The Colony picture Collaboration

Many repetitive tasks in the lab cost time such as pipetting or picking colonies from agar plates and could technically be performed by robots. We used Opentrons OT-2 as a platform and designed hardware modules and scripts to outsource these tasks. Thereby, we can now offer the Opentrons user community an automated pipeline to streamline laboratory practices in ways that haven’t been possible before.

For the software we decided to use an artificial intelligence (AI). Artificial intelligences however rely on huge data sets to learn their specific task to perfection. In our case, we chose pictures of agar plates with colonies of E. coli as a suitable training set. Our experiments resulted in a big amount of agar plates but it was clear to us pretty quickly that we could never reach a big enough data set just by making photos of our own plates to get an AI with an adequate performance. To achieve this goal, we launched the Colony picture collaboration. We asked other iGEM Teams if they could provide us pictures of their agar plates with E. coli colonies with which we can then train the robot. In order to do that we published a script on how to take the pictures. We made the script as precise as possible to make sure that the data set was as consistent as possible.

Following this, we built a website so they could label the colonies on their images online.

In total 250 colony pictures were added to our data set, vastly increasing the performance of our AI in detecting colonies. As an incentive to participate in this collaboration we gave away prizes to the teams that sent us their pictures, they received a small surprise, an E. coli plushie. The three teams that sent us the most pictures got an engraved trophy out of glass thanks to our sponsor of this collaboration, Doulix.

Earlier this year the iGEM headquarters announced changes in their part submission system, one of which made us extremely happy: BioBricks are now also accepted in Type IIS standard! In our opinion, this is a huge step, as cloning techniques based on Type IIS restriction enzymes are becoming more and more popular in the scientific community due to their numerous advantages over classical cloning methods.
We noticed that more teams converted to MoClo systems in their projects this year but we still think there is a lot that needs to be done for the iGEM community to really embrace this change. In order to help teams with the transition into this new system, we had an idea: What if we could help other teams understand what Type IIS enzymes really are and how they work? If we could share our passion for Modular Cloning and the value of the PhytoBrick standard? If we could introduce them to our Marburg Collection and help removing some of the burdens that come with a switch to a new cloning system?
Therefore we hosted a webinar about Golden Gate, build up a communication platform to give iGEM Teams a chance to troubleshoot their methods and made an Interlab study. Here we evaluated the consistency of Golden Gate Assembly protocols across iGEM teams as well as to give teams the opportunity to gain experience with the assembly method.

This semester we had the pleasure of mentoring UFlorida for their Wiki design. Our member, Rene Inckemann, aided UFlorida in their quest to create a visually accessible Wiki, similar to what we did this past iGEM season. We helped shape UFlorida’s website into an interactive and appealing landscape, while maintaining the integrity of their goal and project. We advised them on their font choices- specifically their use of bold and italicized words-, along with answering questions about our work with the visually disabled community and utilizing our “Accessible Wiki Guide” from the previous year.
Besides answering questions specifically about their project, we also offered valuable information about when to start working on the Wiki and questions about coding. Working with a young team like UFlorida offered us a great mentorship opportunity.

Mike the microbe

We participated in the “Mike the microbe” collaboration of the iGEM Team US AFRL CarrollHS. They sent us their virtual mascots Mike the Microbe and Chia the Chitinase so we could take pictures with them to connect all iGEM teams around the world via social media. It brought us great joy to join to this collaboration and let the two little buddies visit our daily life in our incubators for cyanobacteria.

Postcards Düsseldorf

iGEM Düsseldorf called for their traditional collaboration project, a long year postcard campaign with the purpose to educate and to show the public about the different topics and projects in Synthetic Biology and especially regarding all the iGEM projects. With interesting designs and a short project abstract iGEM teams could spread their ideas using the postcards to share their thinking to each other and the society. Our title and postcard design was about our photosynthetic project „Syntex“. You can see Synechococcus elongatus UTEX 2973 direly needing a refreshing drink, a cute little draft from our team member Jonas.

iGEMxSDGs challenge

IGEM Costa Rica, Tuebingen, and TAS Taipei created an iGEMxSDGs challenge as collaboration. They asked us to choose four of the Sustainable Development Goals (SDGs) proposed by the United Nations (UN). We joined this collaboration challenge and spread it on our social media account. We decided on the following goals:

Who wore it best? #labcoatchallenge

The Stony Brook iGEM Team challenged us to design an outfit for a runway from a standard lab coat. The outfit had to be created by tying, not using duct tape, cut or sew, etc. After designing our outfits four of our members presented their style on our ‘runway’ while paparazzi took their photos. As an outfit we chose a dress highlighting the neckline, a shoulder free dress, a knotted dress and a skirt to bring glamour to the daily routine in the labs. Especially our guys were rocking their outfits as you can see here x

iGEM Spring Festival in Bonn

From 3rd – 5th Mai we met our iGEM colleagues for the Spring Festival in Bonn. Professors of the university of Bonn presented their research fields which gained huge interest. We heard lectures of immunology and neurosciences, as well as reviving mammoths. During the lectures, specific topics were deepened in small seminar groups, such as the ethical tenability of CRISPR applied at humans and other animals. At the poster sessions we got the first time in contact with the other teams’ projects. Afterwards we had the opportunity to vote for the best project, which iGEM Düsseldorf won. Besides that, the meetup was filled with a lot of awarding categories. We competed in the categories for “Best Video”, “Best Poster”, “Best Project” and a single person had the chance to win the award for “Best Meme”. The iGEM Team Bonn offered spontaneously a little football table tournament, where two of our team members won. In the evening we learnt a lot about Bonn as a city from a guide living there for ages. Afterwards, the iGEM Teams met in several groups in restaurants and bars. We merged with iGEM Kaiserslautern and exchanged our projects and ideas for the rest of the evening.
On the second day, the iGEM Team Bonn offered a competition out of three rounds, where we competed against other teams. We were asked iGEM specific questions, had to solve riddles for an escape room and finished a lab challenge afterwards. Our team could compete until the end and won the prize! Thanks again to Doulix for this awesome prize!
We particularly thank the iGEM Team Bonn for the huge effort and the great meetup!

Erlangen collaboration meetup

On the 17th – 19th of May we attended the collaboration meetup hosted by the iGEM Team Erlangen 2019. There, we met the iGEM teams of Straßbourg, Tübingen, Vienna and of course Erlangen. Apart from listening to the interesting talks from the various professors there, we made a lot of new friends and took the chance to talk about possible collaborations with the other teams and also promote our collaborations, such as the colony picking project and the Golden Gate webinar (evtl. verlinken). We would like to thank iGEM Team Erlangen very much for organizing this wonderful meetup and are happy to see them soon in Boston.

Düsseldorf meetup
From 5th – 7th July we went to the HHU for the German meetup. The calendar offered lots of lectures with interesting topics such as the Excellent Cluster of Prof. Andreas Weber “CEPLAS” but also non-scientific aspects like how to do presentations. We tried to visit all of them while presenting our poster in the hall. There we got in touch with other iGEM Teams also learnt about their projects. We promoted our Webinar project and laid the foundation stone for future collaborations. On the second day, iGEM Düsseldorf organized a panel discussion about the issues concerning green genetic engineering. Thereby, we got great input on how to structure our panel discussion and which subjects should be mentioned. Beside the regular program organized by iGEM Düsseldorf we used a lot of chances to get in contact with other teams. After the presentations a couple of tourist guides showed us the beautiful old town of Düsseldorf and explained some interesting historical facts. Afterwards we had again the possibility to meet with other iGEMers in a pub and talk about the projects, especially to find weaknesses or opportunities for collaborations. This really went successfully due to the time we spend with iGEM Team Aachen and Kaiserslautern. The iGEM Team Düsseldorf also arranged a game contest between the teams, where we lost in the final to our good friends from Potsdam. Congrats!

Thanks again to iGEM Düsseldorf for the huge effort and the great meetup!

Vilnius, Lithuania – Biohackathon Lab App 2019
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 UCopenhagen, 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 starting to work more 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,was included in the protocols. In our heads the idea to have a user-friendly GUI grew more and more and soon we found 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 provided us with 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!