Open source plays vital role in scientific advances

By Marilyn de Villiers
Johannesburg, 06 Jul 2018

While the open source movement initially came into being as a way to "democratise" software development, it is now playing an increasingly important role in the development of cutting edge technologies in a wide range of non-IT fields, including medicine and science.

For example, researchers from Chile, who have just been awarded the 2018 PLOS Open Source Toolkit Channel Prize, relied heavily on open source software and hardware for the development of a low-cost fluorescent imaging system.

This system can be used in a wide range of fields including laboratory medicine, pharmacology, environmental biology and molecular biology to image assays. It could also be used in an educational environment for the teaching of biology.

In their article, the researchers make the point that following the impact of free and open source software in software development, open hardware will accelerate hardware development in a similar manner, enabling laboratories around the world to design and make their own equipment.

They believe these designs could replace commercial scientific instrumentation with self-manufacturing, lowering costs by over 90%.

This is precisely what happened when they used open source tools to develop their imaging system.

"The total cost of our device is approximately US$250, including all components, materials, 3D printing [...] Commercial equivalents can cost as much as US$10 000 with less functionality," they said. "Reducing costs and using accessible components lowers the access barrier to scientific experiments and democratises science."

Powerful, low cost

Part of the process involved in producing the imaging system was the development of open source Python code. The code developed by the researchers was used to operate hardware that is used for time-lapse experiments. In addition, a Python module was developed to extract meaningful biological information and analyse data.

In line with the open source philosophy, the researchers have made all the resources developed in the process of producing the imaging system available under open source licences. The Python code developed to operate hardware, run experiments and store the resulting imaging sequences, for example, is available on Github.

PLOS is a non-profit publisher and advocacy organisation which has set up several channels as information resources for various research communities. The PLOS Open Source Toolkit is a global forum for open source hardware and software research and applications. The winners of the various PLOS channel prizes were selected via a Twitter poll.