Open Source!

Open Source

Leveraging Free and Open Source Software and Hardware (FOSS/FOSH) for capacity building in education and research.

The ascent of the internet has brought about many fundamental changes about the way we interact with each other and the world around us. One key aspect of this is the Open Source movement. The ability for anyone with an internet connection to create and share ideas and pieces of code freely over the internet has redefined software engineering from a niche for only for few specialists to the global community. But the open source movement does not stop there. Recent development of key open hardware tools make it possible to build real, physical machines, ranging from simple household items to complex and highly specialized laboratory equipment. Two developments are key: Cheap microcontroller boards, such as the 20-30€ Arduino, and the steeply falling costs of 3D printers (today a state-of-the-art printer can be purchased for well below 1,000 €). Accordingly it is now possible to establish a “home factory” for customized hardware: Mechanical parts are designed on a computer on free software and subsequently printed on a 3D printer, while the electronics are set-up from off-the-shelf electronic components and controlled using microcontrollers and a few lines of code.

Of course, plenty of free-to-download designs for all kind of devices are available on online repositories such as Thingyverse or Instructables. Even the need for a full-fledged computer system is rapidly coming to be obsolete in many applications: Modern mobile phones today carry more processing power than top-end computers only a few years ago. Indeed, the recent release of the Raspberry Pi computer does just that. It costs 30-40 €, is the size of a credit card and boasts processing power comparable to that of a modern iPhone. With an SD card as hard-drive, USB ports, Ethernet connectivity and two display adapters, the RPi easily suffices for many but the more demanding computational tasks needed in a research setting.

Therefore, it is today both affordable and possible to set up a complete home-factory for sophisticated scientific equipment for under 1,000 €. The impact of these possibilities can scarcely be overstated. Products are much cheaper than commercial equivalents, customized to specific demands, and can be produced locally within a few hours. Moreover, free sharing of designs via the internet means that the best designs will rapidly find a vast contributor-base to fix bugs or modify for new applications – a global community for free product design. Critically, the workflow is not overly complicated and requires little previous knowledge – indeed, some of the most influential figures in the open source movement are children and teenagers. The only real limitation is knowledge about the possibilities, and confidence to use them.

Still not convinced? Watch these videos, and/or check out a recent presentation by T Baden on Open Hardware

Key Resources

Open Neuroscience: a website all around Open source projects for use in Neuroscience education and research, run by our Open source Guru: Andre Maia Chagas

Our “Tinkering workshop” in Tübingen, Germany includes 3D printers, Arduino microcontrollers and other low-cost/hi-tech gadgets. Here we develop tools that we think will be useful in an African laboratory setting.

Some projects

3D printable Microcope for histology based on Raspberry Pi

3D printable lens adapter to turn a smartphone into a simple pocket-microcope

3D printed Micromanipulator based on a previous open design from Timothy Marzullo, Backyard brains

3D printed high precision pipettes based on a previous open design from Kevin Walus (UBC, Vancouver, CA)

Arduino Psychophysics experiment by Andre Maia Chagas of OpenNeuroscience

– The TReNDberry Pi

Frequent links to the global biohacker community, e.g. Backyard brains, and many others. E.g. see this collection of Open Lab tools

 

Upcoming training courses

– Workshop at University of Addis Ababa, Ethiopia on “Building your own laboratory equipment” – TBC

– Bioinformatics training using open source approaches at ICIPE, Kenya – TBC

– Module on building extracellular amplifiers from scratch as part of our next neuroscience summer school in Dar es Salaam, Tanzania in August 2014.

 

Past Events and Resources

December, 2013     TReND Christmas campaign to raise funds towards a 3D printer for African labs.

August, 2013        Building Extracellular amplifiers from scratch, and lectures on use of free and open software and hardware tools – as part of our summer schools

August, 2012        Building Extracellular amplifiers from scratch, and lectures on use of free and open software and hardware tools – as part of our summer schools

 

Open Source Team:

Tom B, Centre for Integrative Neuroscience (CIN), University of Tübingen, Germany

Andre M C, Centre for Integrative Neuroscience (CIN), University of Tübingen, Germany

Jelena A, WT-MRC Stem Cell Institute, University of Cambridge, UK

Lucia L PG, Centre for Integrative Genomics (CIG), University of Lausanne, Switzerland

Angelo T, UCL, London, UK

Horst S, Innowep, Würzburg, Germany

 

Some further reading:

Pearce, Joshua M. The Case for Open Source Appropriate Technology. Environment, Development and Sustainability (2012). pdf

 

 

Massively scalable

Because these technologies are free (or very cheap) compared to commercial alternatives, introduction of FOSS/FOSH approaches to African teachers and scientists is essentially only limited by the generation of awareness about them and basic training in their use.

Why it is important

There is no reason that African scientists should not be at the forefront of the Open Source movement, in terms of both implementation and development.

Why it is unique

It is not – that’s the whole point.

Who do we target

Researchers, both junior and senior to achieve a carry-on effect onto their peers and students.