Team:CLSB-UK/Collaborations
Collaborations
Teamwork makes the dream work
Contents
Collaborations
We collaborated with Judd, Carroll High School, University of Westminster and EPFL. We helped them with a mixture of modeling, and wiki development and they have helped us massively in return - giving us advice, testing our hardware and software, reviewing our guide for high school teams and letting us use their facilities.
Judd School
Judd-UK is the only other UK high school team. Luckily, they’re only a short train journey away.
Their collaborations page mentions us too!
What we did for them
We met near the start of the iGEM cycle and discussed both wiki development and modeling, giving them lots of advice and actionable tips - these are available for all high schools in our high school guide. We helped them derive their differential equations and explained some reaction kinetics.
We later advised them on modeling. We suggested ways of modeling their inducible promoter and advised them on solving differential equations, both analytically and numerically. We also helped them find constants for transcription and translation as they are also using a cell free extract. We checked the matlab code for their final model. Their results validated their model. Take a look at their modeling page for details
At the UK iGEM meetup we gave them ideas about what to do for human practices.
What they did for us
They tested our synthetic biology bot giving us useful feedback including suggesting the team lookup feature, the ability to repeat a step in the protocol (as opposed to just next and back), which we implemented. They also suggested having a command to skip to a particular step which we tried to implement but found it wasn’t feasible as it caused conflicts with the part lookup feature.
They tested our combined densitometer and fluorometer. They found that we could hold the light sensor more securely using blue tack, or possibly superglue rather than the electrical tape we had been using. They also suggested we save a recording number rather than just whether or not a reading had been recorded and add the ability to download only the ‘recorded’ data. We implemented this, making data analysis easier and the fluorometer more powerful.
They helped us with our high school teams guide by giving us detailed feedback that we incorporated into the final guide. They gave us lots more advice for the ‘idea’ section of the guide, and helped provide us with other pertinent points for the ‘why enter,’ ‘fundraising’ and ‘equipment’ sections.
Showing Judd-UK our fluorometer and densitometer
Teaching Westminster the basics of wiki development
Westminster (Biobusters)
We met Westminster several times - and thoroughly enjoyed the iGEM UK meetup they organized!
You may be interested in seeing their collaborations page.
What we did for them
We gave University of Westminster advice on how to use the iGEM wiki editing tools, Mediawiki templates, as well as pointing them to some good HTML, CSS and JavaScript learning resources.
What they did for us
We collaborated with the Westminster iGEM team in order to carry our iGEM’s interlab study. We do not have a plate reader at CLS, but Westminster kindly agreed to let us use theirs to carry out the measurements. Their PI, Dr Smith, was invaluable in helping us setup and use the machines - we are very grateful for her time and effort. Take a look at our results on our InterLab page.
Carroll High School
Although an ocean away, we communicated a lot with fellow high school team, CarrollHS.
We’re happy to have made it onto their collaborations page.
What we did for them
We helped Carroll High School with several parts of the wiki. We first explained the way the iGEM wiki is structured and how to use Mediawiki formatting and templates. We later troubleshooted parts of their wiki, writing code to fix problems they were having in their navbar, footer and with the overall layout.
What they did for us
They reviewed our guide for high school teams wanting to enter iGEM, and gave us suggestions to make it more user friendly - for example, we included the extra concluding paragraph on their advice
Attribution: Logo provided by Carroll HS.
Attribution: Logo provided by EPFL
EPFL (aptasense)
EPFL were also working with toehold switches, and they gave us great advice on how to overcome our problem homologous miRNAs. We designed a second series of switches having read the paper they recommended, and the advantages of these switches make our sensor better suited to clinical use. Take a look at our design and integrated human practices pages for more.
Oxford (see cruzi)
Oxford’s modeling team checked our MATLAB code and differential equations. They pointed out that our parameters were not dimensionally homogeneous, which we fixed. They also sent us Karzburn’s 2011 paper, ‘Coarse grained dynamics of a protein synthesis in a cell free system’, where we found a value for our constant of translation. They also ran stochastic simulations for us - take a look at our modeling page to see the results.
Attribution: Logo provided by Oxford iGEM
High school teams guide
We’d like to thank the high school teams who kindly completed the survey about their iGEM experiences. Their input was vital to the high school guide we produced.
We explain the common problems and how they can be overcome, providing actionable advice on everything from fundraising to lab work, including tips from a PI’s perspective. We hope that it inspires new high schools to take part in and succeed in the competition.
UK iGEM Meetup
On the 17th and 18th of August, we attended the UK iGEM meetup hosted by the Westminster, UCL and Warwick iGEM teams. This was a great opportunity for us to present our project to others. We delivered a formal presentation, and explained our project at poster sessions. We were also able to find out more about other teams’ projects and their work.
We were able to set up links with some of the teams there which led to some of our collaborations. In addition, it was useful to talk to other teams with more experience and get advice on things like poster design or presentation skills.
Attribution: Dr Caroline Smith, Westminster iGEM
