1- Developing workshops on DNA for a broad audience
Education is a very important part of the iGEM competition, and as part of our iGEM experience we thought of ways to make science, and more specifically Molecular / Synthetic Biology, more accessible to the general public.
Getting Kiwis to give up their DNA at the Apériscience event in February
Our first opportunity in science education came in February. We were invited to develop workshops for a science popularization event called Apérisciences. The workshops directly preceded a conference entitled "DNA superstar or supercop" (presented by Catherine Bourgain) at the Public Library in Massy. We addressed a diverse audience, including primary, middle and high school students and their families, For this event, we created a workshop on DNA extraction from kiwis to make DNA a tangible matter for people. We attempted to introduce molecular biology techniques such as electrophoresis and explain our project to a broad non-scientist audience.
Reflecting on the experience from February and the necessary improvements, we developed additional materials, checklists and advice that we hoped to be able to use at another event, when the lock down would be over.
Hosting our improved workshops at a science museum along with our iGEM partners
Our team, iGEM GO Paris-Saclay had the idea of creating a long-term partnership between our iGEM team and the Cité des Sciences et de l'Industrie, one of the biggest science museums in Europe. Initial contacts were made in March before the lockdown. We started planning the event with the help of Valérie Lerouyer, and chose to invite our partner iGEM teams (Sorbonne_U, Evry Paris-Saclay, Bettencourt and Ionis) because we felt it was important to be able to share this event with them. With the reopening of museums, we were able to host our improved workshops on October 3rd and 4th in the Cité de la Science et de l'Industrie in Paris. We also presented our respective projects.
During this 2-day event, four workshops attracted great interest: "An introductory quiz: can you tell me where to find DNA?", "Extracting DNA from kiwi", "Measuring DNA size" and "the DNA compaction challenge". Our public included people only starting to discover the exciting world of Biological Sciences, but also people wishing to delve deeper and expand their knowledge in this area. Our eager team members welcomed any questions relating to our workshops and to Biology in general, which led to a lot of interesting and insightful conversations. We also developed a paper questionnaire and QR code to obtain feedback from our participants, gauge their understanding of the topics we presented and get new ideas for things people might wish to learn about. Thanks to this, we also gained insights into the difficulty our visitors had to understand the notion of entangled genes - inspiring us to create diagrams of our advances.
In addition to the fun we had with the general public, it was a pleasure to expand our collaboration with our partner iGEM teams with whom we had worked so hard on organizing our Parisian MeetUp.
PDF File DNA workshops.
2 - Sharing among scientists: Tutorial course on the software CAMEOS
We know that iGEM is a learning experience, where every team has valuable knowledge to impart. At the beginning of our project, team members and supervisors alike faced problems with installing and utilising the CAMEOS software. Learning to navigate the software took some time, and we decided we could make life easier for future iGEM teams and synthetic biology reserarchers who might want to use Gene Entanglement in their own projects by creating a user-friendly CAMEOS tutorial.
We developed a full tutorial course on the software CAMEOS. This course explains how to run the software, including how to generate the inputs needed by the program and how to analyze the outputs with other computational biology tools. The tutorial only requires a basic knowledge of computer science to be completed, but even without access to terminal commands, it is designed to be easy to follow.
You can follow the tutorial on this page.
Who is this tutorial for?
This course aims to help biology students and future iGEMers, as well as synthetic biology researchers, to be more familiar with CAMEOS and sequence entanglement. We think that sequence entanglement tools are a fantastic idea and are bound to become more and more popular in the coming years. Students will need a basic knowledge of computer science, including how to use a Linux environment with superuser rights, which is the only pre-requisite for this course. All course parts are desgined to be indepedent and the course can still be followed without running the terminal commands.
Why did we develop it?
Our first experience with using the CAMEOS algorithm was that it is difficult to know where to start especially if you are not a computational biologist. We found its documentation to be a bit lacking and with this iGEM project and our interactive course we aimed to resolve this problem. We fully re-documented the software processes to facilitate its use by everyone, illustrating CAMEOS with accessible examples.
Most iGEM GO Paris-Saclay team members managed to install and run CAMEOS on their computer in a collaborative videoconference of about ~ 2.5 hours. For the next step, unfortunately very few people on our team managed to generate all inputs needed for CAMEOS to run it with their own proteins. This hurdle was also one of the motivations behind this tutorial.
What will they learn?
In the first part, students will learn how to use the programming language Julia, and how to download and run the software. We will detail how to solve certain problems we encountered when installing the software. By the end of the part, students will be able to generate their first entangled sequences.
The second part deals with the generation of CAMEOS inputs. Students will be able to generate all necessary files from a single protein Multiple Sequence Alignment (MSA) using our bash script. We explain the use of each command line in the script, and what the resulting files are used for in the CAMEOS algorithm. By the end of this part, students will be able to entangle their own genes.
In the third part, students will learn how to select the optimal sequences using our script calculating pareto optimality. We will go over online tools to help non-computational biologists analyze their entangled sequences. We will also present lacking features from the CAMEOS software which are important to consider in the process of designing a BioBrick.
Finally, in the case study, students will become familiar with the different databases to retrieve homologous sequences necessary to run CAMEOS and the tools to perform the Multiple Sequence Alignments. Our case study explores which kind of alignments would be the best for entangling sequences with CAMEOS. This study opens a few questions and might provide some tracks to explore in the research field.
Who tested it?
Outside of our team, our tutorial course was tested by none other than the IOANNINA iGEM 2021 team, as part of a collaboration. Their feedback helped us improve parts of the tutorial including command lines that were missing or poorly explained. Overall, one member managed to follow all the steps from our tutorial despite not being a seasoned user of Linux terminal commands.