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Member blog & video: Training in bioinformatics sponsored by CONNECTED

Edith Avedi, one of our network members, has written this blog specially for the CONNECTED website. Edith successfully applied for CONNECTED funding to attend a bioinformatics course which began in January 2019 at The Swedish University of Agricultural Sciences.

Bioinformatics course, Sweden

Edith Avedi pictured with fellow network member and course delegate Adedapo Adediji (left), and CONNECTED Management Board member Professor Richard Hopkins (centre)

Training in bioinformatics at SLU Sweden, sponsored by CONNECTED

by Edith Avedi

Through CONNECTED I got an opportunity to train in bioinformatics at SLU in Sweden for nine weeks. During this period I have learned a lot, and from the best teachers.

The module of the course comprised lecturers, tutorials and assignments; it was basically hands-on training. The nature of the training is in a manner that allows a seamless flow from one aspect to the other, hence making understanding easy.

During this training we were taken through basics, such as online blast and biological databases. Thereafter we were taken through sequencing technologies, De novo assembly, genome annotation, RNA sequencing, Eukaryotic annotation, metabarcording, virus metagenomics and well as protein sequence and structure analysis.

This training has equipped me with step-wise skills on how to explore, analyse and interpret molecular data, and I am now also knowledgeable in several useful free softwares.

Through international trade, pathogens are moved from one country to the other. Current diagnostics approaches in most developing countries rely on having prior knowledge of the target pathogens, and so are not effective in identifying new pathogens or associated variants that are likely to be introduced.

Prof Erik Bongcam Rudloff

Prof Erik Bongcam Rudloff addresses delegates at the bioinformatics course

Therefore the use of next generation sequencing approaches such as Nanopore, PacBio and Illumina is not only cheap but also saves time. However, this leads to massive data generation that needs computational knowledge, hence the importance of this course. At KEPHIS, Kenya, we are in the process of adopting these high throughput technologies in our plant health quarantine and certification scheme. The knowledge gained during this training will be utilised at the institution to ensure we import and export safe planting materials, in surveillance programs, and in generating peer reviewed publications.

Scroll down to watch a short video of Edith talking about the course

Sharing the new learning

I will train my colleagues (some are Msc and PhD students) and students on internship on the various aspects learnt.

Our plant quarantine laboratory is a COMESA reference laboratory; therefore we analyse samples from the COMESA region, and also offer training on diagnostics.

Bioinformatics class, CONNECTED network

Bioinformatics class at The Swedish University of Agricultural Sciences, Uppsala, Sweden

I will have bioinformatics included in the training syllabus. We also train various institutions, both government and private, as well as institutions of higher learning on plant health issues. Therefore, it will be important to have them taught a unit in bioinformatics too.

During this period, I have made good friends and created new networks through interactions with many students from across the world. My most memorable moment is on realising that so many different free softwares for bioinformatics are open source and can be installed just by typing “conda install”.

Whereas my biggest achievement is having used the knowledge to analyse my virus metagenomic data which is part of my PhD project. I leave SLU as an expert in bioinformatics. Thank you CONNECTED for this opportunity.

Edith Avedi works for the national plant protection organization of Kenya (KEPHIS) as a plant health inspector. She is based at the Plant Quarantine and Biosecurity Station –Muguga. Her main duties are carrying out surveillances and diagnostics of pathogens of quarantine significance particularly viruses and viroids.