Difference between revisions of "Team:Cambridge-JIC/Design"

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<h1>Problem statement</h1>
 
<h1>Problem statement</h1>
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<p>The use of fluorescent markers is central to many iGEM projects. In fact, the most widely used coding BioBrick on the iGEM Parts Registry is that encoding GFP, with 514 uses. However, the tool generally used to characterise a construct’s fluorescence - a fluorescence microscope - is prohibitively expensive for most iGEM teams, costing over $30,000.
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<p>The use of fluorescent markers is central to many iGEM projects. In fact, the most widely used coding BioBrick on the iGEM Parts Registry is that encoding GFP, with 514 uses. However, the tool generally used to characterise a construct’s fluorescence - a fluorescence microscope - is prohibitively expensive for most iGEM teams, costing over $30,000.</p>
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<p>Therefore the problem we set out to tackle was <i> to design a cost-effective but precise method of quantifying fluorescence from the fluorescent proteins most commonly used in iGEM. </i></p>
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Therefore the problem we set out to tackle was <i> to design a cost-effective but precise method of quantifying fluorescence from the fluorescent proteins most commonly used in iGEM. </i></p>
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<h1>Design criteria</h1>
 
<h1>Design criteria</h1>
 
<p>The criteria any design <b>must</b> meet are: </p>
 
<p>The criteria any design <b>must</b> meet are: </p>
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<ul><li><p>Able to characterise GFP fluorescence</li></p></ul>
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<ul><p>Able to characterise GFP fluorescence</ul></p>
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<p>Other desired characteristics of our product were:</p>
 
<p>Other desired characteristics of our product were:</p>
 
<center><div style="margin-right: 40px"><img src="https://static.igem.org/mediawiki/2015/c/c8/CamJIC-Design-Table.png" style="width:100%; max-width: 800px">
 
<center><div style="margin-right: 40px"><img src="https://static.igem.org/mediawiki/2015/c/c8/CamJIC-Design-Table.png" style="width:100%; max-width: 800px">
 
   <p>© All About 3D Printing, 2015</p></center></div>
 
   <p>© All About 3D Printing, 2015</p></center></div>
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<h1>Design criteria</h1>
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<h1>Potential Solutions</h1>
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<p>The criteria any design <b>must</b> meet are: </p>
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<p>We designed a low-cost, open-source fluorescence microscope built mainly out of off-the-shelf and 3D-printable components. Anyone with access to our designs and a 3D printer should be able to build one for themselves. We compared how our design fared on our design criteria to a conventional fluorescence microscope:
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<center><div style="margin-right: 40px"><img src="https://static.igem.org/mediawiki/2015/5/51/CamJIC-Design-Conventional.png" style="width:100%; max-width: 800px">
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  <p>© All About 3D Printing, 2015</p></center></div>
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<center><div style="margin-right: 40px"><img src="https://static.igem.org/mediawiki/2015/4/45/CamJIC-Design-New.png" style="width:100%; max-width: 800px">
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  <p>© All About 3D Printing, 2015</p></center></div>
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<ul><p>Able to characterise GFP fluorescence</ul></p>
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<h1>Design Implications</h1>
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<p>OpenScope has the potential to change many areas beyond our initial goal of making fluorescence imaging accessible to iGEM team. Its low cost and ease of assembly open up many opportunities:</p>
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<ul>
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<li><p>Education: OpenScope could be used to introduce secondary-school students to fluorescence microscopy. Its low cost means it is well within a school’s budget, and is in fact cheaper than most school microscopes. Printing and assembling the microscope itself could also be an educational experience.</p></li>
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<li><p>Research: Most research labs are able to afford a commercial fluorescence microscope, but budget constraints mean there is usually one for the entire lab (with a specialised room) and time needs to be booked on it. This restricts its use significantly. Having several OpenScopes alongside it would enable researchers to quickly image new samples, or perform things like time-lapse imaging. OpenScope could also be integrated into other equipment like fume hoods or incubators.</p></li>
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<li><p>On the move: OpenScope is light weight and can be battery powered. This makes it ideal for fieldwork where a conventional fluorescence microscope would be impossible to carry. Its ability to be remote controlled means it can also be left in remote areas and be accessed at any point.</p></li>
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<li><p>Developing Countries: Its low cost makes it accessible to labs in developing countries, and its ease of assembly and service allows labs to use it without having to rely on spare parts and technical support from a distant company.</p></li>
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<p>Other desired characteristics of our product were:</p>
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<center><div style="margin-right: 40px"><img src="https://static.igem.org/mediawiki/2015/c/c8/CamJIC-Design-Table.png" style="width:100%; max-width: 800px">
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  <p>© All About 3D Printing, 2015</p></center></div>
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<h1>Environmental Impact</h1>
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<p>We looked at the potential environmental effects of all the components of OpenScope throughout their lifetime. Most of these components are mass-produced (with the exception of the 3D printed chassis) so the start of OpenScope’s lifecycle is managed already to industry standards.</p>
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<ul>
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<li><p>Chassis: OpenScope/’s chassis (which makes up the majority of its mass) is made of polylactic acid (PLA). PLA is a polymer derived from sugarcane or other plants, and is fully biodegradable. Thus the chassis itself has very little environmental impact.</p></li>
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<li><p>Raspberry Pi and Arduino: Raspberry Pi and Arduino are printed circuit boards which contain silicon chips. Some of their components, such as lead, cadmium or mercury, could be hazardous at the end of their life if they are not recycled or disposed of safely. However, the risks of environmental harm from these are significantly lower than those in the electronics we use every day.</p></li>
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<li><p>Optics and LEDs: These are made primarily of glass and plastic, which have limited to no environmental impact.</p></li>
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<h1>Social Impact</h1>
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<p>OpenScope, if it becomes widespread, has the potential to greatly expand the scope of fluorescence microscopy. The cost of fluorescence microscopes will no longer be as much of a barrier to synthetic biology research, making this kind of research much more accessible and widespread. Other tools can be developed which incorporate OpenScope, leading to other useful equipment being developed. The open-source licensing strategy we’ve used means anyone can develop on our hardware and software, leading to more equipment being developed based on OpenScope and some of our changes being introduced in other commercial initiatives as well. </p>
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Revision as of 09:58, 14 September 2015

CAMBRIDGE-JIC

Problem statement

The use of fluorescent markers is central to many iGEM projects. In fact, the most widely used coding BioBrick on the iGEM Parts Registry is that encoding GFP, with 514 uses. However, the tool generally used to characterise a construct’s fluorescence - a fluorescence microscope - is prohibitively expensive for most iGEM teams, costing over $30,000.

Therefore the problem we set out to tackle was to design a cost-effective but precise method of quantifying fluorescence from the fluorescent proteins most commonly used in iGEM.

Design criteria

The criteria any design must meet are:

  • Able to characterise GFP fluorescence

Other desired characteristics of our product were:

© All About 3D Printing, 2015

Potential Solutions

We designed a low-cost, open-source fluorescence microscope built mainly out of off-the-shelf and 3D-printable components. Anyone with access to our designs and a 3D printer should be able to build one for themselves. We compared how our design fared on our design criteria to a conventional fluorescence microscope:

© All About 3D Printing, 2015

© All About 3D Printing, 2015

Design Implications

OpenScope has the potential to change many areas beyond our initial goal of making fluorescence imaging accessible to iGEM team. Its low cost and ease of assembly open up many opportunities:

  • Education: OpenScope could be used to introduce secondary-school students to fluorescence microscopy. Its low cost means it is well within a school’s budget, and is in fact cheaper than most school microscopes. Printing and assembling the microscope itself could also be an educational experience.

  • Research: Most research labs are able to afford a commercial fluorescence microscope, but budget constraints mean there is usually one for the entire lab (with a specialised room) and time needs to be booked on it. This restricts its use significantly. Having several OpenScopes alongside it would enable researchers to quickly image new samples, or perform things like time-lapse imaging. OpenScope could also be integrated into other equipment like fume hoods or incubators.

  • On the move: OpenScope is light weight and can be battery powered. This makes it ideal for fieldwork where a conventional fluorescence microscope would be impossible to carry. Its ability to be remote controlled means it can also be left in remote areas and be accessed at any point.

  • Developing Countries: Its low cost makes it accessible to labs in developing countries, and its ease of assembly and service allows labs to use it without having to rely on spare parts and technical support from a distant company.

Environmental Impact

We looked at the potential environmental effects of all the components of OpenScope throughout their lifetime. Most of these components are mass-produced (with the exception of the 3D printed chassis) so the start of OpenScope’s lifecycle is managed already to industry standards.

  • Chassis: OpenScope/’s chassis (which makes up the majority of its mass) is made of polylactic acid (PLA). PLA is a polymer derived from sugarcane or other plants, and is fully biodegradable. Thus the chassis itself has very little environmental impact.

  • Raspberry Pi and Arduino: Raspberry Pi and Arduino are printed circuit boards which contain silicon chips. Some of their components, such as lead, cadmium or mercury, could be hazardous at the end of their life if they are not recycled or disposed of safely. However, the risks of environmental harm from these are significantly lower than those in the electronics we use every day.

  • Optics and LEDs: These are made primarily of glass and plastic, which have limited to no environmental impact.

Social Impact

OpenScope, if it becomes widespread, has the potential to greatly expand the scope of fluorescence microscopy. The cost of fluorescence microscopes will no longer be as much of a barrier to synthetic biology research, making this kind of research much more accessible and widespread. Other tools can be developed which incorporate OpenScope, leading to other useful equipment being developed. The open-source licensing strategy we’ve used means anyone can develop on our hardware and software, leading to more equipment being developed based on OpenScope and some of our changes being introduced in other commercial initiatives as well.

Useful Software

Below is a list of software programs that we have found useful for developing open-source hardware, supplemented with other commonly used programs:

  1. OpenSCAD – a free, open-source, parametric CAD platform used to design 3D objects for printing (available from here)

  2. Tracker – a free, open-source, video analysis and modelling tool. Used to track moving objects in videos and extract data (available from here)

  3. Cura 3D – a free, open-source 3D printer interface from Ultimaker. Used to control printer settings (available from here)

  4. Fiji - a free, open-source image processing and analysis platform. Particularly useful for microscopy (available from here)

  5. Inkscape – a free, open-source vector graphics package. Extremely useful for 2D design followed by linear extrusion (available from here)

  6. DesignSpark – a free electronics design software for PCB prototyping. Has an online library of over 80,000 parts (available from here)

  7. Scribus – a free, open-source graphics software. Particularly useful for publishing (available from here)

  8. Python – a free, open-source, programming language that allowed us to put together software quickly

  9. Nginx – A FOSS lightweight web server on top of which we built our web interfaces.

  10. OpenCV – A FOSS released under a BSD license that provides a library for image processing software (available from here)

For a detailed list of free, open-source software programs available, look here.