Team:Edinburgh OG/Collaborations

PhagED: a molecular toolkit to re-sensitise ESKAPE pathogens

Collaboration with Newcastle team

Following our iGEM Northern Meet-up, we asked Newcastle to help us to convert our deterministic model of interactions between phages and bacteria into stochastic one. Although nobody from their team had previous experience in modelling using Python packages, StochPy in particular, they received extensive training in modelling in general that proved to be very useful for us.

During over 2 hours long Skype session with Bradley Brown and his team members we worked thought our model together bit by bit trying to find a solution. We shared the basic principle behind StochPy and our draft models, whereas Newcastle proposed a working solution. The result of this collaboration is reflected in our GitHub page with a commit title “Introduction of Newcastle help in stochastic model”. This collaboration is also mentioned on the official Newcastle 2017 wiki Collaborations page.

Collaboration with Edinburgh UG team

Throughout the project we have extensively collaborated with the Edinburgh_UG team. The collaboration resulted essential for both teams to develop their projects.

Collaboration 1

2017 Edinburgh OG and UG teams worked together to deliver a presentation for the Synthetic Biology Society at the University of Edinburgh on October 11th. The main focus of our presentation was to raise awareness and promote iGEM competition through an introduction to iGEM history and principles and the explanation of our projects.To achieve this, we explained how iGEM have helped us to develop practical and problem-solving skills, to come up with solutions to world problems and finally helped us to collaborate and integrate our project and ideas into the real world.

The audience, 30 people from both under and postgraduate degrees, seemed to be very motivated to join the 2018 team, asking many questions about the detailed procedure of application.

Collaboration 2

We helped the Edinburgh UG team incorporate stochastic modelling into their project. Up until this point, they were having difficulty modelling the catalysis of recombination by site-specific recombinases. With our feedback they were able to develop a complete model that allowed for their designs to be tested in silico.

Collaboration 3

Edinburgh UG team provided us with the Escherichia coli strain BL21(DE3) and C600. The former was important for testing the T7 phage, the latter essential to correctly fold and produce P1 phage particles. Finally, the Edinburgh UG team provided us with an electroporator to introduce our CRISPR systems into lambda phage.