Difference between revisions of "Team:Marburg/Hardware"

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<h1>Hardware</h1>
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<h3>Best Hardware Special Prize</h3>
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<p>In addition to encouraging teams to work with DNA parts and build biological devices in the lab, iGEM also encourages other types of technical solutions for synthetic biology. This can include physical devices (hardware) related to robotic assembly, microfluidics, low-cost measurement devices, to name a few examples. There are many exciting opportunities for hardware innovation in synthetic biology.
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      <h1 class="heading">
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        H A R D W A R E
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      </h1>
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      <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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        class="logo"
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        alt="Syntex Logo">
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    <div style="margin-top: 10vh;">
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      <section class="section">
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        <h1 class="title">Hardware</h1>
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        <p style="text-align: justify;">
 +
          Since last year’s iGEM team Marburg won the OT-2 in the Opentrons Robot Challenge, this year’s team built upon it and extended the amount of workflows, which could be performed with it.
 +
A large number of OT-2 protocols have been developed, ranging from Golden Gate specific protocols over plasmid purification using Wizard® MagneSil® Plasmid Purification System to even colony picking.
 +
However, this software would not be able to function without suitable hardware. To facilitate proper workflows in the OT-2, which is structured slotwise, new adapters, mounts and a variation of different tube holders had to be developed.
 +
By designing and creating the required devices with a computer-aided design (CAD) software and a 3D printer, it was easy, cheap and fast to produce custom made labware, which would perfectly fit our needs.
 +
As well as our developed software, all our software specific and additional created hardware designs are made open-source in our <a href="https://github.com/igemsoftware2019/iGemMarburg2019">Github repository</a> under the CERN Open Hardware Licence version 1.2 (CERN OHL v1.2), whereby it will benefit the whole iGEM community in order to simplify the work in the lab, with and even without the OT-2.
 +
Our hardware consists of the following devices:
 +
<br>
 +
                <br>
 +
            </p>
 +
            <h2 class="title">The Colony Picking Unit (CPU)</h2>
 +
            <div><p>
 +
              This hardware package contains STL files and instructions for everything that is needed to transform an OT-2 into a low-cost colony picker. This includes a STL file for the Raspberry Pi and ArduCAM mount, which will be fixed onto the OT-2 arm, a STL file for the light table, suitable for 90 mm petri dishes as well as for plates in SBS format, and a detailed instruction on how to solder and install the LEDs, Arduino and cables into the 3D printed light table.
 +
            </p>
  
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<p>
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            <figure style="float: right; margin-left: 25px;">
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Teams who are interested in working with hardware in their project, or as a side project, are encouraged to apply for the Best Hardware award.
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                <img style="height: 400px; width: 600px"
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<br><br>
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                    src="https://static.igem.org/mediawiki/2019/6/62/T--Marburg--mountbelow.JPG"
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To compete for the <a href="https://2019.igem.org/Judging/Awards">Best Hardware prize</a>, please describe your work on this page and also fill out the description on the <a href="https://2019.igem.org/Judging/Judging_Form">judging form</a>.
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                    alt="OT-2 arm mount below">
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<br><br>
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                <img style="height: 400px; width: 600px"
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You must also delete the message box on the top of this page to be eligible for this prize.
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                    src="https://static.igem.org/mediawiki/2019/c/c4/T--Marburg--mountside.JPG"
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</p>
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                    alt="OT-2 arm mount side">
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</p>
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                <figcaption style="max-width: 600px">
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</div>
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                    Fig.1 - 3D printed Raspberry Pi 4 Model B and ArduCAM mount for the OT-2 arm consisting of top and base parts.
 +
                </figcaption>
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            </figure>
  
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            <br>
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<h3>Inspiration</h3>
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<p>You can look at what other teams did to get some inspiration! <br />
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Here are a few examples:</p>
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<ul>
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<li><a href="https://2018.igem.org/Team:Valencia_UPV/Hardware">2018 Valencia UPV</a></li>
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<li><a href="https://2018.igem.org/Team:Unesp_Brazil/Hardware">2018 Unesp Brazil</a></li>
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<li><a href="https://2016.igem.org/Team:Valencia_UPV">2016 Valencia UPV</a></li>
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<li><a href="https://2016.igem.org/Team:Aachen">2016 Aachen </a></li>
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<li><a href="https://2015.igem.org/Team:TU_Delft">2015 TU Delft  </a></li>
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<li><a href="https://2015.igem.org/Team:TU_Darmstadt">2015 TU Darmstadt</a></li>
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</ul>
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</div>
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</div>
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            <script src="https://embed.github.com/view/3d/igemsoftware2019/iGemMarburg2019/master/Hardware/Camera_mount_base.stl"></script>
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            <script src="https://embed.github.com/view/3d/igemsoftware2019/iGemMarburg2019/master/Hardware/Camera_mount_top.stl"></script>
  
 +
            <br>
  
 +
            <figure style="float: right; margin-left: 25px;">
 +
                <img style="height: 400px; width: 600px"
 +
                    src="https://static.igem.org/mediawiki/2019/4/41/T--Marburg--lighttablemodule.JPG    "
 +
                    alt="Light table module">
 +
                <figcaption style="max-width: 600px">
 +
                    Fig.2 - 3D printed light table containing LED’s and an Arduino fitting perfectly into one OT-2 slot.
 +
                </figcaption>
 +
            </figure>
 +
 +
            <br>
 +
 +
            <script src="https://embed.github.com/view/3d/igemsoftware2019/iGemMarburg2019/master/Hardware/Light_table.stl"></script>
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            <script src="https://embed.github.com/view/3d/igemsoftware2019/iGemMarburg2019/master/Hardware/Light_table_lid.stl"></script>
 +
 +
            <br>
 +
 +
 +
 +
 +
            <h2 class="title">The Plasmid Purification add-on</h2>
 +
            <div><p>
 +
              This add-on consists of an STL file describing the measurements of an adapter for the BioShake D30-T elm shaker from QInstruments to perfectly fit into slot 3 or slot 10 of the OT-2. The adapter combined with the file “CoordinatesOrdered.json” make the BioShake D30-T elm shaker accessible as labware in the OT-2 and are required to perform the plasmid purification with Promegas Wizard® MagneSil® Plasmid Purification System.
 +
            </p>
 +
 +
            <figure align=center>
 +
                <img style="height: 500px; width: 300px"
 +
                    src="https://static.igem.org/mediawiki/2019/e/e9/T--Marburg--shakeradapter.JPG"
 +
                    alt="Shaker SBS adapter">
 +
                <figcaption style="max-width: 1400px">
 +
                    Fig.3 - 3D printed adapter for the BioShake D30-T elm shaker from QInstruments fitting perfectly into an OT-2 slot.
 +
                </figcaption>
 +
            </figure>
 +
            <br>
 +
 +
            <script src="https://embed.github.com/view/3d/igemsoftware2019/iGemMarburg2019/master/Hardware/Shaker-SBS-Adapter.stl"></script>
 +
 +
 +
 +
 +
            <h2 class="title">Additional Labware</h2>
 +
            <h3 class="title">Cuvette holder</h3>
 +
            <div><p>
 +
              We created this labware suitable for 40 cuvettes and additionally fitting into an OT-2 slot to easily carry and fill cuvettes automatedly. Of course, this cuvette holder can also be used for manually filling cuvettes.
 +
            </p>
 +
 +
            <figure align=center>
 +
                <img style="height: 500px; width: 300px"
 +
                    src="https://static.igem.org/mediawiki/2019/2/24/T--Marburg--k%C3%BCvettenhalter.JPG"
 +
                    alt="Cuvette Holder">
 +
                <figcaption style="max-width: 1400px">
 +
                    Fig.4 - 3D printed cuvette holder in SBS format fitting perfectly into an OT-2 slot.
 +
                </figcaption>
 +
            </figure>
 +
            <br>
 +
 +
            <script src="https://embed.github.com/view/3d/igemsoftware2019/iGemMarburg2019/master/Hardware/Cuvette-SBS.stl"></script>
 +
 +
 +
 +
 +
            <h3 class="title">90 mm Petri dish SBS adapter</h3>
 +
            <div><p>
 +
              Automating the whole cloning process in the OT-2 includes not only colony picking, but also plating. That is why we designed an adapter for 90 mm petri dishes to fit into an OT-2 slot with SBS format. Protocols for plating with the OT-2 on agar plates in this adapter were developed and are freely available.
 +
 +
            </p>
 +
 +
            <figure align=center>
 +
                <img style="height: 500px; width: 300px"
 +
                    src="https://static.igem.org/mediawiki/2019/8/88/T--Marburg--90mmSBS.JPG"
 +
                    alt="90 mm to SBS adapter">
 +
                <figcaption style="max-width: 1400px">
 +
                    Fig.5 - 3D printed 90 mm Petri dish to SBS adapter fitting perfectly into an OT-2 slot.
 +
                </figcaption>
 +
            </figure>
 +
            <br>
 +
 +
            <script src="https://embed.github.com/view/3d/igemsoftware2019/iGemMarburg2019/master/Hardware/90mm-SBS.stl"></script>
 +
 +
 +
 +
 +
            <h3 class="title">50 ml falcon tube holder</h3>
 +
            <div><p>
 +
              Every now and then a large amount of liquids is required and needs to be stored. 50 ml falcon tubes are often the right choice to do so. We designed a 50 ml falcon tube holder to carry 6 of 50 ml falcons. Additionally, this holder was designed in SBS format to also fit into the OT-2 for automated workflows.
 +
 +
            </p>
 +
 +
            <figure align=center>
 +
                <img style="height: 500px; width: 300px"
 +
                    src="https://static.igem.org/mediawiki/2019/3/30/T--Marburg--falcontubeholder.JPG"
 +
                    alt="Falcon tube holder">
 +
                <figcaption style="max-width: 1400px">
 +
                    Fig.6 - 3D printed  50 mm Falcon Tube holder in SBS format fitting perfectly into an OT-2 slot.
 +
                </figcaption>
 +
            </figure>
 +
            <br>
 +
 +
            <script src="https://embed.github.com/view/3d/igemsoftware2019/iGemMarburg2019/master/Hardware/Falcon-SBS.stl"></script>
 +
 +
 +
 +
 +
 +
 +
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 +
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        <article>
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          <h1 class="title"></h1>
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          <p style="text-align: justify; margin-bottom: 1em;">
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          </p></div>
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        </article>
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Revision as of 00:48, 22 October 2019

H A R D W A R E

Hardware

Since last year’s iGEM team Marburg won the OT-2 in the Opentrons Robot Challenge, this year’s team built upon it and extended the amount of workflows, which could be performed with it. A large number of OT-2 protocols have been developed, ranging from Golden Gate specific protocols over plasmid purification using Wizard® MagneSil® Plasmid Purification System to even colony picking. However, this software would not be able to function without suitable hardware. To facilitate proper workflows in the OT-2, which is structured slotwise, new adapters, mounts and a variation of different tube holders had to be developed. By designing and creating the required devices with a computer-aided design (CAD) software and a 3D printer, it was easy, cheap and fast to produce custom made labware, which would perfectly fit our needs. As well as our developed software, all our software specific and additional created hardware designs are made open-source in our Github repository under the CERN Open Hardware Licence version 1.2 (CERN OHL v1.2), whereby it will benefit the whole iGEM community in order to simplify the work in the lab, with and even without the OT-2. Our hardware consists of the following devices:

The Colony Picking Unit (CPU)

This hardware package contains STL files and instructions for everything that is needed to transform an OT-2 into a low-cost colony picker. This includes a STL file for the Raspberry Pi and ArduCAM mount, which will be fixed onto the OT-2 arm, a STL file for the light table, suitable for 90 mm petri dishes as well as for plates in SBS format, and a detailed instruction on how to solder and install the LEDs, Arduino and cables into the 3D printed light table.

OT-2 arm mount below OT-2 arm mount side
Fig.1 - 3D printed Raspberry Pi 4 Model B and ArduCAM mount for the OT-2 arm consisting of top and base parts.


Light table module
Fig.2 - 3D printed light table containing LED’s and an Arduino fitting perfectly into one OT-2 slot.


The Plasmid Purification add-on

This add-on consists of an STL file describing the measurements of an adapter for the BioShake D30-T elm shaker from QInstruments to perfectly fit into slot 3 or slot 10 of the OT-2. The adapter combined with the file “CoordinatesOrdered.json” make the BioShake D30-T elm shaker accessible as labware in the OT-2 and are required to perform the plasmid purification with Promegas Wizard® MagneSil® Plasmid Purification System.

Shaker SBS adapter
Fig.3 - 3D printed adapter for the BioShake D30-T elm shaker from QInstruments fitting perfectly into an OT-2 slot.

Additional Labware

Cuvette holder

We created this labware suitable for 40 cuvettes and additionally fitting into an OT-2 slot to easily carry and fill cuvettes automatedly. Of course, this cuvette holder can also be used for manually filling cuvettes.

Cuvette Holder
Fig.4 - 3D printed cuvette holder in SBS format fitting perfectly into an OT-2 slot.

90 mm Petri dish SBS adapter

Automating the whole cloning process in the OT-2 includes not only colony picking, but also plating. That is why we designed an adapter for 90 mm petri dishes to fit into an OT-2 slot with SBS format. Protocols for plating with the OT-2 on agar plates in this adapter were developed and are freely available.

90 mm to SBS adapter
Fig.5 - 3D printed 90 mm Petri dish to SBS adapter fitting perfectly into an OT-2 slot.

50 ml falcon tube holder

Every now and then a large amount of liquids is required and needs to be stored. 50 ml falcon tubes are often the right choice to do so. We designed a 50 ml falcon tube holder to carry 6 of 50 ml falcons. Additionally, this holder was designed in SBS format to also fit into the OT-2 for automated workflows.

Falcon tube holder
Fig.6 - 3D printed 50 mm Falcon Tube holder in SBS format fitting perfectly into an OT-2 slot.