“Early on in our iGEM journey we discovered that Aalto-Helsinki was working on a biosensor project, just as us. Initial conversations lead to the discovery of shared goals between our teams -mainly our wish to develop comprehensive ODE modelling and incorporate ethical considerations in our project work. Our dry-lab collaboration soon proved beneficial for our teams, and this lead to a partnership throughout the season eventually extending to human practice collaborations as well. The professional (and social) exchange has not only provided us with directly useful ideas and trouble-shooting, but inspired us throughout our whole process to be open minded and think critically about our models and assumptions. It has help us understand how to communicate our project in various levels of details and convey our ideas successfully. We are extremely happy to have had the pleasure of working with Aalto-Helsinki!” -UCopenhagen
DRY-LAB PARTNERSHIP
Introduction
In May, when we first talked with the Copenhagen iGEM team, we discussed the possibility of starting a dry-lab collaboration, since both teams wanted to model similar things on their respective projects. Throughout the iGEM competition we have had three meetings in which we have exchanged several thoughts about each other's models.
First Meeting
Our first meeting was held on 16.06.2020. In this meeting each team explained their project to the other one. We gave insights into the pathways that we were working with and explained in detail which parts we were aiming to model and which softwares we would use.
In this first meeting, our team already had done a simple MatLAB Simbiology model. We explained to the Copenhagen team that we were aiming to use MatLAB and Rosetta softwares. With MatLAB, we wanted to model our whole biosensor pathway and we would use Rosetta to predict modifications in the ligand binding site of the transcription factor MphR, that would increase the binding affinity for its ligands, macrolide antibiotics. To see more about our models, visit our modelling page. We gave the Copenhagen team advice when using the Rosetta software and some insights on how to use it.
In this meeting, we agreed on exchanging our MatLAB models in order for the other team to revise them and give some feedback on how to improve them in the following meeting.
Second Meeting
Our second meeting was held on 04.08.2020. For this meeting, each team had revised the other team’s model in order to give feedback.
When going through our MatLAB Simbiology model, the Copenhagen team had some important points to highlight. Mainly, they made us see we over-simplified our model and some more parameters and reactions should be considered. In particular, the reactions to be considered were mRNA decay of MphR and the diffusion of macrolide antibiotics inside the cell.
From our part, we mainly commented on Copenhagen’s presentation of the model. Their pathway is quite complex and has lots of steps, so we suggested that a clearer presentation of how it works could make it easier for the reader to understand it. For that, we mentioned the possibility of presenting a graph of the whole pathway and changing the ODEs names to more intuitive ones, rather than letters with numbers.
At the end of the meeting, both teams agreed on making the changes proposed by the other team, send the model with the changes and meet again to go through them.
Third Meeting
Our third meeting was held on the 14.09.2020 and was meant to be the final dry-lab meeting regarding our models.
When going through our MatLAB Simbiology model the Copenhagen team didn’t have any comments as we have improved the model following their suggestions in the previous meeting.
From our part, we concluded that the MatLAB model of the Copenhagen team was much more understandable than previously. We only made them aware that one of the graphs that the model output had an unexpected decay of one of the components of their model. Apart from that, we concluded the presentation of the model had significantly improved since the last time.
Finally, in this meeting we agreed on revising each other’s dry-lab wikis in order to give some feedback and see if we could improve our modelling pages. We also agreed on having a Partnership since our collaboration was meaningful for both teams and we helped each other significantly.
Conclusion
In conclusion, throughout the iGEM 2020 competition we have been in constant communication with the Copenhagen team in order to help each other with the MatLAB models. From our part, thanks to Copenhagen's feedback, we have added a bit more complexity in our model and from their part, they have given a more detailed presentation of their model in order for the reader to be able to understand it.
HUMAN PRACTICES PARTNERSHIP
Nordic Ethics Workshop
During our first meeting with the Copenhagen team we decided we wanted to extend our collaboration to the Human Practices side of our projects as well. During the meeting we discussed many possibilities for collaboration and came to the conclusion that our projects would greatly benefit from a workshop where we could discuss and troubleshoot our projects from an ethical perspective. From this we then created the Nordic Ethics Workshop to which we also invited iGEM Stockholm, iGEM Uppsala and Trondheim NTNU.
Even though we were responsible for organizing the workshop, the Copenhagen team gave their insight into how we could best do the setup for the workshop, which helped a lot in the planning. In cooperation we managed to create a great afternoon, which brought all the Nordic teams together to discuss and troubleshoot our projects. To read more about the details from the workshop visit our collaborations page.
Meeting after Nordic Ethics Workshop
We met with the Copenhagen team separately after the workshop to further discuss and troubleshoot our projects from an ethics perspective. Team Copenhagen had done an in-depth estimation of our possible carbon footprint, should we start to manufacture our product. The calculations were based largely on estimations and assumptions, but it gave us a good idea about where most of our carbon emissions would come from and helped us to visualize the processes we would need in order to make our project into a product.
We, on the other hand, had done a more extensive troubleshoot of team Copenhagen's project, where we answered questions team Copenhagen had about their project and brought up thoughts and questions we had. We especially focused on the ethics of using their product on humans and hopefully gave the Copenhagen team good points to think about and consider about their project.
