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

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

A list of design criteria for our hardware.

Potential Solutions

We have designed a low-cost, open-source microscope built mainly from off-the-shelf and 3D-printable components. Anyone with access to our designs and a 3D printer should will be able to build one for themselves. Comparisons were made of OpenScope to that of a conventional microscope:

Commercial fluorescence microscopes score 19 points.

Our OpenScope design scores 24 points on this scale.

Design Implications

OpenScope has huge potential to increase accessibility to microscopy to areas out with the iGEM project:

• 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 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

The potential environmental impact of the components of OpenScope were analysed over their lifetime . Most of these components are mass-produced (with the exception of the 3D printed chassis).

• 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 [1]. Being a thermoplastic it has the ability to be recycled into many different products at the end of its life.

• 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 to the environment if they are not recycled or disposed of safely [2]. The risks associated with these are significantly lower than most daily use electronics.

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

Social Impact

OpenScope has the potential to become widespread and greatly expand the accessibility of microscopy. The cost of microscopes will no longer be so much of a barrier to synthetic biology research. 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 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.

References

[1] Yutaka Tokiwa; Buenaventurada P. Calabia; Charles U. Ugwu; Seiichi Aiba, "Biodegradability of Plastics", 2009, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2769161/.

[2] Lucy McAllister, "The Human and Environmental Effects of E-Waste", 2015, http://www.prb.org/Publications/Articles/2013/e-waste.aspx/.