Difference between revisions of "Team:Sherbrooke/Description"

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<h2> Project Description </h2>
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<h2 align="center">Re-inventing the lab: Development of a highly flexible, affordable and open source robotic automation platform</h2>
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<br>
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<p>
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Almost everyone working or studying in biology have heard about liquid handlers and robots dedicated to biological sciences. Despite the fact that many know about them, and could potentially use them in their lab, very few scientists actually use automation.
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</p>
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<p>
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One of the main difficulties is getting access to one of these robots. They are expensive and only highly funded laboratories can afford them.  However, even if students or scientists have access to an automation platform, they often barely use it. 1) The consumables used by these robots are expensive and can cost up to 10 times more than the usual consumables found in a laboratory, which is simply too pricey for most research groups to afford for day to day operations. 2) Robots are generally built for specific protocols with high-throughput applications in mind, and lack the flexibility required to easily expand their application range. 3) Many lower throughput but still time-consuming and repetitive experiments cannot be performed by current robots because specific modules that support their automation are not available or too costly.  4) Third party modules are generally not compatible between manufacturers because of proprietary hardware and software. 5) Other problems like complicated not sufficiently flexible software tools (with costly updates) or the need to have dedicated personnel trained to run the robots discourage many potential users.
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</p>
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<p>
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Our team has developed an affordable, modular and open source robotic automation platform to address these problems. Our platform and accessory modules are built from affordable off-the-shelf or 3D-printed parts, bringing the acquisition cost to a point where most laboratories can afford it. Our software has an easy to use, yet powerful, graphical interface that uses a well-designed and flexible database to store protocols along with labware and modules’ specifications.
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<p>
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In addition to our basic platform, many modules were created:<br>
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<ul>
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<li>Single channel pipette using a special tip holder that can accommodate any standard tips (2 µl, 200 µl and 1000 µl);</li>
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<li>Multi-channel pipette (8 channels) with tip holder compatible with any standard tips (2 µl, 200 µl and 1000 µl);</li>
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<li>Gripper for tubes, plates and tip boxes;</li>
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<li>Centrifuge for 1.5 ml and 5 ml tubes;</li>
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<li>A magneto- caloric module for 1.5 ml tube (heat or cool 1.5 ml tube, and apply magnetic field for protocols using magnetic beads);</li>
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<li>A magneto-caloric module for 96-well plate tube (heat or cool 96-well plate, and apply magnetic field for protocols using magnetic beads);</li>
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<li>Turbido Agitator Caloric module (heat or cool a 2.5 cm glass tube, mix the liquid using a magnetic stir bar, and measure optical density in real-time even in the presence of ambient light).</li>
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</ul>
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</p>
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<p>
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As the hardware and the software are open source, creating or interfacing new modules that works with the platform can be easily done!
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</p>
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<p>
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Using our modules and software, the BIOBOT platform will allow the automation of many synthetic biology applications. For example, a recombineering experiment could be performed in a totally automated fashion by including the following steps: cell culture, optical density measurement, cell wash and preparation by centrifugation, electroporation, recovery of transformed cells, and plating. To do so, a “scarless” genome editing deletion system is being constructed using an inducible toxin and a double selectable marker (amilCP and KanR). Those markers will make the cells blue and resistant to kanamycin, a feature that could serve the robot to eventually be able to see which colonies are most likely to be good. A second recombineering step could remove this cassette without any residual “scar” sequence through a counterselection using the inducible toxin. The details about these parts and the related experiments are shown in Biologic Parts section.
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<p>Tell us about your project, describe what moves you and why this is something important for your team.</p>
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<div class="imageContainer">
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<br />
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<img width="50%" src="https://static.igem.org/mediawiki/2015/8/84/Team_Sherbrooke_3D_Whole_Platform.png" /><br/>
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<p>Robotic Platform Main Assembly</p>
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<h5>What should this page contain?</h5>
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<ul>
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<li> A clear and concise description of your project.</li>
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<li>A detailed explanation of why your team chose to work on this particular project.</li>
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<li>References and sources to document your research.</li>
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<li>Use illustrations and other visual resources to explain your project.</li>
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<h2>Also in "Project"</h2>
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<a href="https://2015.igem.org/Team:Sherbrooke/Experiments"><li>Experiments & Protocols</li></a>
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<a href="https://2015.igem.org/Team:Sherbrooke/Results"><li>Results</li></a>
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<a href="https://2015.igem.org/Team:Sherbrooke/Design"><li>Design</li></a>
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</ul>
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<h4>Advice on writing your Project Description</h4>
 
  
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We encourage you to put up a lot of information and content on your wiki, but we also encourage you to include summaries as much as possible. If you think of the sections in your project description as the sections in a publication, you should try to be consist, accurate and unambiguous in your achievements.
 
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Judges like to read your wiki and know exactly what you have achieved. This is how you should think about these sections; from the point of view of the judge evaluating you at the end of the year.
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<h4>References</h4>
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<p>iGEM teams are encouraged to record references you use during the course of your research. They should be posted somewhere on your wiki so that judges and other visitors can see how you though about your project and what works inspired you.</p>
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<h4>Inspiration</h4>
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<p>See how other teams have described and presented their projects: </p>
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<ul>
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<li><a href="https://2014.igem.org/Team:Imperial/Project"> Imperial</a></li>
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<li><a href="https://2014.igem.org/Team:UC_Davis/Project_Overview"> UC Davis</a></li>
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<li><a href="https://2014.igem.org/Team:SYSU-Software/Overview">SYSU Software</a></li>
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</ul>
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Latest revision as of 18:54, 3 October 2015

Re-inventing the lab: Development of a highly flexible, affordable and open source robotic automation platform


Almost everyone working or studying in biology have heard about liquid handlers and robots dedicated to biological sciences. Despite the fact that many know about them, and could potentially use them in their lab, very few scientists actually use automation.

One of the main difficulties is getting access to one of these robots. They are expensive and only highly funded laboratories can afford them. However, even if students or scientists have access to an automation platform, they often barely use it. 1) The consumables used by these robots are expensive and can cost up to 10 times more than the usual consumables found in a laboratory, which is simply too pricey for most research groups to afford for day to day operations. 2) Robots are generally built for specific protocols with high-throughput applications in mind, and lack the flexibility required to easily expand their application range. 3) Many lower throughput but still time-consuming and repetitive experiments cannot be performed by current robots because specific modules that support their automation are not available or too costly. 4) Third party modules are generally not compatible between manufacturers because of proprietary hardware and software. 5) Other problems like complicated not sufficiently flexible software tools (with costly updates) or the need to have dedicated personnel trained to run the robots discourage many potential users.

Our team has developed an affordable, modular and open source robotic automation platform to address these problems. Our platform and accessory modules are built from affordable off-the-shelf or 3D-printed parts, bringing the acquisition cost to a point where most laboratories can afford it. Our software has an easy to use, yet powerful, graphical interface that uses a well-designed and flexible database to store protocols along with labware and modules’ specifications.

In addition to our basic platform, many modules were created:

  • Single channel pipette using a special tip holder that can accommodate any standard tips (2 µl, 200 µl and 1000 µl);
  • Multi-channel pipette (8 channels) with tip holder compatible with any standard tips (2 µl, 200 µl and 1000 µl);
  • Gripper for tubes, plates and tip boxes;
  • Centrifuge for 1.5 ml and 5 ml tubes;
  • A magneto- caloric module for 1.5 ml tube (heat or cool 1.5 ml tube, and apply magnetic field for protocols using magnetic beads);
  • A magneto-caloric module for 96-well plate tube (heat or cool 96-well plate, and apply magnetic field for protocols using magnetic beads);
  • Turbido Agitator Caloric module (heat or cool a 2.5 cm glass tube, mix the liquid using a magnetic stir bar, and measure optical density in real-time even in the presence of ambient light).

As the hardware and the software are open source, creating or interfacing new modules that works with the platform can be easily done!

Using our modules and software, the BIOBOT platform will allow the automation of many synthetic biology applications. For example, a recombineering experiment could be performed in a totally automated fashion by including the following steps: cell culture, optical density measurement, cell wash and preparation by centrifugation, electroporation, recovery of transformed cells, and plating. To do so, a “scarless” genome editing deletion system is being constructed using an inducible toxin and a double selectable marker (amilCP and KanR). Those markers will make the cells blue and resistant to kanamycin, a feature that could serve the robot to eventually be able to see which colonies are most likely to be good. A second recombineering step could remove this cassette without any residual “scar” sequence through a counterselection using the inducible toxin. The details about these parts and the related experiments are shown in Biologic Parts section.


Robotic Platform Main Assembly


Also in "Project"