Difference between revisions of "Team:Marburg/Collaborations"

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     <div class="container">
 
     <div class="container">
 
       <h1 class="title">
 
       <h1 class="title">
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         UC Davis Collaboration
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         The Colony-Picture Project
 
       </h1>
 
       </h1>
 
       <p>
 
       <p>
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         UC Davis iGEM team is one of the winners of Opentron competition in 2019, where as prize Opentron gave out OT-2 pipetting robots to ten iGEM
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         One of our goals was to build a reasonable colony picking robot to outsource the tiring task
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         teams, whose applications are the most convincing. iGEM Marburg won one OT-2 during last year’s edition of the competition and got contacted
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        of colony picking by hand. Automated lab processes have improved in recent years and are
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         for collaboration by iGEM UC Davis along with other said competition winners from 2018 and 2019.
+
         being improved today and in the future. We used an Opentron and we constructed modules
 +
        and scripts, that allow other iGEM Teams to turn their own OT-2 into a colony picking robot
 +
         as well.
 
       </p>
 
       </p>
 
       <p>
 
       <p>
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         The goal for this inter-lab collaboration is to collect data and determine the accuracy of the OT-2 compared to humans. To do this, UC Davis
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         To achieve this goal, we initiated this Collaboration because we needed to train the artificial
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         conceived a protocol to perform serial dilutions of silica beads and fluorescence both manually and with OT-2. In total iGEM Marburg did four
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         intelligence with a lot of data, so that it is able to recognize the colonies by itself. We asked
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        dilutions; twice with OT-2 and twice manually. The data is then sent to UC Davis via the spreadsheet designed by them. Finally iGEM Marburg
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         other iGEM Teams if they could provide us with pictures of their agar plates with E. Coli
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         made a Slack channel for all iGEM teams with OT-2 to be in contact with one another; further increasing exchange and collaboration. More
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         colonies with which we could train the robot. In order to do that we published a script, code
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         information about this collaboration can be found on UC Davis wiki.
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        and module we created.
 
       </p>
 
       </p>
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    </div>
 
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  </section>
 
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  <section class="section">
 
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    <div class="container">
 
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      <h1 class="title">
 
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        Biohackathon Lab App 2019
 
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      </h1>
 
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      <h2 class="subtitle">
 
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        Vilnius, Lithuania
 
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      </h2>
 
 
       <p>
 
       <p>
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         In August 2019 our Team participated in the Biohackathon Lab App, organized by the Vilnius-Lithuania Team 2019. Together with the iGEM Teams
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         To participate all that was needed was 9 cm diameter agar plates with E. Coli colonies, a 12-
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         Stockholm and Copenhagen, as well as several non-iGEM Teams we sat together for a weekend packed with problems, ideas and neat solutions.
+
        inch (or larger) screen and a 12-megapixel camera (phone or SLR). Other criteria were evenly
 +
        distributed, easily distinguishable colonies that don’t clump together and using LB medium
 +
        only. The first step was taking the picture. For this purpose, the screen had to be set to the
 +
        highest level of brightness and display a white image. Then the transparent paper we sent
 +
         the teams had to be placed on top of the monitor and on top of that the agar plate was
 +
        placed and the lid removed. Subsequently, the picture was taken from a 90 degree angle
 +
        whereby light reflections should be avoided.
 
       </p>
 
       </p>
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       <p>
+
       <p style="display: hidden;">
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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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         Following this, the images taken had to be labeled using a web-based tool. The picture had
 +
        to be converted into a jpeg file and then uploaded in the weblink. In the weblink the option
 +
        ‘rectangle’ had to be chosen. Afterwards, the single colonies were marked. In the end the
 +
        pictures were saved and exported as a json-file and then uploaded in a folder in the google
 +
        drive.
 
       </p>
 
       </p>
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       <p>
+
       <p style="display: hidden;">
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         During this time we were in the middle of our works with the Opentrons OT-2 and soon realized that some of our biologists had trouble
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         Next, we fed the robot the data.
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        integrating protocols in the robot themselves, as this is primarily done by writing the protocol in Python and pushing it directly to the
+
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        robot – no convenient application to change parameters, such as the amount of reactions, of the protocol included. In our heads the idea to
+
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        have a user-friendly GUI grew more and more and soon we saw ourselves standing in the Vilnius University Life Sciences Center.
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       </p>
 
       </p>
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       <p>
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       <p style="display: hidden;">
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        “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
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         As an incentive to participate in this Collaboration we gave away prizes. The first ten teams
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        perfect fit to complement our small team: Nour Alsamsam was happy to join us for this weekend and lend us his coding skills – huge thank you
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         that send us 100 pictures got a small surprise, an E. Coli soft toy. The team that sent us the
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        to you, Nour!
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         most pictures got a bigger surprise, a ….. @Team.
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      </p>
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−
      <p>
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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
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        in such a short time – it was clear for us, that we would continue with this project later on!
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      </p>
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      <p>
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        In conclusion, the Biohackathon was an awesome and productive meeting of the iGEM Teams Stockholm, Copenhagen, Vilnius and Marburg. We talked
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        about our projects, offered each other feedback on current issues in the lab and shared many ideas.
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      </p>
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      <p>
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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
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        perspective on our project and are now looking forward to meet the other teams again at the Giant Jamboree!
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      </p>
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    </div>
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  </section>
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  <section class="section" style="display: none;">
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    <div class="container">
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      <h1 class="title">
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         Golden Gate webinar
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      </h1>
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      <p>
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        In our second big collaboration we organized, created and hold a live webinar about Golden
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        Gate cloning to teach and to indroduce other iGEM Teams this special cloning method in
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        contrast to the alternative conventional cloning methods. Through this method and our
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        webinar it fascilate other teams who are already using this method to get deeper insights to
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         Golden Gate cloning. Besides for iGEM Teams, who are unfamiliar with that method, they
+
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        could get an overview why this method is so efficient in labs who are going to clone in cells.
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        Finally we wanted to show again that our Marburg collection and the Marburg collection 2.0
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        is (still) availaible for every iGEM Team.
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      </p>
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−
      <p>
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        During a 1,5 h online webinar our team presented with our advisor René Inckemann the
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        topics and methods like: Golden Gate cloning, what is so special about this cloning method,
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        how to create a genetic toolbox and showed students how the software Genious works for
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        designing DNA parts. This webinar was hold on three different dates with three different time
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        (30/07/2019 - 10:00 CET, 31/07/2019 - 18:00 CET and 08/08/2019 - 24:00 CET) so that
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        every iGEM Teams in all continents had the possibility to attend to their favourite time fitting
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        next to their busy daylife with iGEM. During the live webinar people get the chance to read a
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        FAQ about the webinar itself or they could just group chat with us to ask questions, give
+
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        feedback and/or just chatting with us and the other participans.
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−
      </p>
+
−
      <p>
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−
         Alongside to the live webinar we created a slack workspace called GoldenGateCloning
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        especially for the iGEM Teams who wanted to participate. In different channels the iGEM
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        teams could ask us questions beforehand about the webinar progamme on ON-24, get
+
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        summarized information about Golden Gate cloning, FAQ etc. Channels that we were
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        created: #Automation of g gate, #Chassis adaptions, #FAQ, #Fun-and-spam, #General,
+
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        #Golden-gate-database and #Golden-gate-protocol. Therefore the students could download
+
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        via our G-Drive folders that contain protocols for the Golden Gate cloning, so that teams can
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−
        easily use this method for their own project. There were also a handout about a summary
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        and an explanation about Golden Gate cloning, Type IIS Restriction Enzymes, Standartised
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        Golden Gate cloning parts and texts about „How to create your own toolbox (LV 0 – 2)“.
+
−
      </p>
+
−
      <p>
+
−
        Furthermore the iGEM Teams had the possibility to get the slides from our holded webinars
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−
        to have a look again for their own purpose. In G-Drive the people could also find the Genious
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        Files for their teams, so that the iGEM teams can try constructing their own in-silico parts
+
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        using these files. To sum up all these offered materials enable other teams our cloning
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        protocolls and presentation slides. Via the slack channel we offer FAQ, support and help at
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−
        any time via the different channels.
+
−
      </p>
+
−
      <p>
+
−
        At the end of our collaboration webinar over 70/80 iGEM-teams all around the world
+
−
        registrated and participated in our webinar (see table/picture: XWorldmap?). Also Doulix as a
+
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        company attended to our webinar and said after their participation: „Great webinar about
+
−
        Golden Gate of iGEMmarburg2019!“ (info@doulix.com on Twitter). All in all we got a lot of
+
−
        positive feedbacks about our collaboration webinar and we helped/supported a lot of teams
+
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        regarding to biobricks/ genetic toolboxes, Genious and how to use the golden gate method
+
−
        for current/future clonings in your own labs.
+
 
       </p>
 
       </p>
 
     </div>
 
     </div>

Revision as of 13:51, 14 September 2019

The Colony-Picture Project

One of our goals was to build a reasonable colony picking robot to outsource the tiring task of colony picking by hand. Automated lab processes have improved in recent years and are being improved today and in the future. We used an Opentron and we constructed modules and scripts, that allow other iGEM Teams to turn their own OT-2 into a colony picking robot as well.

To achieve this goal, we initiated this Collaboration because we needed to train the artificial intelligence with a lot of data, so that it is able to recognize the colonies by itself. We asked other iGEM Teams if they could provide us with pictures of their agar plates with E. Coli colonies with which we could train the robot. In order to do that we published a script, code and module we created.

To participate all that was needed was 9 cm diameter agar plates with E. Coli colonies, a 12- inch (or larger) screen and a 12-megapixel camera (phone or SLR). Other criteria were evenly distributed, easily distinguishable colonies that don’t clump together and using LB medium only. The first step was taking the picture. For this purpose, the screen had to be set to the highest level of brightness and display a white image. Then the transparent paper we sent the teams had to be placed on top of the monitor and on top of that the agar plate was placed and the lid removed. Subsequently, the picture was taken from a 90 degree angle whereby light reflections should be avoided.

Following this, the images taken had to be labeled using a web-based tool. The picture had to be converted into a jpeg file and then uploaded in the weblink. In the weblink the option ‘rectangle’ had to be chosen. Afterwards, the single colonies were marked. In the end the pictures were saved and exported as a json-file and then uploaded in a folder in the google drive.

Next, we fed the robot the data.

As an incentive to participate in this Collaboration we gave away prizes. The first ten teams that send us 100 pictures got a small surprise, an E. Coli soft toy. The team that sent us the most pictures got a bigger surprise, a ….. @Team.