Reflections on a bioinformatics training course funded by CONNECTED
Rose Tafadzwa Masekesa is a CONNECTED network member who wrote this blog having successfully applied for CONNECTED funding to attend a bioinformatics course which began in January 2020 at The Swedish University of Agricultural Sciences.
As an avid molecular virologist, my passions lie in identifying and protecting plants from the devastating effects of viruses. As I enjoyed experimenting in the lab more, I tended to strengthen my wet lab skills consequently generating lots of biological data where I depended on outsourcing for analysis and interpretation of the Next Generation Sequencing (NGS) data.
As one can imagine this was a recipe for disaster as interpretations of some results were puzzling to say the least. The one Bioinformatics “skill” I could confidently boast of was the ability to perform a rudimentary BLAST search on NCBI.
So armed with my one competency in bioinformatics, I arrived at SLU a complete novice but eager to learn.
I take my hat off to Prof. Eric Bongcam-Rudloff and his team for having a well-structured, easy to follow and in-depth course that managed to create common ground for individuals with different levels of expertise in bioinformatics.
The course was a nice balance between lectures and hands-on analysis/interpretation training with an emphasis on skills development. Learning was a pleasure as each topic was taught by a group of experts who spoke from personal experience.
The course covered essential components of the bioinformatics workflow, including, to mention just a few:
- accessing raw NGS data from various databases
- performing quality checks on NGS data
- data trimming for quality purposes
- de novo genome assembly
- differential gene expression analysis
- structural/functional annotation
- pan genome, and
- comparative analysis.
Our class was composed of individuals from 16 nations from across the world, who were working on diverse research projects ranging from insect genomics, to animal genomics, to plant genomics, and this helped to enliven discussions.
Now with close to three months of training under my belt, I am more competent in the field of High Throughput DNA/RNA sequencing data analysis and interpretation.
As such, I plan to engage in collaborations with other CONNECTED members in the country and region in our efforts to combat plant viruses.
I also intend to aid in the NGS data analysis and interpretation capacity building initiative amongst CONNECTED members, sharing not only the knowledge gained at SLU but also the free software that I received for analysis of NGS data.
It is also my intention to transfer the knowledge and skills that I learnt in the bioinformatics course by conducting regular workshops with research colleagues at the University of Zimbabwe where I am employed. The purpose of these workshops will be to introduce or reinforce concepts in bioinformatics, to demonstrate the actual practical application of gained skills in problem-solving and use the workshops as a networking platform within the University of Zimbabwe that will enable greater collaboration between departments such as Entomology, Pathology, Plant Breeding and Molecular Biology.
In addition, I plan to create/update plant-virus procedure/protocol documents (desk manuals, standard operating procedures, flowcharts or checklists) by including relevant bioinformatics steps that allow for more comprehensive outcomes in terms of diagnostics and analysis of plant vector-borne diseases.
I also plan to establish a mentorship relationship with the newer members of staff in the Crop Science Department who recently graduated. This will aid skills and knowledge transfer in terms of bioinformatics.
Lastly, I intend to engage in mind mapping exercises with individuals or small groups of colleagues which will help map out their thought processes, and point out areas where bioinformatics could play a critical role in enriching the research.
I am immensely grateful to CONNECTED for affording me this unique opportunity to enrich not only my informatics skills but also those of the region.
Thank you CONNECTED.
Rose Tafadzwa Masekesa (PhD) is a plant molecular virologist working as a lecturer and researcher in the Crop Science department, University of Zimbabwe. Her research focuses on molecular characterization of plant viruses as well as plant protection from viruses through tissue culture and genetic transformation means.