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 ictures. 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.

Webinar - Educating about Golden Gate cloning

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We wanted to reach as many teams as possible with our webinar on Golden Gate cloning, Type IIS enzymes, their benefits and how to use all of this in their own projects. We started planning everything that we thought should be in the webinar, from the biological function of the Type IIS enzymes and how they differ from Type II enzymes, over its applications in Synthetic Biology like modular cloning to the in-depth strategies when designing your own parts and actually building them in the lab.
During this planning step we realized, that some of the teams that are already working with Golden Gate might not benefit as much from an entry level webinar. Consequently, we thought about integrating more complex design questions that we could share with the community. We finished our webinars with a practical part, showing the part-design in Geneious Prime – the sequence analysis software we used throughout the year. Firstly, we explained the different levels that can be built with Golden Gate and then introduced some more complex designs that are also possible with Golden Gate cloning, such as the construction of whole operons or space holder parts. Through this we hoped to also reach teams that use Golden Gate themselves, showing them the possibilities this cloning system offers.
To reach as many teams on the globe as possible we set up webinars on three different times to cover as many time zones within a comfortable time frame – hoping that this will allow more iGEM teams to participate. The one and a half hour webinars were held on July 30th 10am CET, July 31st 6pm CET and the last time on 8th August 12pm CET by our instructor René Inckemann with the support of three of our team members. We were happy that in total 18 teams participated, as well as some students from the universities of Marburg and Gießen and even a few fellow scientists from the Max-Planck-Institute for terrestrial microbiology. In total we counted around 70 participants. We were also really happy to see Sota Hirano from Doulix on our webinar, who gave us some awesome feedback, stating that he did learn new things about Golden Gate which he was not aware of before! We thank all the following teams for participating in this awesome event:

Team Aachen
Team Athens
Team Amazonas-Brazil
Team CMU-Q
Team ITESO
Team Soundbio
Team UFPR-Curitiba Brazil
Team Delft
Team BOKU-Viena
Team Düsseldorf
Team IlSc-BAngalore
Team Kaiserslautern
Team Leiden
Team Macau
Team Macau
FAU-Tartz-TUIT
Team FAU-Erlangen
Team Quens-Canada

If you would like to learn about Golden Gate assembly please feel free to watch our webinar through this Link:
Webinar 30.07.2019
Webinar 31.07.2019
Webinar 09.08.2019

Slack Channel and gDrive - Global networking in the Golden Gate community

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Although we were quite pleased with the result of our webinar, we thought about how to further connect this Golden Gate community, so we created a Slack workspace for everyone that is working with this method, enabling us all to exchange protocols and ideas or troubleshoot issues that might arise. So far there are close to 50 members, but we hope to find more enthusiasts willing to share their knowledge!
All files used for the webinar are openly available. You can find our protocols, handouts, slides as well as the files we used for the practical part in Geneious to construct parts in-silico in our shared Google Drive. Through this we hope to make it easier for other teams willing to start with Golden Gate cloning, as they can start designing their first own in-silico parts with our guidance.

The main documents of the Golgen Gate Webinar
→ Download: Golden Gate webinar slide 2019
→ Download:Handout Golden Gate webinar
→ Download:Golden Gate protocoll

To try out the described in-silico cloning you can download the needed sequences as geneious file here.
→ Download:Sequences Webinar

Slack Channel and gDrive - Global networking in the Golden Gate community

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Interlab - Accelerate Golden Gate Assembly

Interlab - Accelerate Golden Gate Assembly As we are constantly working on improving the efficiency of Golden Gate. We clearly saw the main bottleneck of the reaction was the long assembly time in the cycler. In the webinar and in ourGolden Gate community weprovided protocols with three different cycler settings for different applications. Although these threeprotocols were tested before, they were never compared to each other in their efficiency.
We conducted our own Interlab study in collaboration with the iGEM Teams from TUDelft , HUmboldt Berlin and TU Kaiserslautern In order to find the best protocol, we supplied the teams with specific Level 0 parts,that should be assembled to a Level 1 vector using the three different cycler conditions. The provided parts areshown in this table:

5' Connector	BBa_K2560075 /
Promoter	J23119 BBa_K2560031
RBS	B0034 BBa_K2560008
CDS	sfGFP BBa_K2560042
Terminator	B0015 BBa_K2560035
3' Connector	BBa_K2560080
ORI:	ColE1 BBa_K2560036
Antibiotic-Resistance-Cassette	Kan-RFP BBa_K2560056

The Golden Gate reactions should be pipetted together using the given parts and then betransformed in E. coliand be plated with similar amounts on agar plates. A colony with a correct assembled vector would have afunctioning Transcription Unit which expresses GFP, which can be clearly distinguished from RFP expressing colonies which only carries the antibiotic cassette and false non fluorescent colonies.
The ratio of green to non-green colonies was used to evaluate which of the three protocols yielded in the highest transformation efficiency and the highest rate of positive clones.

The handout with the used protocols can be downloaded here

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!