of Environment at the National Customs, UNODC Environment Crime Project Specialist, Wood Productive Innovation and Technology Transfer Center of Peru and some NGOs involved in Wildlife Diversity Protection.
Applications are now open for CABANA Travel Fellowships to participate in 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)
- CABANA Travel Fellowships will be awarded to scientists (mainly PhD students or young postdoctorals) from Latin-America eligible countries (i.e. countries indicated in the Application Form), that send a communication to the X International Conference on Bioinformatics - SoIBio+10.
- CABANA Travel Fellowships will offer to the selected fellows a grant to cover the Registration fees, the Hotel accommodation and the Return Flights to the X International Conference on Bioinformatics - SoIBio+10. The grant has a maximum limit of £1125 per fellow. The registration and the accommodation will be directly paid to the Conference once the applicant is selected. The flight will be reimbursed to each travel fellow upon submission of a travel claim form (that will be provided by CABANA) which should include copy of the air ticket and boarding passes.
- CABANA Travel Fellowships will be awarded according to the quality of the scientific communication sent to the X International Conference on Bioinformatics - SoIBio+10, but also considering the CV and the needs of the applicant. Early-stage researchers, women and underrepresented groups are especially encouraged to apply.
- For the application the candidates have to fill this CABANA Application Form (https://forms.gle/DqM5jZ1R6xQzF7Yj6) and at the same time fill the SoIBio+10 Registration Form in the website of the Conference. In the CABANA form the following documents will be asked to you: (i) copy of the title and abstract (500 words) of the communication sent to the Conference; (ii) a brief CV (not more than 2 pages indicating degree, current status and institution); (iii) a brief budget calculating approximately the cost of your flight (i.e. return tickets to Montevideo) .
- The deadline for the application of the CABANA Travel Fellowships is midnight UTC on Saturday, September 15th.
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.’
Back in Peru after her CABANA secondment, Hannele Lindqvist-Kreuze shares the outcomes from her secondment
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.