UC Davis Collaboration

UC Davis iGEM team is one of the winners of Opentron competition in 2019, where as prize Opentron gave out OT-2 pipetting robots to ten iGEM teams, whose applications are the most convincing. iGEM Marburg won one OT-2 during last year’s edition of the competition and got contacted for collaboration by iGEM UC Davis along with other said competition winners from 2018 and 2019.

The goal for this inter-lab collaboration is to collect data and determine the accuracy of the OT-2 compared to humans. To do this, UC Davis conceived a protocol to perform serial dilutions of silica beads and fluorescence both manually and with OT-2. In total iGEM Marburg did four dilutions; twice with OT-2 and twice manually. The data is then sent to UC Davis via the spreadsheet designed by them. Finally iGEM Marburg made a Slack channel for all iGEM teams with OT-2 to be in contact with one another; further increasing exchange and collaboration. More information about this collaboration can be found on UC Davis wiki.

Biohackathon Lab App 2019

Vilnius, Lithuania

In August 2019 our Team participated in the Biohackathon Lab App, organized by the Vilnius-Lithuania Team 2019. Together with the iGEM Teams Stockholm and Copenhagen, as well as several non-iGEM Teams we sat together for a weekend packed with problems, ideas and neat solutions.

With the task of creating an Application that tackles a self-found problem, we sat together and brainstormed about what could be done.

During this time we were in the middle of our works with the Opentrons OT-2 and soon realized that some of our biologists had trouble integrating protocols in the robot themselves, as this is primarily done by writing the protocol in Python and pushing it directly to the robot – no convenient application to change parameters, such as the amount of reactions, of the protocol included. In our heads the idea to have a user-friendly GUI grew more and more and soon we saw ourselves standing in the Vilnius University Life Sciences Center.

“We” were two biologists and one mathematician, so we talked to some of the other participants that did not have a team yet and found the perfect fit to complement our small team: Nour Alsamsam was happy to join us for this weekend and lend us his coding skills – huge thank you to you, Nour!

Together we tried our best to come up with a suitable app and presented it in the end, having more ideas in our heads than we could implement in such a short time – it was clear for us, that we would continue with this project later on!

In conclusion, the Biohackathon was an awesome and productive meeting of the iGEM Teams Stockholm, Copenhagen, Vilnius and Marburg. We talked about our projects, offered each other feedback on current issues in the lab and shared many ideas.

We are very grateful that we got the opportunity to meet so many experts from different fields, which really helped getting a fresh perspective on our project and are now looking forward to meet the other teams again at the Giant Jamboree!

Golden Gate webinar

In our second big collaboration we organized, created and hold a live webinar about Golden Gate cloning to teach and to indroduce other iGEM Teams this special cloning method in contrast to the alternative conventional cloning methods. Through this method and our webinar it fascilate other teams who are already using this method to get deeper insights to Golden Gate cloning. Besides for iGEM Teams, who are unfamiliar with that method, they could get an overview why this method is so efficient in labs who are going to clone in cells. Finally we wanted to show again that our Marburg collection and the Marburg collection 2.0 is (still) availaible for every iGEM Team.

During a 1,5 h online webinar our team presented with our advisor René Inckemann the topics and methods like: Golden Gate cloning, what is so special about this cloning method, how to create a genetic toolbox and showed students how the software Genious works for designing DNA parts. This webinar was hold on three different dates with three different time (30/07/2019 - 10:00 CET, 31/07/2019 - 18:00 CET and 08/08/2019 - 24:00 CET) so that every iGEM Teams in all continents had the possibility to attend to their favourite time fitting next to their busy daylife with iGEM. During the live webinar people get the chance to read a FAQ about the webinar itself or they could just group chat with us to ask questions, give feedback and/or just chatting with us and the other participans.

Alongside to the live webinar we created a slack workspace called GoldenGateCloning especially for the iGEM Teams who wanted to participate. In different channels the iGEM teams could ask us questions beforehand about the webinar progamme on ON-24, get summarized information about Golden Gate cloning, FAQ etc. Channels that we were created: #Automation of g gate, #Chassis adaptions, #FAQ, #Fun-and-spam, #General, #Golden-gate-database and #Golden-gate-protocol. Therefore the students could download via our G-Drive folders that contain protocols for the Golden Gate cloning, so that teams can easily use this method for their own project. There were also a handout about a summary and an explanation about Golden Gate cloning, Type IIS Restriction Enzymes, Standartised Golden Gate cloning parts and texts about „How to create your own toolbox (LV 0 – 2)“.

Furthermore the iGEM Teams had the possibility to get the slides from our holded webinars to have a look again for their own purpose. In G-Drive the people could also find the Genious Files for their teams, so that the iGEM teams can try constructing their own in-silico parts using these files. To sum up all these offered materials enable other teams our cloning protocolls and presentation slides. Via the slack channel we offer FAQ, support and help at any time via the different channels.

At the end of our collaboration webinar over 70/80 iGEM-teams all around the world registrated and participated in our webinar (see table/picture: XWorldmap?). Also Doulix as a company attended to our webinar and said after their participation: „Great webinar about Golden Gate of iGEMmarburg2019!“ (info@doulix.com on Twitter). All in all we got a lot of positive feedbacks about our collaboration webinar and we helped/supported a lot of teams regarding to biobricks/ genetic toolboxes, Genious and how to use the golden gate method for current/future clonings in your own labs.