Overview

"When it comes to software, I much prefer free software, because I have very seldom seen a program that has worked well enough for my needs, and having sources available can be a life-saver."

Linus Torvalds

An important part of our project was the screening for substrates All this data was generated using a Hamilton robot for liquid handling. This robot enabled us to find the right organism to degrade our oily waste product. Such experiments are generally a great tool, to validate the growth on particular substrates or the degradation of toxic compounds. Furthermore, they can be used to compare different strains. However, we realized that it is a technology not everyone has access to.

To challenge this, we started a hardware project aiming to develop a cheap alternative to the Hamilton robot. A small device, that would enable hackerspaces and highschoolers to easily acquicire and compare growth data for their projects. To make this device as cheap as possible, we reduced the Hamilton to its key features:

Results

We build a working prototype that:

• can be rebuild at a cost of approx. US$ 150
• Demonstrate its functionality
• Integrate feedback from prospective users
• Provide all source files for other developers

Theory

Growth rates and spectrophotometry

Basic concept - measuring OD

When assessing growth of microorganisms, it is necessary to be able to obtain and interpret information about population size, or at least concentration at a given time. Optical Density (OD\(_{600}\)) measurement is a widely used, suitable method known by everyone familiar with biotechnology. This principle is based on spectrophotometry, where a light transmission of 600 nm passes through biological material and the resulting transmittance, \(\Phi\) is measured at the receiver end. Because biological material reflects light, higher biological density reflects more light, giving lower transmittance readings. Thus, at full transmittance, \(\Phi_{\text{ref}}\), OD\(_{600}\) should be equal to 0.

For the Microfermentation Platform, OD\(_{600}\) at time t is calculated from the Lambert-Beer law REFERENCE: $$ \text{OD}_{600,t} = -\log\Bigg(\frac{\Phi_t}{\Phi_{\text{ref}}}\Bigg) $$ Where the light source is an LED, with its intensity controlled by some input voltage, and the transmittance is measured by a sensor and recorded as a voltage.

Growth curves of microorganisms

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From Spectrophotometer to Fermenter

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User testing

This device is meant to go out to fellow iGEMers and Hackerspaces. So intuitively we brought it to our friends from the local hackerspace Biologigaragen and our highschool student Tobias

Higschool student: Tobias

Tobias had no problems following the protocol we wrote. He liked the menu and the overall design. However, he mentioned that it was difficult to take the cuvettes out again from the robot because the holder is embedded very deeply in the housing. He helped himself by removing a panel and accessing the chambers from the side. A future prototype might be build slightly larger in order to increase comfort.

However, we also detected one major flaw. The protocol given to him did not include a point about regulating the airflow and the pump was only switched on while running the fermentation. Therefore he did not adjust it, causing most of the liquids to spill out in the housing and causing the program to crash. Consequently we adapted the protocol and the program so that the airflow could be regulated correctly prior to fermentation.

Hackerspace: Biologigaragen

Proof of concept

During the development, the design had to be tested several times and the results are shown there. After testing the protocol with Tobias, we ran a final test to prove that the overall concept is working now. The results are shown below

Prototyping

The prototype was build using laser cutting, 3D-printing and printed custom boards (PCB). It is controlled by an Arduino UNO R3 that was programmed using the Arduino IDE. All the files are created in the native formats of open source programs. We have used the following programs and recomend them, as the source files are in the respective native formats. In addition, all these programs have great communities to help, if you get stuck.

Make your own

We built this prototype with the purpose to share it with hackerspaces, highschools and other iGEM teams world wide. We cannot afford shipping devices all over the world but with the files below, you can recreate your own device, you will only need the ArduinoIDE out of the softwares mentioned before.

In principle, you can send the files out to different manufacturers and they will ship you the requested parts. We recomend this option for the circuit board, because US$ 16 for 10 copies is very good value for money. Especially if you have never soldered before, you might need one or 2 boards before you get a feeling for it.

For laser cutting and 3D-printing, we recommend you to ask around first. Especially 3D-printers are increasingly popular and the next fablab might be closer than you think. This will not only save you some money but bring you in contact with other makers.

Acknowledgements

We have worked very hard this summer to create this device and achieved something that seemed totally out of reach only a few months ago. This would not have been possible without the help of other people. We would especially like to thank our supervisor Chris and Martin and Erik to pushing this project into the right direction. To see who else helped us along the way, see the full credit on our Acknowledgements page