Get To Know Biopython
For science communication, we created five online tutorials on Biopython. Which can be used as a fun and practical introduction to computational biology. The idea for these tutorials came from Bram’s summer internship. There, he wished to implement python code in his internship report to, among others, calculate the expected length of a PCR fragment. It sometimes took days to create a functional script to compute all those tasks. Sometimes, the available resources on the internet are not enough or not specific enough to help in the creation of these scripts. Also, the available tutorials on YouTube are often too long, too general and not really application-driven.
Therefore, we got the idea for this series of five online tutorials on Biopython for daily life. After a brainstorming session with Ir. Louis Coussement, Bram started with creating our tutorial series: “From Sequences to Similarity”. Our tutorials distinct themselves from other YouTube tutorials on Biopython by its hands-on use, detailed code, easy explanation and short duration. You can directly adapt the code for your own use. We wish to focus on the practical implementation of certain Biopython functionalities instead of providing efficient coding.
We made six videos in total: One introductory video on installing the necessary software and on where to find the source code, followed by the five Biopython tutorials. These tutorials are in chronological order and build further on each other to complete the story in the fifth and last tutorial. First, we show how to download a sequence in FASTA format directly from the web by only using the accession number for the sequence. Secondly, we show how to calculate the expected length of a PCR fragment using the forward and reverse primer sequences. Thirdly, episode three is devoted to a BLAST (Basic Local Alignment Search Tool) search on a pre-defined nucleotide sequence. And last but not least, episodes four and five show a pairwise and multiple sequence alignment procedure and we finish with the creation of a phylogenetic tree.
And, of course, we kept the most impressive part of the series as last! In the fifth and final episode, we create a phylogenetic tree from a file with only country names and accession numbers. To make it really as practical and contemporary as possible, we almost only used nucleotide sequences of different SARS-Cov2 isolates!
To wrap up: We believe that our Youtube tutorial series “From Sequences to Similarity” is a very useful and easy way to introduce students, scientists and other interested people to (Bio)python and its usage in molecular biology. We focus on the use of the code in real-world examples rather than getting to know python better. It was also very interesting and fun to build these videos! Bram had an excellent chance to improve his python coding and video creation skills. Taken all these interesting facts together, our series of Biopython tutorials are very suitable for a golden medal for science communication!
You can watch them at the bottom of this page, on our youtube channel or you can click Bubbly to navigate you there!
We Did More Than Tutorials!
Besides the tutorials, we also brought our project outside our team. We communicated our project to academic and professional experts and researchers from our university. Besides that, we wished to disseminate our project to other interested people. We also used several social media channels. Finally, we also communicated our project with flyers, a press release, and a very informative crowdfunding page.