Team:Cambridge-JIC/Design

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

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

OpenSCAD Design

We are using an open-source software called OpenSCAD to design our components. Here the focus is on the CAD aspect, making it extremely powerful for designing machine parts. It is not an interactive modeller, and instead reads a script and compiles a 3D image. This allows configurable parameters to be programmed in to the designs.

When creating lens holders for the Optics Bench, this became extremely useful as the parameters for each lens could be filled in individually. A single design was readily modified to make each individual component. The software outputs .scad files, which can then be converted to .stl for printing.

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.