Difference between revisions of "Team:Sherbrooke/Description"

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<h2> Project Description </h2>
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<h2 align="center">Re-inventing de lab: Development of a highly flexible, affordable and open source robotic automation platfom</h2>
  
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<p class="normal">A lot of technology fields are growing at an incredible fast pace. Just think of transport electrification with Tesla’s Model S, further and further space travel such as ESA Rosetta space mission, SpaceX's project to recycle space rocket, or simply your newly released cell phone. For instance, biology is part of those fields that are evolving incredibly fast. But, the automation of biology technics in research and robotisation in biology are not still developed enough nor it is affordable to most laboratory. In an era where everything is automated with robot almost as soon it is feasible, biology lab researchers are still working heart and soul, day and night, to perform repetitive and time consuming lab manipulations that could easily be done by a robot.</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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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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Professor Sébastien Rodrigue, biologist at the University of Sherbrooke located in Quebec, Canada, wanted to bring manipulations of biology lab to an upper level. He decided to propose a project to the electrical and software engineering students at the university to design and built an automatic robotic platform that could do so. Our group of student gratefully accepted this thrilling challenge and so the BIOBOT project officially started.
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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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In addition to our basic platform, many modules were created:<br>
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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 denisity in real-time even in the presence of ambient light).</li>
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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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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 class="normal">The project will help him to bring lab manipulation to another level and to do so, an automated robotic platform with compatible auxiliary modules will be designed and built. This platform includes a Cartesian robot, a tool holding support with pipettes and a gripper, a centrifuge and auxiliary modules that include an ingenious mix of magnetism control, temperature control and instrumentation. All of these modules are explained in details in our Wiki’s Design page.</p>
 
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<p class="normal">Our platform will then be able to perform many pipetting operations, using a single-channel or a multi-channel pipette. It will also perform lab protocols that required control of temperature for solution in 1.5 mL and 96-well plate. For this kind of vessel, magnetisation to agglomerate particle on the vessel's inner-wall. One of the module will calculate turbidity of the solution in a glass test-tube that will be placed in the module. A centrifuge will also be interfaced with the robotic platform to be used during the protocols. Lastly, a gripper will be available when any labware need to be moved around, such as tip box or tubes.</p>
 
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<p class="normal">In addition to all its functionality, our platform have the advantage to be modular. That means that most of the module on the entire platform can be used independently of all the others. Our platform is also Open-Source so everyone can benefit of our work and adapt the platform to their needs. Compared to others platforms available on the market at the moment and that does the same actions as ours, the BIOBOT platform can perform many different types of operations, and it is also really affordable.</p>
 
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<p class="normal">Furthermore, the BIOBOT platform will hopefully be able to perform a recombineering experiment in a totally automated fashion including steps like: cell culture, optical density follow up, cell wash and preparation, electroporation, recuperation and plating. To do so, a clean deletion system will be 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 good. A second recombineering experiment could remove this cassette without any scars through counterselection with toxin induction. The details about the parts used and the experiments are shown in Biologic Parts section</p>
 
 
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Revision as of 14:15, 17 September 2015

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

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 denisity 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.


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