Team:Newcastle/Collaborations
Collaboration
Over the course of the summer we have collaborated with a number of different iGEM teams and attended a number of different events including iGEM meetups at home in the UK and abroad in Europe. As well as conferences, like IWBDA, where we discussed our project with researchers in the field to gather their thoughts and feedback. We have documented these collaborations below.
Exeter
Team Exeter kindly helped us by conducting thermal conductivity experiments on LB and M9 media. These were important in allowing us to correctly model the temperature change caused by running an electric current through common bacterial growth media. They found that the conductivity of both M9 and LB to be very similar to that of water. Whilst water has a thermal conductivity of 598.4 mW/Km (miliwatts per metre kelvin) at room temperature Exeter found that LB has a slightly higher thermal conductivity at 605 (+/- 20) mW/Km and M9 a slightly lower thermal conductivity of 570 (+/- 30) mW/Km.
This data was incorporated into our modelling and helped us identify which media to use in our later conductivity experiments. It also gave us some useful pointers for exploring other fluids with different specific heat capacities. Thanks Exeter!
European iGEM Meetup
This years, European iGEM Meetup was hosted by teams EVRY and IONIS in Paris. Some of our team members attended this event which consisted of a poster session on the Saturday morning where we presented our project and started to identify other teams who were working on similar projects or who might need access to equipment we had for collaboration. We got lots of good feedback on our project, and particularly our poster design, which lead to it being redesigned for the later Westminster Meetup. In the afternoon there were two round table dicussions with members of the synthetic biology community. Of particular interest to us was the talk on biosecurity which contained useful information on considerations for our human practices around biosecurity and introduced us to the concept of 'dual purpose' constructs which is something we discuss further in our safety work.
Westminster Meetup
On the 17-18th of August a half of Newcastle University iGEM 2016 team went to UK iGEM teams meet up in University of Westminster where we had to display our poster and make the presentation.
The presentation went well, but a few improvements could be made. First of all, the clear structure of the presentation that had separate sections for introduction, microfluidics and breadboard, genetics and human practices worked well. We will try to make our next presentation very structural as well. Also, a breadboard design picture should be included in order to help people visualize how our final product looks like. Our human practices part looked very integrative and different compared with other teams and now we should continue and actually develop a human practices simulator. Finally, chronological order in some parts of the presentation such as human practices were easy for listeners to understand and follow so we are planning to use this approach in other parts of our presentation.
The poster was received positively as well. However, when comparing ours with the ones of other teams we have indicated a few areas which could be improved. First of all, our poster could have contained less text and maybe bullet points to make it more attractive. By reducing the amount of text in the poster we are also able to make the heading and text larger. Finally, we would like to make the sections of our final poster more separate than before. Even though this poster had a better separation than the previous one, the components description were a little bit scattered and thus harder to follow.
IWDBA 2016
Whilst half of our Team was at the Westminster iGEM meetup the others half were in Newcastle attending IWBDA 2016, the international workshop on biodesign automation. There we heard from a number of researchers in fields related to synthetic biology and were able to explain our idea to them on order to get feedback. We found that the feedback was positive once people fully understood our idea but that we were not explaining our end product, the plug and play kit, very well. We resolved to make better use of props such as the existing electronics kits for children at future presentation opportunities. Whilst gathering feedback on our idea we were fortunate to find someone working on the same area, but from the opposite end - using electronics to sense signals from the bacteria. In particular, Luis Ortiz of Boston University was using pH probes to sense the bacteria and integrate this information into a computer system. He gave us useful information on altering the pH of a growth media using bacteria which is something we investigated further as an alternative way of changing the resistance of our growth media in our various 'resistor' constructs. We also heard from researchers working on new micofluidics fabrication techniques involving the etching of plastics rather than moulding PDMS. We investigated this further when considering our 'environmental responsibility' from both a human practices and safety perspective.
Whilst at IWBDA we also had the pleasure of meeting the 2016 Leiden iGEM team and to hear about their idea and discuss the progress of both our projects.
Edinburgh Meetup
The Northern iGEM Meetup was held on the 29th of July at the University of Edinburgh. This was an opportunity for teams from Scotland and Northern England to get together and present on the work they had done so far. As we had not completed many experiments at this point we presented a similar presentation to that one we delivered to sixth form students at our schools taster day for syntehtic biology. We thought this would be a good opportunity to start on our human practices work and so covered information about our project and where we can see our research and ideas in the coming years. We also made sure to pose some important ethical issues that we had been encoutering in our project to the audience in order to guage their responses.
We also used the Northern Meetup to look for new collaboration opportunities. It was here we met the Edinburgh undergraduate iGEM team. Like us they were working on a project interfacing bacteria and eletronics, in this case on creating a modular system for storing data in DNA. Also like us, they had encountered problems explaining their work to other people and getting feedback from them. This was particulalry important to them as the end-product of their technology is a system useable by consumers.
We explained to them that we were creating a computer game based ‘thought experiment’ designed to stimulate discussion around the consequences of using our technology as part of our human practices and offered to integrate their storage system into our thought experiment so that they could use it to get feedback. They thought this was an excellent idea and we invited them down to Newcastle to meet with us and discuss how they wanted their system to be presented within our 'thougt experiment'.
Edinburgh
Following on from our first meeting at the Northern iGEM Meetup the Edinburgh undergraduate team came down to Newcastle to discuss their idea and collaboration in more detail. The problem they are tackling through their iGEM project is that much of today’s digitally generated data must be archived for a long periods of time. Often this is required by law.
To overcome the limitations of current archival storage systems, like cost and low density the Edinburgh team were investigating the use of a DNA storage system which has a much higher information density and lasts a longer time, thereby reducing costs. They hoped that their technology would eventually form part of consumer products. Serving large libraries and institutions with significant amounts of archived data, like the National Library of Scotland.
Well aware of the concerns of the public around the use of genetically modified organisms the Edinburgh team wanted a way to explain their technology and gather feedback on people’s perceptions of it. As we were building a game based ‘thought experiment’ designed to stimulate discussion on the consequences of using our technology in real world scenarios for our own project we felt this would also be suitable for use by the Edinburgh team. You can read more about why we chose this approach on our human practices background page.
We agreed that we would aim to guide the user to consider some uses of their technology and to think through the effects of its use. The Edinburgh team were particularly keen for us to explore the privacy concerns around long term data storage, so we set out to design a level of our game that would explain the notion of DNA storage and the security aspects that the Edinburgh team were implementing.
Through their meetings with , Dr Kami Vaniea and Dr Aggelos Kiayias, they had found that there was already some skepticisim around whether or not encryption was really necessary in their system. By providing them with a tool that showed how they encryption would work in some of their threat scenarios we hoped to make it eaiser to explain and justify their approach.
Consequently, we integrated an illustration of their storage and encryption scheme, implemented in a simplified form in JavaScript whilst maintaining the core principles, into our .
