Difference between revisions of "Team:Marburg/Collaborations"

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         COLLABORATION <!--  Titel austauschen-->
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         C O L L A B O R A T I O N
 
       </h1>
 
       </h1>
 
       <hr class="line">
 
       <hr class="line">
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       <img src="https://static.igem.org/mediawiki/2019/a/ac/T--Marburg--logo.svg"
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       <img src="https://static.igem.org/mediawiki/2019/a/ac/T--Marburg--logo.svg" class="logo" alt="Syntex Logo">
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         <p style="text-align: justify;"> <!--  Text-->
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         <p style="text-align: justify;">
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           Through this iGEM year we interacted with so many iGEM Teams all around the world. It was a pleasure working
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                Through this iGEM year we interacted with so many iGEM Teams all around the world. It was a pleasure working with
+
          with
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              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.
+
          all the different teams and learn from each other. We got so many impressions about other projects and hope we
−
              A huge Thank you for every team collaboration !
+
          could help with our collaborations.
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          A huge Thank you for every team collaboration !
 +
 
 
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             <h1><!--  Titel von Pop up in schwarzer Box-->
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             <h1>
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               Colony<br>
+
               C O L O N Y<br>
−
            pictures
+
              P I C T U R E S
 
             </h1>
 
             </h1>
 
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                <!-- Untertitel im Popup -->           
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              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.
 
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               <h1 class="title">Colony pictures</h1> <!--  Titel im pop up-->
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               <h1 class="title">Colony Pictures</h1>
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               <section class="section">
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               <section class="section"> <!--  Inhalt Pop up start-->
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                 <h2 class="subtitle">The Colony picture Collaboration</h2>
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                 <h2> <b> The Colony picture Collaboration </b></h2>
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                <p>
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                    <p>  
+
                  <figure Style="float:left; margin-right: 25px;">
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                    <figure Style="float:left; margin-right: 25px;" >
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                    <img style="height: 65ex; width: 50ex"
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                        <img style="height: 65ex; width: 50ex"  
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                      src=https://static.igem.org/mediawiki/2019/5/5e/T--marburg--colony_picking_2.jpeg
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                        src=https://static.igem.org/mediawiki/2019/5/5e/T--marburg--colony_picking_2.jpeg alt="Bild von Roboter Platzhalter">
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                      alt="Bild von Roboter Platzhalter">
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                        <figcaption>
+
                    <figcaption>
−
                            Figure 1: Pipetting Robot (OT-2) colony picking set up.
+
                      Figure 1: Pipetting Robot (OT-2) colony picking set up.
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                        </figcaption>
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                    </figcaption>
−
                        </figure>
+
                  </figure>
−
                        Many repetitive tasks in the lab cost time such as pipetting or picking colonies from agar
+
                  Many repetitive tasks in the lab cost time such as pipetting or picking colonies from agar
−
                        plates and could
+
                  plates and could
−
                        technically be performed by robots. We used Opentrons OT-2 as a platform and designed hardware
+
                  technically be performed by robots. We used Opentrons OT-2 as a platform and designed hardware
−
                        modules and
+
                  modules and
−
                        scripts to outsource these tasks. Thereby, we can now offer the Opentrons user community an
+
                  scripts to outsource these tasks. Thereby, we can now offer the Opentrons user community an
−
                        automated pipeline
+
                  automated pipeline
−
                        to streamline laboratory practices in ways that haven’t been possible before.”
+
                  to streamline laboratory practices in ways that haven’t been possible before.”
−
                   
+
 
−
                    </p>  </p>
+
                </p>
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                    <br>
+
                 </p>
−
                    <p> 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.
+
−
                    </p>
+
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                    <br> <br> <br> <br>
+
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                    <figure Style="text-align:center">
+
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                        <img style="height: 50ex; width: 75ex"
+
−
                            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>
+
−
                    <br>
+
−
                    <p> Following this, we built a website so they could label the colonies on their images online.
+
−
                    </p>
+
−
                    <br>
+
−
                    <figure Style="text-align:center">
+
−
                        <img style="height: 50ex; width: 80ex"
+
−
                            src="https://static.igem.org/mediawiki/2019/0/0b/T--marburg--collonycollab_website.png"
+
−
                            alt="colony picking website">
+
−
                        <figcaption>
+
−
                            Figure 3: Website for colony picutre labeling.
+
−
                        </figcaption>
+
−
                    </figure>
+
−
                    <br>
+
−
                    <p> 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.
+
−
                    </p>
+
−
                 </p>  
+
 
                 <br>
 
                 <br>
−
                 <br> <!-- Inhalt vom pop up, wenn nur Text dann <p>, wenn mit bilder etc extra ein <div> drum machen-->
+
                <p> For the software we decided to use an artificial intelligence (AI). Artificial intelligences
−
              </section> <!-- Inhalt Pop up start-->
+
                  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.
 +
                </p>
 +
                 <br> <br> <br> <br>
 +
                <figure Style="text-align:center">
 +
                  <img style="height: 50ex; width: 75ex"
 +
                    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>
 +
                <br>
 +
                <p> Following this, we built a website so they could label the colonies on their images online.
 +
                </p>
 +
                <br>
 +
                <figure Style="text-align:center">
 +
                  <img style="height: 50ex; width: 80ex"
 +
                    src="https://static.igem.org/mediawiki/2019/0/0b/T--marburg--collonycollab_website.png"
 +
                    alt="colony picking website">
 +
                  <figcaption>
 +
                    Figure 3: Website for colony picutre labeling.
 +
                  </figcaption>
 +
                </figure>
 +
                <br>
 +
                <p> 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.
 +
                </p>
 +
                </p>
 +
              </section>
 
             </div>
 
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             <h1>
 
             <h1>
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                    The Golden Gate <br> collaboration
+
              T H E<span style="visibility: hidden;">A</span>G O L D E N<span style="visibility: hidden;">A</span>G A T E<br>
 +
              C O L L A B O R A T I O N
 
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               <h1 class="title">The Golden Gate collaboration</h1>
 
               <h1 class="title">The Golden Gate collaboration</h1>
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              style="text-align: justify;">
+
 
               <p>
 
               <p>
−
                    Earlier this year the iGEM headquarters announced changes in their part submission system, one of
+
                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,
+
                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
+
                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
+
                and more popular in the scientific community due to their numerous advantages over classical cloning
−
                    methods.
+
                methods.
−
                    <br>
+
                <br>
−
                    We noticed that more teams converted to MoClo systems in their projects this year but we still think
+
                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
+
                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:
+
                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
+
                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
+
                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
+
                introduce them to our Marburg Collection and help removing some of the burdens that come with a
−
                    switch to a new cloning system?
+
                switch to a new cloning system?
−
                    <br>
+
                <br>
−
                    Therefore we hosted a webinar about Golden Gate, build up a communication platform to give iGEM
+
                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
+
                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
+
                consistency of Golden Gate Assembly protocols across iGEM teams as well as to give teams the
−
                    opportunity to gain experience with the assembly method.
+
                opportunity to gain experience with the assembly method.
−
                    <br>
+
                <br>
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                    <br>
+
                <br>
 
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                <label for="collapsible2_1" class="lbl-toggle">
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                                <h3 class="title">Webinar - Educating about Golden Gate cloning </h3>
+
                  <h3 class="title">Webinar - Educating about Golden Gate cloning </h3>
−
                            </label>
+
                </label>
−
                            <div class="collapsible-content">
+
                <div class="collapsible-content">
−
                                <div class="content-inner" style="text-align: justify; text-align-last: left;">
+
                  <div class="content-inner" style="text-align: justify; text-align-last: left;">
−
                                    <p>
+
                    <p>
−
                                    <br>
+
                      <br>
−
                                        <figure Style="text-align:center"><!-- dynamisches bild-->
+
                      <figure Style="text-align:center">
−
                                            <img style="height: 50ex; width: 50ex"
+
                        <!-- dynamisches bild-->
−
                                                src="https://static.igem.org/mediawiki/2019/0/01/T--marburg--Webinar_button.png" alt="Webinarbutton">
+
                        <img style="height: 50ex; width: 50ex"
 +
                          src="https://static.igem.org/mediawiki/2019/0/01/T--marburg--Webinar_button.png"
 +
                          alt="Webinarbutton">
 +
                      </figure>
 +
                      <br>
 +
                      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.
 +
                      <br>
 +
                      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.
 +
                      <br>
 +
                      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:
 +
                      <br>
 +
                      <br>
 +
                      <a href="https://2019.igem.org/Team:Aachen/collaborations">Team Aachen</a> <br>
 +
                      <a href="https://2019.igem.org/Team:Athens/Collaborations">Team Athens</a> <br>
 +
                      <a href="https://2019.igem.org/Team:Amazonas-Brazil/Collaborations">Team
 +
                        Amazonas-Brazil</a> <br>
 +
                      <a href="https://2019.igem.org/Team:CMUQ/Collaborations">Team CMU-Q</a> <br>
 +
                      <a href="https://2019.igem.org/Team:ITESO_Guadalajara/Collaborations">Team ITESO</a>
 +
                      <br>
 +
                      <a href="https://2019.igem.org/Team:SoundBio//Collaborations">Team Soundbio</a> <br>
 +
                      <a href="https://2019.igem.org/Team:UFPR-Curitiba-Brazil/Collaborations">Team
 +
                        UFPR-Curitiba Brazil</a> <br>
 +
                      <a href="https://2019.igem.org/Team:TUDelft/Collaborations">Team Delft</a> <br>
 +
                      <a href="https://2019.igem.org/Team:BOKU-Vienna/Collaborations">Team BOKU-Viena</a> <br>
 +
                      <a href="https://2019.igem.org/Team:Duesseldorf/Collaborations">Team Düsseldorf</a> <br>
 +
                      <a href="https://2019.igem.org/Team:IISc-Bangalore/Collaborations">Team IlSc-BAngalore</a>
 +
                      <br>
 +
                      <a href="https://2019.igem.org/Team:TU_Kaiserslautern/Collaborations">Team Kaiserslautern</a>
 +
                      <br>
 +
                      <a href="https://2019.igem.org/Team:Leiden/Collaborations">Team Leiden</a> <br>
 +
                      <a href="https://2019.igem.org/Team:UM_Macau/Collaborations">Team Macau</a> <br>
 +
                      <a href="https://2019.igem.org/Team:PuiChing_Macau/Collaborations">Team Macau</a> <br>
 +
                      <a href="https://2019.igem.org/Team:Tartu_TUIT/Collaboration">FAU-Tartz-TUIT</a> <br>
 +
                      <a href="(https://2019.igem.org/Team:FAU_Erlangen/Collaborations">Team FAU-Erlangen</a>
 +
                      <br>
 +
                      <a href="https://2019.igem.org/Team:Queens_Canada/Collaborations">Team Quens-Canada </a>
 +
                      <br>
 +
                      <br>
 +
                      <div>
 +
                        <figure Style="text-align:center">
 +
                          <!-- Bild solte mittig sein -->
 +
                          <img style="height:60ex; width:80ex"
 +
                            src="https://static.igem.org/mediawiki/2019/f/f1/T--marburg--Doulix_webinar.jpeg"
 +
                            alt="Bilder Webinar">
 +
                          <figcaption>
 +
                            Figure 3: Participants watching our Golden Gate webinar all over the world.
 +
                          </figcaption>
 +
                        </figure>
 +
                      </div>
 +
 
 +
                      <br>
 +
                      If you would like to learn about Golden Gate assembly please feel free to watch our
 +
                      webinar through this Link:
 +
                      <br>
 +
                      <a href="https://www.youtube.com/watch?v=-UUUG2iL7og">Webinar 30.07.2019 </a> <br>
 +
                      <a href="https://www.youtube.com/watch?v=Aq-6MlaVWww">Webinar 31.07.2019 </a> <br>
 +
                      <a href="https://www.youtube.com/watch?v=Aq-6MlaVWww">Webinar 09.08.2019 </a> <br>
 +
                    </p>
 +
                  </div>
 +
                </div>
 +
 
 +
 
 +
                <br>
 +
                <div class="wrap-collabsible">
 +
                  <input id="collapsible2_2" class="toggle" type="checkbox">
 +
                  <label for="collapsible2_2" class="lbl-toggle">
 +
                    <h3 class="title">Slack Channel and gDrive - Global networking in the Golden Gate community</h3>
 +
                  </label>
 +
                  <div class="collapsible-content">
 +
                    <div class="content-inner" style="text-align: left; text-align-last: left;">
 +
                      <div>
 +
                        <p>
 +
                          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!<br>
 +
                          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.
 +
                          <br> <br>
 +
                          The main documents of the Golgen Gate Webinar <br>
 +
                          → Download: <a
 +
                            href="https://static.igem.org/mediawiki/2019/0/0a/T--marburg--GG_webinar_slides.pdf">Golden
 +
                            Gate webinar slide 2019 </a><br>
 +
                          → Download:<a
 +
                            href="https://static.igem.org/mediawiki/2019/0/09/T--CMUQ--goldenGateWebinarHandout.pdf">Handout
 +
                            Golden Gate webinar </a> <br>
 +
                          → Download:<a
 +
                            href="https://static.igem.org/mediawiki/2019/c/c2/T--marburg--GG_protocoll_white.pdf">Golden
 +
                            Gate protocoll </a>
 +
                          <br>
 +
                          <br>
 +
                          To try out the described in-silico cloning you can download the needed sequences as
 +
                          geneious file here. <br>
 +
                          → Download:<a href="https://2019.igem.org/File:T--marburg--Sequences_Webinar.zip">Sequences
 +
                            Webinar </a> <br>
 +
                        </p>
 +
                      </div>
 +
                    </div>
 +
                  </div>
 +
                </div>
 +
                <!--hier interlab hin-->
 +
                <div class="wrap-collabsible">
 +
                  <input id="collapsible2_3" class="toggle" type="checkbox">
 +
                  <label for="collapsible2_3" class="lbl-toggle">
 +
                    <h3 class="title">Slack Channel and gDrive - Global networking in the Golden Gate community</h3>
 +
                  </label>
 +
                  <div class="collapsible-content">
 +
                    <div class="content-inner" style="text-align: left; ">
 +
                      <div>
 +
                        <p>
 +
                          <h4>Interlab - Accelerate Golden Gate Assembly</h4>
 +
                          <p>
 +
                            <figure Style="float:left; margin-left: 25px;">
 +
                              <img style="height: 50ex; width: 40ex"
 +
                                src="  https://static.igem.org/mediawiki/2019/7/79/T--marburg--interlab_button.svg"
 +
                                alt="Interlab button">
 +
                            </figure>
 +
                            <br> <br>
 +
                            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.<br>
 +
                            We conducted our own Interlab study in collaboration with the iGEM Teams from
 +
                            <a href="https://2019.igem.org/Team:TUDelft"> TUDelft </a>,
 +
                            <a href="https://2019.igem.org/Team:Humboldt_Berlin"> HUmboldt Berlin </a> and
 +
                            <a href="https://2019.igem.org/Team:TU_Kaiserslautern"> TU Kaiserslautern </a>
 +
                            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:
 +
                            <br> <br> <!-- Tabelle Links noch rein -->
 +
                            <table>
 +
                              <tbody>
 +
                                <tr>
 +
                                  <td style="text-align: center">5' Connector </td>
 +
                                  <td style="text-align: center"> <a href="link 1"> BBa_K2560075 </a>/
 +
                                </tr>
 +
                                <tr>
 +
                                  <td style="text-align: center">Promoter </td>
 +
                                  <td style="text-align: center"> <a href="link 2"> J23119 BBa_K2560031 </a>
 +
                                </tr>
 +
                                <tr>
 +
                                  <td style="text-align: center">RBS </td>
 +
                                  <td style="text-align: center"> <a href="link 2"> B0034 BBa_K2560008 </a>
 +
                                </tr>
 +
                                <tr>
 +
                                  <td style="text-align: center">CDS </td>
 +
                                  <td style="text-align: center"> <a href="link 3"> sfGFP BBa_K2560042 </a>
 +
                                </tr>
 +
                                <tr>
 +
                                  <td style="text-align: center">Terminator </td>
 +
                                  <td style="text-align: center"> <a href="link 4"> B0015 BBa_K2560035 </a>
 +
                                </tr>
 +
                                <tr>
 +
                                  <td style="text-align: center">3' Connector </td>
 +
                                  <td style="text-align: center"> <a href="link 5"> BBa_K2560080 </a>
 +
                                </tr>
 +
                                <tr>
 +
                                  <td style="text-align: center">ORI: </td>
 +
                                  <td style="text-align: center"> <a href="link 6"> ColE1 BBa_K2560036 </a>
 +
                                </tr>
 +
                                <tr>
 +
                                  <td style="text-align: center">Antibiotic-Resistance-Cassette</td>
 +
                                  <td style="text-align: center"> <a href="link 7"> Kan-RFP BBa_K2560056 </a>
 +
                                </tr>
 +
 
 +
                              </tbody>
 +
                            </table>
 +
                            <br> <!-- Tabelle -->
 +
                            <br> <br> <br>
 +
                            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. <br>
 +
                            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.
 +
                            <br> <br>
 +
                            <figure Style="text-align:center">
 +
                              <img style="height: 60ex; width:80ex"
 +
                                src="https://static.igem.org/mediawiki/2019/9/91/T--marburg--interlab_package.jpeg"
 +
                                alt="Interlab oackage">
 +
                              <figcaption>
 +
                                Fig 1: Interlab package.
 +
                              </figcaption>
 +
                            </figure>
 +
                            <br>
 +
                            <br>
 +
                            The handout with the used protocols can be downloaded <a
 +
                              href=https://static.igem.org/mediawiki/2019/a/a0/T--marburg--Interlab_protocoll.pdf> here </a>
 +
                              </p> </p> </div> </div> </div> </div> </div> </div> </div> </div> <!--popup3-->
 +
                              <div class="sub" onclick="popup('rbn3')">
 +
                                <div class="sub-header">
 +
                                  <h1>
 +
                                    Berlin/Delft
 +
                                  </h1>
 +
                                  <hr>
 +
                                </div>
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                                <div class="sub-content">
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                                  <p>
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                                  </p>
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                                </div>
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                              </div>
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                              <div id="rbn3" class="popup">
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                                <div class="popup-container">
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                                  <div class="popup-header">
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                                    <h1 class="title">Berlin/Delft Collaborations</h1>
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                                    <button type="button" onclick="hide('rbn3')">X</button>
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                                  </div>
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                                      <p>
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                                        <figure Style="float:right; margin-left: 25px;">
 +
                                          <img style="height: 15ex; width: 35ex"
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                                            src="  https://static.igem.org/mediawiki/2019/9/9b/T--marburg--berlin_logo_richtig.png"
 +
                                            alt="Berlin logo">
 
                                         </figure>
 
                                         </figure>
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                                        iGEM Berlin engineered the freshwater algae Chlamydomonas reinhardtii to degrade
 +
                                        Polyethylene
 +
                                        terephthalate
 +
                                        (PET). For this goal they also built a bioreactor for their chassis. We sent
 +
                                        them our UTEX
 +
                                        strain to test if
 +
                                        their photobioreactor is capable to cultivate other phototrophic organisms as
 +
                                        well. They gained
 +
                                        additional
 +
                                        experiences on growth conditions for phototrophic organisms and we could see our
 +
                                        strains grow in
 +
                                        a
 +
                                        bioreactor environment.
 
                                         <br>
 
                                         <br>
−
                                         We wanted to reach as many teams as possible with our webinar on Golden Gate cloning,
+
                                         Click here to learn more about there project <a
−
                                        Type IIS enzymes, their benefits and how to use all of this in their own projects. We
+
                                          href="https://2019.igem.org/Team:Humboldt_Berlin"> Chlamylicious </a>
−
                                        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.
+
 
                                         <br>
 
                                         <br>
−
                                        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.
 
 
                                         <br>
 
                                         <br>
−
                                         To reach as many teams on the globe as possible we set up webinars on three different
+
                                         <br> <br> <br>
−
                                         times to cover as many time zones within a comfortable time frame – hoping that this
+
                                         <h> <b>Delft Collaborations </b></h> <!-- Delf-->
−
                                         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
+
                                         <figure Style="float:left; margin-right: 25px;">
−
                                         of three of our team members.
+
                                          <img style="height: 60 ex; width: 40ex"
−
                                        We were happy that in total 18 teams participated, as well as some students from the
+
                                            src="https://static.igem.org/mediawiki/2019/5/5e/T--marburg--Skype_DELF.jpeg"
−
                                         universities of Marburg and Gießen and even a few fellow scientists from the
+
                                            alt=" DELFT Bild">
−
                                        Max-Planck-Institute for terrestrial microbiology. In total we counted around 70
+
                                          <figcaption> Fig. 1: Skype talk with TU Delft</figcaption>
−
                                        participants. We were also really happy to see Sota Hirano from Doulix on our webinar,
+
                                         </figure>
−
                                        who gave us some awesome feedback, stating that he did learn new things about Golden
+
 
−
                                         Gate which he was not aware of before!
+
                                         <figure Style="float:right; margin-left: 25px;">
−
                                        We thank all the following teams for participating in this awesome event:
+
                                          <img style="height: 30ex; width: 30ex"
 +
                                            src="https://static.igem.org/mediawiki/2019/d/d4/T--marburg--DELF_logo_richtig.svg"
 +
                                            alt="DELF logo">
 +
 
 +
                                         </figure>
 
                                         <br>
 
                                         <br>
 +
                                        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 <a
 +
                                          href="https://2019.igem.org/Team:TUDelft">
 +
                                          project SCI-PHI 29 </a>
 +
 
                                         <br>
 
                                         <br>
−
                                        <a href="https://2019.igem.org/Team:Aachen/collaborations">Team Aachen</a> <br>
+
                                      </p>
−
                                        <a href="https://2019.igem.org/Team:Athens/Collaborations">Team Athens</a> <br>
+
                                    </div>
−
                                        <a href="https://2019.igem.org/Team:Amazonas-Brazil/Collaborations">Team
+
                                    <br>
−
                                            Amazonas-Brazil</a> <br>
+
                                    <br>
−
                                        <a href="https://2019.igem.org/Team:CMUQ/Collaborations">Team CMU-Q</a> <br>
+
                                    <br>
−
                                         <a href="https://2019.igem.org/Team:ITESO_Guadalajara/Collaborations">Team ITESO</a>
+
                                  </div>
 +
                                </div>
 +
                              </div>
 +
                              <div class="sub" onclick="popup('rbn4')">
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                                <!--UC Davis pop up-->
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                                <div class="sub-header">
 +
                                  <h1>
 +
                                    UC DAVIS
 +
                                  </h1>
 +
                                  <hr>
 +
                                </div>
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                                <div class="sub-content">
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                                  <p>
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                                  </p>
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                              </div>
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                              <div id="rbn4" class="popup">
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                                  <div class="popup-header">
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                                    <h1 class="title">UC Davis collaboration</h1>
 +
                                    <button type="button" onclick="hide('rbn4')">X</button>
 +
                                  </div>
 +
                                  <div class="popup-content">
 +
                                    <div>
 +
                                      <p>
 +
                                         <figure Style="float:left; margin-right: 25px;">
 +
                                          <img style="height: 50ex; width: 40ex"
 +
                                            src="https://static.igem.org/mediawiki/2019/4/49/T--marburg--UCD_OT2.jpeg"
 +
                                            alt="UCD OT2">
 +
                                        </figure>
 +
                                        UC Davis iGEM team is one of the winners of the Opentrons competition in 2019.
 +
                                        iGEM Marburg
 +
                                        won one OT-2
 +
                                        during last
 +
                                        year’s edition of the competition and got contacted for a collaboration by iGEM
 +
                                        UC Davis
 +
                                        along with other
 +
                                        winners from
 +
                                        2018 and 2019.
 +
                                        The goal for this automation InterLab collaboration was to collect data to
 +
                                        determine the
 +
                                        accuracy and
 +
                                        reproducibility of
 +
                                        the OT-2 compared to humans. To do this, UC Davis proposed to perform the
 +
                                        standard iGEM
 +
                                        protocol on serial
 +
                                        dilutions
 +
                                        with silica beads and fluorescein, each manually and with an OT-2. In total iGEM
 +
                                        Marburg did
 +
                                        four dilutions;
 +
                                        twice with
 +
                                        an OT-2 and twice manually. The data was then sent to UC Davis via the
 +
                                        spreadsheet designed
 +
                                        by them.
 +
                                        Finally, iGEM
 +
                                        Marburg aided by creating a Slack channel for all iGEM teams with an OT-2 to
 +
                                        facilitate
 +
                                        better communication
 +
                                        and
 +
                                        exchange in the future.
 +
                                        <br><br>
 +
                                        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).
 
                                         <br>
 
                                         <br>
−
                                         <a href="https://2019.igem.org/Team:SoundBio//Collaborations">Team Soundbio</a> <br>
+
                                         For the fluorescence the r2 value from the OT2 data beats human r2 value with
−
                                         <a href="https://2019.igem.org/Team:UFPR-Curitiba-Brazil/Collaborations">Team
+
                                        0.94 and 0.90,
−
                                            UFPR-Curitiba Brazil</a> <br>
+
                                         respectively.
−
                                         <a href="https://2019.igem.org/Team:TUDelft/Collaborations">Team Delft</a> <br>
+
                                        Interestingly, for the silica beads, manual measurements yielded a more
−
                                         <a href="https://2019.igem.org/Team:BOKU-Vienna/Collaborations">Team BOKU-Viena</a> <br>
+
                                         satisfactory result
−
                                         <a href="https://2019.igem.org/Team:Duesseldorf/Collaborations">Team Düsseldorf</a> <br>
+
                                        with r2 value of
−
                                         <a href="https://2019.igem.org/Team:IISc-Bangalore/Collaborations">Team IlSc-BAngalore</a>
+
                                        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.
 
                                         <br>
 
                                         <br>
−
                                        <a href="https://2019.igem.org/Team:TU_Kaiserslautern/Collaborations">Team Kaiserslautern</a>
 
 
                                         <br>
 
                                         <br>
−
                                         <a href="https://2019.igem.org/Team:Leiden/Collaborations">Team Leiden</a> <br>
+
                                         <figure Style="text-align:center">
−
                                        <a href="https://2019.igem.org/Team:UM_Macau/Collaborations">Team Macau</a> <br>
+
                                          <img style="height: 50ex; width: 50ex"
−
                                        <a href="https://2019.igem.org/Team:PuiChing_Macau/Collaborations">Team Macau</a> <br>
+
                                            src="https://static.igem.org/mediawiki/2019/c/cc/T--marburg--UC_Davis_Graphic_1.png"
−
                                        <a href="https://2019.igem.org/Team:Tartu_TUIT/Collaboration">FAU-Tartz-TUIT</a> <br>
+
                                            alt=" UCD Graphic 1">
−
                                        <a href="(https://2019.igem.org/Team:FAU_Erlangen/Collaborations">Team FAU-Erlangen</a>
+
                                          <img style="height: 50ex; width: 50ex"
−
                                        <br>
+
                                            src=" https://static.igem.org/mediawiki/2019/a/a7/T--marburg--UC_Davis_Graphic_2.png"
−
                                        <a href="https://2019.igem.org/Team:Queens_Canada/Collaborations">Team Quens-Canada </a>
+
                                            alt=" UC Davis Graphic 2">
−
                                        <br>
+
                                          <figcaption1>
−
                                        <br>
+
                                            <br> Figure 1: a)OT-2 vs manual fluorescein measurement experiment. OT-2
−
                                        <div>
+
                                            performed better
−
                                        <figure Style="text-align:center"> <!-- Bild solte mittig sein -->
+
                                            with r2 value of 0.94 compared to 0.90 of human. b)OT-2 vs manual silica
−
                                            <img style="height:60ex; width:80ex"
+
                                            beads measurement experiment. Human performed better
−
                                                src="https://static.igem.org/mediawiki/2019/f/f1/T--marburg--Doulix_webinar.jpeg"
+
                                            with r2 value of 0.90 compared to 0.82 of OT-2.
−
                                                alt="Bilder Webinar">
+
−
                                            <figcaption>
+
−
                                                Figure 3: Participants watching our Golden Gate webinar all over the world.
+
 
                                             </figcaption>
 
                                             </figcaption>
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                                         </figure>  
+
                                         </figure>
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                                    </div>
+
−
                                     
+
 
                                         <br>
 
                                         <br>
−
                                        If you would like to learn about Golden Gate assembly please feel free to watch our
+
                                      </p>
−
                                        webinar through this Link:
+
                                      <br>More information about this collaboration such as individual team data can be
−
                                        <br>
+
                                      found on UC
−
                                        <a href="https://www.youtube.com/watch?v=-UUUG2iL7og">Webinar 30.07.2019 </a> <br>
+
                                      Davis wiki:
−
                                        <a href="https://www.youtube.com/watch?v=Aq-6MlaVWww">Webinar 31.07.2019 </a> <br>
+
                                      <a href="https://2019.igem.org/Team:UC_Davis/Collaborations"> Wiki UC Davis
−
                                        <a href="https://www.youtube.com/watch?v=Aq-6MlaVWww">Webinar 09.08.2019 </a> <br>
+
                                         Collaboration </a>
−
                                    </p></div>
+
                                      <br>
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                            </div>
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                          </p>
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              <br>
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              <div class="wrap-collabsible">
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                <input id="collapsible2_2"
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                  class="toggle"
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                  type="checkbox">
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                <label for="collapsible2_2"
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                  class="lbl-toggle">
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                  <h3 class="title">Slack Channel and gDrive - Global networking in the Golden Gate community</h3>
+
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                </label>
+
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                <div class="collapsible-content">
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                  <div class="content-inner"
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                    style="text-align: left; text-align-last: left;">
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                    <div><p>
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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!<br>
+
−
                            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.
+
−
                            <br> <br>
+
−
                            The main documents of the Golgen Gate Webinar <br>
+
−
                            → Download: <a
+
−
                                href="https://static.igem.org/mediawiki/2019/0/0a/T--marburg--GG_webinar_slides.pdf">Golden
+
−
                                Gate webinar slide 2019 </a><br>
+
−
                            → Download:<a
+
−
                                href="https://static.igem.org/mediawiki/2019/0/09/T--CMUQ--goldenGateWebinarHandout.pdf">Handout
+
−
                                Golden Gate webinar </a> <br>
+
−
                            → Download:<a
+
−
                                href="https://static.igem.org/mediawiki/2019/c/c2/T--marburg--GG_protocoll_white.pdf">Golden
+
−
                                Gate protocoll </a>
+
−
                                <br>
+
−
                                <br>
+
−
                            To try out the described in-silico cloning you can download the needed sequences as
+
−
                            geneious file here. <br>
+
−
                            → Download:<a
+
−
                                href="https://2019.igem.org/File:T--marburg--Sequences_Webinar.zip">Sequences
+
−
                                Webinar </a> <br>
+
−
                  </p></div>
+
−
                  </div>
+
−
                </div>
+
−
              </div>
+
−
              <!--hier interlab hin-->
+
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              <div class="wrap-collabsible">
+
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                    <input id="collapsible2_3"
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                      class="toggle"
+
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                      type="checkbox">
+
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+
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                      class="lbl-toggle">
+
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                      <h3 class="title">Slack Channel and gDrive - Global networking in the Golden Gate community</h3>
+
−
                    </label>
+
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                    <div class="collapsible-content">
+
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                      <div class="content-inner"
+
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                        style="text-align: left; ">
+
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                        <div><p>
+
−
                                <h4>Interlab - Accelerate Golden Gate Assembly</h4>
+
−
                                <p>
+
−
                                    <figure Style="float:left; margin-left: 25px;">
+
−
                                        <img style="height: 50ex; width: 40ex" src="  https://static.igem.org/mediawiki/2019/7/79/T--marburg--interlab_button.svg"
+
−
                                            alt="Interlab button">
+
−
                                    </figure>
+
−
                                    <br> <br>
+
−
                                    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.<br>
+
−
                                    We conducted our own Interlab study in collaboration with the iGEM Teams from
+
−
                                    <a href="https://2019.igem.org/Team:TUDelft"> TUDelft </a>,
+
−
                                    <a href="https://2019.igem.org/Team:Humboldt_Berlin"> HUmboldt Berlin </a> and
+
−
                                    <a href="https://2019.igem.org/Team:TU_Kaiserslautern"> TU Kaiserslautern </a>
+
−
                                    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:
+
−
                                    <br> <br> <!-- Tabelle Links noch rein -->
+
−
                                    <table>
+
−
                                            <tbody>
+
−
                                                <tr>
+
−
                                                    <td style="text-align: center">5' Connector </td>
+
−
                                                    <td style="text-align: center"> <a href="link 1"> BBa_K2560075 </a>/
+
−
                                                </tr>
+
−
                                                <tr>
+
−
                                                        <td style="text-align: center">Promoter </td>
+
−
                                                        <td style="text-align: center"> <a href="link 2">  J23119 BBa_K2560031 </a>
+
−
                                                </tr>
+
−
                                                <tr>
+
−
                                                        <td style="text-align: center">RBS </td>
+
−
                                                        <td style="text-align: center"> <a href="link 2">  B0034 BBa_K2560008 </a>
+
−
                                                </tr>
+
−
                                                <tr>
+
−
                                                        <td style="text-align: center">CDS </td>
+
−
                                                        <td style="text-align: center"> <a href="link 3"> sfGFP BBa_K2560042  </a>
+
−
                                                </tr>
+
−
                                                <tr>
+
−
                                                        <td style="text-align: center">Terminator </td>
+
−
                                                        <td style="text-align: center"> <a href="link 4"> B0015 BBa_K2560035  </a>
+
−
                                                </tr>
+
−
                                                <tr>
+
−
                                                        <td style="text-align: center">3' Connector </td>
+
−
                                                        <td style="text-align: center"> <a href="link 5">  BBa_K2560080 </a>
+
−
                                                </tr>
+
−
                                                <tr>
+
−
                                                        <td style="text-align: center">ORI: </td>
+
−
                                                        <td style="text-align: center"> <a href="link 6"> ColE1 BBa_K2560036  </a>
+
−
                                                </tr>
+
−
                                                <tr>
+
−
                                                        <td style="text-align: center">Antibiotic-Resistance-Cassette</td>
+
−
                                                        <td style="text-align: center"> <a href="link 7">  Kan-RFP BBa_K2560056  </a>
+
−
                                                </tr>
+
−
                                               
+
−
                                            </tbody>
+
−
                                         </table>
+
−
                                    <br> <!-- Tabelle -->
+
−
                                    <br> <br>  <br>
+
−
                                    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. <br>
+
−
                                    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.
+
−
                                    <br> <br>
+
−
                                    <figure Style="text-align:center">
+
−
                                        <img style="height: 60ex; width:80ex"
+
−
                                            src="https://static.igem.org/mediawiki/2019/9/91/T--marburg--interlab_package.jpeg"
+
−
                                            alt="Interlab oackage">
+
−
                                        <figcaption>
+
−
                                            Fig 1: Interlab package.
+
−
                                        </figcaption>
+
−
                                    </figure>
+
−
                                    <br>
+
−
                                    <br>
+
−
                                    The handout with the used protocols can be downloaded <a
+
−
                                        href=https://static.igem.org/mediawiki/2019/a/a0/T--marburg--Interlab_protocoll.pdf>
+
−
                                        here </a> </p>
+
−
                           
+
−
                      </p></div>  
+
 
                       </div>
 
                       </div>
 +
 +
                      <br>
 +
 
                     </div>
 
                     </div>
 
                   </div>
 
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                </div>
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                <div class="sub" onclick="popup('rbn5')">
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                  <!-- UFlorida-->
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                  <div class="sub-header">
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                     <h1>
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                      UFLORIDA
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                    <hr>
 
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                     Berlin/Delft
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            </h1>
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                      <h1 class="title">UFlorida</h1>
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              <h1 class="title">Berlin/Delft Collaborations</h1>
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            </div>
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−
            <div class="popup-content"
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              style="text-align: justify;">
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              <div><p>
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                    <figure Style="float:right; margin-left: 25px;">
+
−
                            <img style="height: 15ex; width: 35ex" src="  https://static.igem.org/mediawiki/2019/9/9b/T--marburg--berlin_logo_richtig.png"
+
−
                                alt="Berlin logo">
+
−
                        </figure>
+
−
                    iGEM Berlin engineered the freshwater algae Chlamydomonas reinhardtii to degrade Polyethylene
+
−
                    terephthalate
+
−
                    (PET). For this goal they also built a bioreactor for their chassis. We sent them our UTEX
+
−
                    strain to test if
+
−
                    their photobioreactor is capable to cultivate other phototrophic organisms as well. They gained
+
−
                    additional
+
−
                    experiences on growth conditions for phototrophic organisms and we could see our strains grow in
+
−
                    a
+
−
                    bioreactor environment.
+
−
                    <br>
+
−
                    Click here to learn more about there project <a
+
−
                        href="https://2019.igem.org/Team:Humboldt_Berlin"> Chlamylicious </a>
+
−
                    <br>
+
−
                    <br>
+
−
                  <br> <br> <br>
+
−
                    <h> <b>Delft Collaborations </b></h> <!-- Delf-->
+
−
                 
+
−
                 
+
−
                  <figure Style="float:left; margin-right: 25px;" >
+
−
                        <img style="height: 60 ex; width: 40ex"src="https://static.igem.org/mediawiki/2019/5/5e/T--marburg--Skype_DELF.jpeg" alt=" DELFT Bild">
+
−
                    <figcaption> Fig. 1: Skype talk with TU Delft</figcaption>
+
−
                    </figure>
+
−
                     
+
−
                    <figure Style="float:right; margin-left: 25px;">
+
−
                            <img style="height: 30ex; width: 30ex" src="https://static.igem.org/mediawiki/2019/d/d4/T--marburg--DELF_logo_richtig.svg"
+
−
                                alt="DELF logo">
+
−
                           
+
−
                        </figure>
+
−
                    <br>
+
−
                    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 <a href="https://2019.igem.org/Team:TUDelft">
+
−
                        project SCI-PHI 29 </a>
+
−
                    
+
−
                    <br>
+
−
              </p></div>
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              <br>
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              <br>
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              <br>
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            </div>
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          </div>
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        </div>
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        <div class="sub"
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          onclick="popup('rbn4')"> <!--UC Davis pop up-->
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          <div class="sub-header">
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            <h1>
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−
              UC DAVIS
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            </h1>
+
−
            <hr>
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          </div>
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          <div class="sub-content">
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            <p>
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            </p>
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          </div>
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        </div>
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        <div id="rbn4"
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          class="popup">
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          <div class="popup-container">
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            <div class="popup-header">
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              <h1 class="title">UC Davis collaboration</h1>
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              <button type="button"
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                 onclick="hide('rbn4')">X</button>
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            </div>
+
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            <div class="popup-content">
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            <div> <p>
+
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                    <figure Style="float:left; margin-right: 25px;">
+
−
                            <img style="height: 50ex; width: 40ex" src="https://static.igem.org/mediawiki/2019/4/49/T--marburg--UCD_OT2.jpeg"
+
−
                                alt="UCD OT2">
+
−
                        </figure>
+
−
                UC Davis iGEM team is one of the winners of the Opentrons competition in 2019. iGEM Marburg
+
−
                won one OT-2
+
−
                during last
+
−
                year’s edition of the competition and got contacted for a collaboration by iGEM UC Davis
+
−
                along with other
+
−
                winners from
+
−
                2018 and 2019.
+
−
                The goal for this automation InterLab collaboration was to collect data to determine the
+
−
                accuracy and
+
−
                reproducibility of
+
−
                the OT-2 compared to humans. To do this, UC Davis proposed to perform the standard iGEM
+
−
                protocol on serial
+
−
                dilutions
+
−
                with silica beads and fluorescein, each manually and with an OT-2. In total iGEM Marburg did
+
−
                four dilutions;
+
−
                twice with
+
−
                an OT-2 and twice manually. The data was then sent to UC Davis via the spreadsheet designed
+
−
                by them.
+
−
                Finally, iGEM
+
−
                Marburg aided by creating a Slack channel for all iGEM teams with an OT-2 to facilitate
+
−
                better communication
+
−
                and
+
−
                exchange in the future.
+
−
                 <br><br>
+
−
                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).
+
−
                <br>
+
−
                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.
+
−
                <br>
+
−
                <br>
+
−
                <figure Style="text-align:center">
+
−
                    <img style="height: 50ex; width: 50ex"src="https://static.igem.org/mediawiki/2019/c/cc/T--marburg--UC_Davis_Graphic_1.png"
+
−
                        alt=" UCD Graphic 1">
+
−
                    <img style="height: 50ex; width: 50ex"src=" https://static.igem.org/mediawiki/2019/a/a7/T--marburg--UC_Davis_Graphic_2.png"
+
−
                        alt=" UC Davis Graphic 2"> 
+
−
                    <figcaption1>
+
−
                        <br> 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.
+
−
                    </figcaption>   
+
−
                </figure>
+
−
                <br>
+
−
            </p>
+
−
            <br>More information about this collaboration such as individual team data can be found on UC
+
−
            Davis wiki:
+
−
            <a href="https://2019.igem.org/Team:UC_Davis/Collaborations"> Wiki UC Davis Collaboration </a>
+
−
            <br>
+
−
              </p></div>
+
−
           
+
−
              <br>
+
−
       
+
−
            </div>
+
−
          </div>
+
−
        </div>
+
−
        <div class="sub"
+
−
          onclick="popup('rbn5')"> <!-- UFlorida-->
+
−
          <div class="sub-header">
+
−
            <h1>
+
−
              UFLORIDA
+
−
            </h1>
+
−
            <hr>
+
−
          </div>
+
−
          <div class="sub-content">
+
−
            <p>
+
−
            </p>
+
−
          </div>
+
−
        </div>
+
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        <div id="rbn5"
+
−
          class="popup">
+
−
          <div class="popup-container">
+
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            <div class="popup-header">
+
−
              <h1 class="title">UFlorida</h1>
+
−
              <button type="button"
+
−
                onclick="hide('rbn5')">X</button>
+
−
            </div>
+
−
            <div class="popup-content"
+
−
              style="text-align: justify;>
+
 
               <div></div><p>
 
               <div></div><p>
 
                     <br>
 
                     <br>
  
−
                     <figure  Style="float:left; margin-right: 25px;">
+
                     <figure  Style=" float:left; margin-right: 25px;">
−
                            <img style="height: 30ex; width: 40ex" src="https://static.igem.org/mediawiki/2019/f/f7/T--Florida--iGEMWeb1.png" alt="Florida">
+
                      <img style="height: 30ex; width: 40ex"
−
                            <figcaption>
+
                        src="https://static.igem.org/mediawiki/2019/f/f7/T--Florida--iGEMWeb1.png" alt="Florida">
−
                           
+
                      <figcaption>
−
                            </figcaption>
+
−
                        </figure>
+
−
                    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.
+
−
                    <br>
+
−
                    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.
+
−
                    <br>
+
  
−
                    <figure style="align-content:center;">
+
                      </figcaption>
 +
                      </figure>
 +
                      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.
 +
                      <br>
 +
                      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.
 +
                      <br>
 +
 
 +
                      <figure style="align-content:center;">
 
                         <img src="https://static.igem.org/mediawiki/2019/2/29/T--marburg--UFlorida_Rene.jpeg" alt="Florida">
 
                         <img src="https://static.igem.org/mediawiki/2019/2/29/T--marburg--UFlorida_Rene.jpeg" alt="Florida">
 
                         <figcaption>
 
                         <figcaption>
−
                            Fig. 1: Skypecall with UFlorida
+
                          Fig. 1: Skypecall with UFlorida
 
                         </figcaption>
 
                         </figcaption>
−
                    </figure>
+
                      </figure>
 +
                      <br>
 +
                      </p>
 +
                    </div>
 
                     <br>
 
                     <br>
−
              </p></div>
+
                    <br>
−
              <br>
+
                  </div>
−
              <br>
+
                </div>
−
            </div>
+
                <div class="sub" onclick="popup('rbn6')">
−
          </div>
+
                  <!-- mini collabs-->
−
          <div class="sub"
+
                  <div class="sub-header">
−
          onclick="popup('rbn6')"> <!-- mini collabs-->
+
                    <h1>
−
          <div class="sub-header">
+
                      INTERACTIONS WITH <br>
−
            <h1>
+
                      OTHER TEAMS
−
              INTERACTIONS WITH <br>
+
                    </h1>
−
              OTHER TEAMS
+
                    <hr>
−
            </h1>
+
                  </div>
−
            <hr>
+
                  <div class="sub-content">
−
          </div>
+
                    <p>
−
          <div class="sub-content">
+
                    </p>
−
            <p>
+
                  </div>
−
            </p>
+
                </div>
−
          </div>
+
                <div id="rbn6" class="popup">
−
        </div>
+
                  <div class="popup-container">
−
        <div id="rbn6"
+
                    <div class="popup-header">
−
          class="popup">
+
                      <h1 class="title">UFlorida</h1>
−
          <div class="popup-container">
+
                      <button type="button" onclick="hide('rbn6')">X</button>
−
            <div class="popup-header">
+
                    </div>
−
              <h1 class="title">UFlorida</h1>
+
                    <div class="popup-content" style="text-align: justify;">
−
              <button type="button"
+
                      <div></div>
−
                onclick="hide('rbn6')">X</button>
+
                      <p>
−
            </div>
+
 
−
            <div class="popup-content"
+
                        <b>Mike the microbe</b>
−
              style="text-align: justify;">
+
                        <figure Style="text-align:center">
−
              <div></div><p>
+
                          <img src="  https://static.igem.org/mediawiki/2019/b/b0/T--marburg--Mike_microbe.png"
−
                   
+
−
                    <b>Mike the microbe</b>  
+
−
                    <figure Style="text-align:center">
+
−
                        <img src="  https://static.igem.org/mediawiki/2019/b/b0/T--marburg--Mike_microbe.png"
+
 
                             alt=" Mike the Mircrobe">
 
                             alt=" Mike the Mircrobe">
−
                        <figcaption>
+
                          <figcaption>
 
                             Figure 1: Mike the mircrobe in our lab.
 
                             Figure 1: Mike the mircrobe in our lab.
−
                        </figcaption>
+
                          </figcaption>
−
                    </figure>
+
                        </figure>
−
                    We participated in the “Mike the microbe” collaboration of the iGEM Team US AFRL CarrollHS. They
+
                        We participated in the “Mike the microbe” collaboration of the iGEM Team US AFRL CarrollHS. They
−
                    sent us
+
                        sent us
−
                    their virtual mascots Mike the Microbe and Chia the Chitinase so we could take pictures with them to
+
                        their virtual mascots Mike the Microbe and Chia the Chitinase so we could take pictures with
−
                    connect
+
                        them to
−
                    all iGEM teams around the world via social media. It brought us great joy to join to this
+
                        connect
−
                    collaboration and
+
                        all iGEM teams around the world via social media. It brought us great joy to join to this
−
                    let the two little buddies visit our daily life in our incubators for cyanobacteria.
+
                        collaboration and
−
                    <br>
+
                        let the two little buddies visit our daily life in our incubators for cyanobacteria.
−
                    <br>
+
                        <br>
−
                </p>
+
                        <br>
−
                <br>
+
                      </p>
−
                <p>
+
                      <br>
−
                    <h4><b>Postcards Düsseldorf</b></h4>     <!-- Postcard challenge-->
+
                      <p>
 +
                        <h4><b>Postcards Düsseldorf</b></h4> <!-- Postcard challenge-->
 
                         iGEM Düsseldorf called for their traditional collaboration project, a long year postcard
 
                         iGEM Düsseldorf called for their traditional collaboration project, a long year postcard
 
                         campaign with the
 
                         campaign with the
Line 810: Line 820:
 
                         <br>
 
                         <br>
 
                         <figure Style="text-align:center">
 
                         <figure Style="text-align:center">
−
                            <img src="    https://static.igem.org/mediawiki/2019/f/fe/T--marburg--Postcard.png"
+
                          <img src="    https://static.igem.org/mediawiki/2019/f/fe/T--marburg--Postcard.png"
−
                                alt="Postcard challenge">
+
                            alt="Postcard challenge">
−
                            <figcaption>
+
                          <figcaption>
−
                                Figure 2: Our Postcard for the Postcard collaboration from Düsseldorf.
+
                            Figure 2: Our Postcard for the Postcard collaboration from Düsseldorf.
−
                            </figcaption>
+
                          </figcaption>
 
                         </figure>
 
                         </figure>
 
                         <br>
 
                         <br>
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                </p>
+
                      </p>
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                <br>
+
                      <br>
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                <p>
+
                      <p>
−
                    <h5><b>iGEMxSDGs challenge</b></h5>
+
                        <h5><b>iGEMxSDGs challenge</b></h5>
−
                    IGEM Costa Rica, Tuebingen, and TAS Taipei created an iGEMxSDGs challenge as collaboration. They
+
                        IGEM Costa Rica, Tuebingen, and TAS Taipei created an iGEMxSDGs challenge as collaboration. They
−
                    asked us to
+
                        asked us to
−
                    choose four of the Sustainable Development Goals (SDGs) proposed by the United Nations (UN). We
+
                        choose four of the Sustainable Development Goals (SDGs) proposed by the United Nations (UN). We
−
                    joined this
+
                        joined this
−
                    collaboration challenge and spread it on our social media account. We decided on the following
+
                        collaboration challenge and spread it on our social media account. We decided on the following
−
                    goals:
+
                        goals:
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                    <br>
+
                        <br>
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                    <figure Style="text-align:center">
+
                        <figure Style="text-align:center">
−
                        <img src="  https://static.igem.org/mediawiki/2019/1/18/T--marburg--SDG_chalenge.png"
+
                          <img src="  https://static.igem.org/mediawiki/2019/1/18/T--marburg--SDG_chalenge.png"
 
                             alt="SGD Challenge">
 
                             alt="SGD Challenge">
−
                        <figcaption>
+
                          <figcaption>
 
                             Figure 3: SDG challenge.
 
                             Figure 3: SDG challenge.
−
                         </figcaption>
+
                          </figcaption>
−
                    </figure>
+
                         </figure>
 +
                        <br>
 +
                      </p>
 +
                      <br>
 +
 
 +
                      <p>
 +
                        <h5><b>Who wore it best? #labcoatchallenge</b></h5>
 +
                        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
 +
                        <br>
 +
                        <figure Style="text-align:center">
 +
                          <img style="height: 75ex; width: 60ex"
 +
                            src="https://static.igem.org/mediawiki/2019/7/74/T--marburg--Labcoat_Burgi.jpeg" alt="labcoat">
 +
                          <figcaption>
 +
                            Figure 4: Our model Burgis for the labcoatchallenge.
 +
                          </figcaption>
 +
                        </figure>
 +
                        <br>
 +
                      </p>
 +
                    </div>
 
                     <br>
 
                     <br>
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                 </p>
+
                    <br>
−
                 <br>
+
                  </div>
 +
                 </div>
 +
                <div class="sub" onclick="popup('rbn7')">
 +
                  <!-- meet up-->
 +
                  <div class="sub-header">
 +
                    <h1>
 +
                      MEETUPS
 +
                    </h1>
 +
                    <hr>
 +
                  </div>
 +
                  <div class="sub-content">
 +
                    <p>
 +
                    </p>
 +
                  </div>
 +
                 </div>
 +
                <div id="rbn7" class="popup">
 +
                  <div class="popup-container">
 +
                    <div class="popup-header">
 +
                      <h1 class="title">Meet ups</h1>
 +
                      <button type="button" onclick="hide('rbn7')">X</button>
 +
                    </div>
 +
                    <div class="popup-content" style="text-align: justify;">
 +
                      <div></div>
 +
                      <p>
  
−
                <p>
+
                        <h2><b>iGEM Spring Festival in Bonn</b></h2>
−
                    <h5><b>Who wore it best? #labcoatchallenge</b></h5>
+
                        From 3rd – 5th Mai we met our iGEM colleagues for the Spring Festival in Bonn. Professors of the
−
                    The Stony Brook iGEM Team challenged us to design an outfit for a runway from a standard lab coat.
+
                        university of Bonn presented their research fields which gained huge interest. We heard lectures
−
                    The
+
                        of immunology and neurosciences, as well as reviving mammoths. During the lectures, specific
−
                    outfit had to be created by tying, not using duct tape, cut or sew, etc. After designing our outfits
+
                        topics were deepened in small seminar groups, such as the ethical tenability of CRISPR applied
−
                    four of
+
                        at humans and other animals. At the poster sessions we got the first time in contact with the
−
                    our members presented their style on our ‘runway’ while paparazzi took their photos. As an outfit we
+
                        other teams’ projects. Afterwards we had the opportunity to vote for the best project, which
−
                    chose a
+
                        iGEM Düsseldorf won. Besides that, the meetup was filled with a lot of awarding categories. We
−
                    dress highlighting the neckline, a shoulder free dress, a knotted dress and a skirt to bring glamour
+
                        competed in the categories for “Best Video”, “Best Poster”, “Best Project” and a single person
−
                    to the
+
                        had the chance to win the award for “Best Meme”. The iGEM Team Bonn offered spontaneously a
−
                    daily routine in the labs. Especially our guys were rocking their outfits as you can see here
+
                        little football table tournament, where two of our team members won. In the evening we learnt a
−
                    x
+
                        lot about Bonn as a city from a guide living there for ages. Afterwards, the iGEM Teams met in
−
                    <br>
+
                        several groups in restaurants and bars. We merged with iGEM Kaiserslautern and exchanged our
−
                    <figure Style="text-align:center">
+
                        projects and ideas for the rest of the evening.
−
                        <img style="height: 75ex; width: 60ex" src="https://static.igem.org/mediawiki/2019/7/74/T--marburg--Labcoat_Burgi.jpeg" alt="labcoat">
+
                        <br>
 +
                        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!
 +
                        <br>
 +
                        We particularly thank the iGEM Team Bonn for the huge effort and the great meetup!
 +
                        <br>
 +
                        <figure Style="text-align:center">
 +
                          <img style="height: 50ex; width: 65ex"
 +
                            src="https://static.igem.org/mediawiki/2019/a/a9/T--marburg--meet_u_bonn.png"
 +
                            alt="Erlangen meetup">
 +
                          <figcaption>
 +
                            Fig. 1: Two representatives of Doulix celebrating with us.
 +
                          </figcaption>
 +
                        </figure>
 +
 
 +
                        <br>
 +
 
 +
                        <h3><b>Erlangen collaboration meetup</b></h3>
 +
                        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.
 +
                        <br>
 +
 
 +
                        <figure Style="text-align:center">
 +
                          <img style="height: 40ex; width: 65ex"
 +
                            src="https://static.igem.org/mediawiki/2019/0/01/T--marburg--meet_up_erlangen.jpeg"
 +
                            alt="Erlangen meetup">
 +
                          <figcaption>
 +
                            Fig. 2: Group photo from the Erlangen mett up (Michael Burgis from Team Marburg in the left
 +
                            side).
 +
                          </figcaption>
 +
                        </figure>
 +
 
 +
                        <br>
 +
 
 +
                        <h><b>Düsseldorf meetup</b></h>
 +
                        <br>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! <br>
 +
 
 +
                        <figure Style="text-align:center">
 +
                          <img style="height: 70ex; width: 50ex"
 +
                            src="https://static.igem.org/mediawiki/2019/e/e4/T--marburg--meet_up_Duesseldorf.jpeg"
 +
                            alt="Du meetup">
 +
                          <figcaption>
 +
                            Fig. 3: Team photo from the Düsseldorf meetup.
 +
                          </figcaption>
 +
                        </figure>
 +
                        <br>Thanks again to iGEM Düsseldorf for the huge effort and the great meetup! <br>
 +
                      </p>
 +
                      <br>
 +
 
 +
                      <h><b> Vilnius, Lithuania – Biohackathon Lab App 2019</b></h>
 +
                      <br>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.
 +
                      <br>
 +
                      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.
 +
                      <br>“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!
 +
                      <br>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!
 +
                      <br>
 +
                      <figure Style="text-align:center">
 +
                        <img src="Pic" alt="Vilnius hacker">
 
                         <figcaption>
 
                         <figcaption>
−
                            Figure 4: Our model Burgis for the labcoatchallenge.
+
                          Fig. 4: Meet up Vilnius, Lithuania .
 
                         </figcaption>
 
                         </figcaption>
−
                    </figure>
+
                      </figure>
 +
 
 +
                      </p>
 +
                    </div>
 
                     <br>
 
                     <br>
−
              </p></div>
 
−
              <br>
 
−
              <br>
 
−
            </div>
 
−
          </div>
 
−
          <div class="sub"
 
−
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−
          <div class="sub-header">
 
−
            <h1>
 
−
              MEETUPS
 
−
            </h1>
 
−
            <hr>
 
−
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          <div class="sub-content">
 
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            <p>
 
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−
        </div>
 
−
        <div id="rbn7"
 
−
          class="popup">
 
−
          <div class="popup-container">
 
−
            <div class="popup-header">
 
−
              <h1 class="title">Meet ups</h1>
 
−
              <button type="button"
 
−
                onclick="hide('rbn7')">X</button>
 
−
            </div>
 
−
            <div class="popup-content"
 
−
              style="text-align: justify;">
 
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              <div></div><p>
 
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                    <h2><b>iGEM Spring Festival in Bonn</b></h2>
 
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                    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.
 
 
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                    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!
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                    We particularly thank the iGEM Team Bonn for the huge effort and the great meetup!
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                            <img style="height: 50ex; width: 65ex" src="https://static.igem.org/mediawiki/2019/a/a9/T--marburg--meet_u_bonn.png" alt="Erlangen meetup">
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                            <figcaption>
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                                    Fig. 1: Two representatives of Doulix celebrating with us.
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                            <h3><b>Erlangen collaboration meetup</b></h3>
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                            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.
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                                    <img style="height: 40ex; width: 65ex" src="https://static.igem.org/mediawiki/2019/0/01/T--marburg--meet_up_erlangen.jpeg" alt="Erlangen meetup">
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                                            Fig. 2: Group photo from the Erlangen mett up (Michael Burgis from Team Marburg in the left side).
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                                </figure>
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                            <h><b>Düsseldorf meetup</b></h>
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                            <br>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!  <br>
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                                    <img style="height: 70ex; width: 50ex" src="https://static.igem.org/mediawiki/2019/e/e4/T--marburg--meet_up_Duesseldorf.jpeg" alt="Du meetup">
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                                    <figcaption>
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                                            Fig. 3: Team photo from the  Düsseldorf meetup.
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                                    <br>Thanks again to iGEM Düsseldorf for the huge effort and the great meetup! <br>
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                            <h><b> Vilnius, Lithuania – Biohackathon Lab App 2019</b></h>
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                            <br>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.
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                            With the task of creating an application that tackles a self-found problem, we sat together and brainstormed about what could be done.
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                            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.
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                            <br>“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!
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                            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!
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                            <br>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.
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                            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!
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                                    <img  src="Pic" alt="Vilnius hacker">
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                                    <figcaption>
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                                            Fig. 4: Meet up Vilnius, Lithuania .
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       </section>
 
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     </div>

Revision as of 19:53, 21 October 2019

C O L L A B O R A T I O N

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.

T H EAG O L D E NAG A T E
C O L L A B O R A T I O N

Berlin/Delft

UC DAVIS

UFLORIDA

INTERACTIONS WITH
OTHER TEAMS

MEETUPS