This year I was accepted to present at the Plymouth Marine Science and Education Foundation conference (PlyMSEF 2016) held at the Plymouth Marine Laboratory (PML). PlyMSEF is for early career scientists interested in marine research to exchange ideas, present their work and expand their network. If you are keen to see what was shared on social media you can have a look at the hashtag #PlyMSEF2016.
The entire day was dedicated to presentations with various breaks to appreciate the posters. A total of 5 sessions covered various aspects of the marine research: Biogeochemistry, Community Ecology, Climate Change, Hydrodynamics and Modelling and the one in which I presented; Stress and Virology.
All the talks were interesting and showed what projects are running at the moment in Plymouth but also the broad variety of marine research in this area. Professor Stephen de Mora (Chief Executive of PML), Professor Manuel Barange (Director of Science at PML) and Dr Willie Wilson (Director of the Sir Alister Hardy Foundation for Ocean Science) were the 3 keynote speakers of the day, and I cannot lie but I was very keen on the talk about viruses from Dr Willie Wilson titled: “It’s life Jim, but not as we know it”. It was honestly the best part, and I loved the production of the podcast a war we need as part of his talk.
My Contribution at the Conference:
Since the audience was interdisciplinary I decided that my goal for this conference was to make everyone interested and excited about viruses as well as let them leave with a clearer understanding of what sequencing reads and contigs are. Lots of people don’t realize how much we don’t know about viruses, so for the viral section I tried to make sure that everyone understood how diverse viruses are and that are fundamental for the marine environment. Unfortunately not much is known as we are only starting to understand it thanks to new tools and sequencing technology advances. I love this part of my project, so it was very easy to show and share my enthusiasm for marine viruses…but it was slightly more challenging for the bioinformatics.
Lots of my friends get very confused every time I try to explain my work, what they don’t understand is some of the terms such as reads or contig. It was a good opportunity to try to explain it simply. If we want to make changes in our society and ensure the earth is a better place for future generations everyone needs to understand the issues brought up by the scientific community. I believe that as scientist we should been able to explain our research not just to other scientists but also make it understandable to everyone.
The following idea came to me the night before the conference and I managed to annoy my housemates in the middle of the night testing it out on them. So, what did I came up with? Here it comes:
Let’s start from the beginning…
DNA is extracted and send for sequencing where nucleotides are assembled to create fragments called reads. We have now some bigger pieces that will vary from 100 to 300 base pairs (bp) or longer (depending on the technology used) just like the different bits of lego. These will have to go through a quality control… and we will have to remove all the pieces that are not usable:
Our aim is to have all our reads in the green area (like in the picture above). Meaning you only keep the pieces you need to build your lego model.
We are now ready to run a de novo assembly! So we will create a new assembly (de novo is the Latin term for new) from scratch using these reads to create longer fragments that will then take the name contigs. My idea was to picture this process like the Tetris game. How does is work:
Our reads, having passed the quality control, will be used like in the Tetris game and our goal is to create an horizontal line this will be our new complete contig. Of course contigs have various lengths and the process is based on complicated algorithms.
With this idea I really hope that people who have listened to my presentation will next time be able to understand the terms “reads”, “contigs” and “de novo assembly” having now a better clue of what these are and hopefully follow the conversation (or at least have the annoying Tetris music stuck in their heads for the rest of the day…or the next time they’ll hear the term de novo assembly).
This is all for now, hope you enjoyed this short blog and please leave some comments on how you liked this explanation!