Difference between revisions of "Team:Marburg/Collaborations"
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<h2 class="subtitle">The Colony picture Collaboration</h2> | <h2 class="subtitle">The Colony picture Collaboration</h2> | ||
<div style="display: flex; flex-direction: row;"> | <div style="display: flex; flex-direction: row;"> | ||
| − | <figure Style=" | + | <figure Style="margin-right: 25px;"> |
| − | <img | + | <img src=https://static.igem.org/mediawiki/2019/5/5e/T--marburg--colony_picking_2.jpeg |
| − | + | ||
alt="Bild von Roboter Platzhalter"> | alt="Bild von Roboter Platzhalter"> | ||
<figcaption> | <figcaption> | ||
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<p style="margin-bottom: 25px;"> | <p style="margin-bottom: 25px;"> | ||
Many repetitive tasks in the lab cost time such as pipetting or picking colonies from agar plates | Many repetitive tasks in the lab cost time such as pipetting or picking colonies from agar plates | ||
| − | and | + | 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 | |
| − | hardware | + | user community an automated pipeline to streamline laboratory practices in ways that haven’t been |
| − | + | possible before. | |
| − | community | + | |
| − | + | ||
| − | before. | + | |
</p> | </p> | ||
<p> | <p> | ||
For the software we decided to use an artificial intelligence (AI). Artificial intelligences | For the software we decided to use an artificial intelligence (AI). Artificial intelligences | ||
| − | however | + | 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 | |
| − | of | + | 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. | |
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
</p> | </p> | ||
</div> | </div> | ||
</div> | </div> | ||
| − | < | + | <div style="display: flex; flex-direction: row;"> |
| − | < | + | <p> |
| − | src="https://static.igem.org/mediawiki/2019/f/f8/T--marburg--taking_colony_pictures.png" | + | Following this, we built a website so they could label the colonies on their images online. |
| − | + | </p> | |
| − | + | <figure> | |
| − | + | <img src="https://static.igem.org/mediawiki/2019/f/f8/T--marburg--taking_colony_pictures.png" | |
| − | + | alt="Pattern for taking the colony picture"> | |
| − | + | <figcaption> | |
| − | + | Figure 2: Pattern for taking the colony picture. | |
| − | + | </figcaption> | |
| − | </ | + | </figure> |
| + | </div> | ||
<figure Style="text-align:center"> | <figure Style="text-align:center"> | ||
<img style="height: 50ex; width: 80ex" | <img style="height: 50ex; width: 80ex" | ||
Revision as of 20:14, 21 October 2019
C O L L A B O R A T I O N S
Through this iGEM year we interacted with so many iGEM Teams all around the world. It was a pleasure working with all the different teams and learn from each other. We got so many impressions about other projects and hope we could help with our collaborations. A huge Thank you for every team collaboration!
C O L O N Y
P I C T U R E S
In our colony picking collaboration we asked other iGEM teams to supply us with data for our picking algorithm. Thanks to this group effort we could build our colony picking unit.
Colony Pictures
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.
T H EG O L D E NG A T E
C O L L A B O R A T I O N
The Golden Gate collaboration
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.
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
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
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
B E R L I N / D E L F T
Berlin/Delft Collaborations
Click here to learn more about there project Chlamylicious
iGEM Delft created an all species encompassing toolbox, based on orthogonal gene
expression and
host
independent plasmid replication. We exchanged multiple times over Molecular
Cloning and toolbox
designs.
Additionally, we sent them parts in the PhytoBricks standard.
Click here to learn more about there project
project SCI-PHI 29
U CD A V I S
UC Davis collaboration
In total, seven teams participated and sent their data to UC Davis which are
shown in the
figure below.
According to UC
Davis, the fluorescence data was standardized using the iGEM MEFL conversion to
standardize
the plate reader
measurements. Subsequently, the data was fitted using a linear regression model,
whose
quality is quantified
using the
r2 metric (it ranges from 0 to 1 with higher value indicates a better fit).
For the fluorescence the r2 value from the OT2 data beats human r2 value with
0.94 and 0.90,
respectively.
Interestingly, for the silica beads, manual measurements yielded a more
satisfactory result
with r2 value of
0.90
compared to 0.82 from OT2 measurements. One possible explanation could be the
speed of the
OT-2: it took
twice as long
to complete this task with the OT-2 compared to a manual trial. This could lead
to the
sedimentation of the
silica beads
as the OT-2 went through their runs; therefore worsening its results. Also, as
shown in Fig.
2b, one team’s
result
deviates a lot from the rest of the teams, maybe if their result is taken from
the overall
evaluation a more
comparable
result between OT-2 and human can be observed.
Figure 1: a)OT-2 vs manual fluorescein measurement experiment. OT-2
performed better
with r2 value of 0.94 compared to 0.90 of human. b)OT-2 vs manual silica
beads measurement experiment. Human performed better
with r2 value of 0.90 compared to 0.82 of OT-2.
More information about this collaboration such as individual team data can be found on UC Davis wiki: Wiki UC Davis Collaboration
U F L O R I D A
UFlorida
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.
I N T E R A C T I O N S
W I T H
O T H E RT E A M S
Interactions with other teams
Mike the microbe
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
M E E T U P S
Meet ups
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.
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!
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!