Over the year we met some wonderful people and worked together to create some beautiful content!
In collaboration with iGEM teams from UCL, Vienna and Cambridge we ran 4 separate workshops, one after the other, in a series focused on Coding with Biology. The rationale behind this was to help address the common gap in coding capabilities that many biological science undergraduates may have, and to help them create models of complex biological systems. This was in part because of the rapid adoption of in silico modelling (as per our modelling page: “science - without the risk of a lab leak”).
Most of the other sessions from the other teams were focused on Python as a programming language. We see the value in this, as Python is a widely used and versatile programming language (we used it in our bioreactor!), but Python can be really slow. Sometimes when modelling dynamic biological systems, this can bottleneck research.
Hence, our session was showing off Julia – a new programming language designed to be as intuitive as Python, and optimised for science and MATLAB or R, and as fast as high-performance computer languages like C/C++. During our session we covered the following:
This was a rewarding and successful experience for all teams involved, and we all learned a lot from each other. For more information on these workshops please visit the Communication Page in our Project section!
We attended a European meet up in Münster, Germany, in late August whereby the WWU Münster team hosted a range of teams from around Europe to come and present their deliverables and get some feedback on their projects. We had a fantastic time networking in Münster and met some amazing teams who gave us unique insights into our poster, promotional video and presentation. All of the feedback has since been suitably taken on board and adaptations have since been made!
More detail on the event can be found on the WWU Münster wiki page.
Our team went on the Exeter iGEM 2022 team’s podcast, Test Tube, and spoke about our project and received feedback from them on a variety of aspects of our project. Speaking to an iGEM audience also allowed us to gauge how much detail was appropriate to address our target audience, which is particularly important when it comes to our deliverables and presenting in Paris. It was also a great opportunity to learn about more technical aspects of podcast recording from the Exeter team and it gave us the opportunity to share our collective knowledge about synthetic biology with the wider world.
In late June we created a questionnaire designed to gain feedback from synbio scientists and students in order to inform our progress and development of our own toolbox. Our questions focused on the most commonly used bioinformatics toolboxes, what people feel are the most specialised toolboxes, and what are considered the best online bioinformatics toolboxes. We also asked about what common shortcomings many toolboxes seem to share and what improvements people consider most important.
According to our responses the most common toolboxes were MATLAB and BLAST for tailored software, and Expasy was the most common online toolbox. Most people shared the same opinion that most user interfaces were unintuitive, outdated, and lacked documentation or adequate instructions. These issues were compounded for mobile users on online websites.
As a result, we have endeavoured to prioritise functionality and ease of use over the number of features our toolbox has. We felt it was better to do a few things really well and really reliably in order to encourage return users. Over time we plan on integrating more features into our toolbox.
Here we worked with Adam Bowie of the University of Sheffield to host a session introducing AlphaFold to the iGEM community, allowing them to gain an insight into how to use the software in their projects. We also included talks from two of our members, Isaac White and Brooks Rady, who presented research on novel protein design and a live demonstration with ColabFold, respectively.
Find out more about the session on the Communication Page.
We organised an online meeting with the Ohio State University iGEM team, in part because their project also included bioreactor design and phages. Whilst their use of phages was not for guided evolution but instead for optimising bacteria-based early sepsis detection, we still managed to share insights with each other regarding in silico bioreactor modelling, creating temperature profiles and mass balancing for bacterial population modelling.