Open Source Hardware is an opportunity for Synthetic Biology research – the DocuBricks approach by Tobias Wenzel

March 1, 2016 PLOS Blogs Synthetic Biology

by Tobias Wenzel

Open Source Hardware is an exciting new trend

Figure 1: OpenFlexture Microscope by Richard Bowman, UK, 3D printed and operated with a Raspberry Pi computer.

“This microscope is one of the cleverest pieces of open source hardware for laboratory use that I have seen so far” said Prof. Jim Haseloff in the Plant Science Department at the University of Cambridge, as he learned about a design by Richard Bowman. Richard, a fellow in the Department of Physics, was frustrated about the difficulty of working with conventional technologies for some of his experiments. For example fitting a growth chamber into a microscope can be a major challenge. Many conventional scientific instruments are designed to be incompatible to possible extensions and are not co-developed by the user community, leading to impractical designs. Thus he built his own digital microscope from a 3D printed chassis and a simple Raspberry Pi computer. The main challenge to solve for high-quality microscopy results was to position and stabilise the sample. He solved this with a one-piece 3D printed flexing mechanism in plastic. Now the microscope is ready for all sorts of adaption, it can even be placed inside commercial incubators or used in education and field uses – all at a tiny fraction of the price of conventional digital microscopes. What a great demonstration of the uses that are enabled by rapid prototyping methods! Increasingly available methods are e.g. 3D printing and laser cutting along with accessible electronic units such as Arduino microcontrollers or Raspberry Pi computers.

OpenTrans — Figure 2: OpenTrons pipetting robot for liquid handling, start-up by early Genspace members, USA

Richard is not alone in his desire to make experiments more reproducible, and customisable as well as automated. In the last few years, Open Ephys and Backyard Brains started providing tools for electrophysiology measurements, OpenTrons and open syringepump designs target the automation of liquid handling, the electrochemical potentiostat Cheapstat was a creation of an iGEM team and was published in 2011, a different iGEM team in 2015 created a fluorescence microscope adaptation of Richard’s initial design to join the ranks of another popular fluorescence microscope by Tom Baden and Andre Chagas from the University of Tuebingen, Germany. The last mentioned scientists also curate the PLOS Open Source Hardware collection where many other examples can be discovered.

Sharing equipment plans is an opportunity for experimental science, especially Synthetic Biology

Another noteworthy collection that demonstrates the fast raising popularity of Open Source Hardware is Joshua Pearce’s Appropedia and his book Open-source Lab. He illustrates the benefits of open scientific information sharing to the reader in depth. Beyond the arguments of openness, Open Source Hardware works well in science since many experimental set-ups are prototypes that are suitable for manual or rapid manufacturing methods and because technical training is widely available in science. Furthermore, it is a job requirement to demonstrate impact in this profession. Extending the publication-like sharing philosophy to hardware has worked well for the pioneers.

Synthetic Biology specifically can benefit from the open community engineering approach to bring the users and designers of complex interdisciplinary equipment closer together. The exchange of designs and protocols comes hand in hand with an increase of reproducibility of experiments, which is a major challenge of the field. The reproducibility is further enhanced by the additional number of eyes that can spot errors in protocols and improve processes without additional development cost. Open Source Hardware works well in businesses too, when equipment is expensive and specialised as is the case for most synthetic biology instruments. For example: OpenIOlabs is a young Cambridge company that (among others) is in the process of open sourcing many expensive equipment parts from the supply chain, in order to make their key products more accessible and IO Rodeo offers open source laboratory equipment for which the user can decide how many parts he wants to buy and what to build on their own. Users then often contribute improvements for free, which has most prominently driven the development cycles of 3D printers.

Many designs come from the DIY community. Are the bio laboratory designs good enough?

Figure 3: NinjaPRC, a thermocycler design for open source DNA amplification, by Shingo Hisakawa, Japan

A lot of existing open source designs come from the do-it-yourself (DIY) and maker community, as the trend only recently reached academia and business more widely. A group of scientists and makers in Cambridge, UK, tried to replicate open source designs for biology laboratory equipment to kickstart a DIY biolab and evaluate the designs along the criteria of safety, quality, adaptability and ease of build. Funded by a mini-grant of the Synthetic Biology Strategic Research Initiative, they attempted designs for electrophoretic gel boxes, a centrifuge, PCR thermocyclers, tube holders, syringe pumps and a 3D printer (more to be found online, soon). Unfortunately, the team discovered more problems than solutions: even in the documentation sets that looked good, essential parts were missing. Some designs referred to specific parts that are not generally available and that had to be shipped from the US for high costs. Most design files where difficult to adapt to other sizes of e.g. acrylic sheets when build from a metric rather than US-imperial material stock. Assembly sets that could be ordered commercially were complete and had decent to good assembly instructions, but the documentations were usually not sufficient to build the hardware without buying the set, thus not fully deserving the label ‘Open Source Hardware’.

Open Source Hardware + good documentation; it just got easier with DocuBricks

There is a lesson to be learned from the incompleteness of commercial assembly-set documentations: Open Source Hardware is more than an assembly instruction. It is also about documenting design files and decisions along its functionality and in a modular fashion, complete with testing and calibration instructions. A good documentation enables the project to grow and improve without the doing of the inventor. Only in this way most projects can enfold their benefit well to society and technology companies. To be sure, documenting a hardware project is not easy and requires time. For this reason a handful scientists at the University of Cambridge (including the author), all with a background in technology and biology, recently started the DocuBricks initiative. DocuBricks is an open source and free software that makes documenting hardware and usage procedures easier. The name is a reference to modularity in the same way as Lego or BioBricks. As the name suggests, the editor part of the software guides the user through a modular documentation structure with relevant fields in a standardised, yet general format. The user can create a hierarchy of documentation bricks, explaining their function, implementation and assembly while referring to a parts library. The result is a XML document and a folder with construction and media files that is displayed with the viewer part of the software (a style sheet and script to enable interactivity).

Over the database with the same name, DocuBrick.com, the projects can be shared and found. The team puts emphasis on impact tracking and acknowledgement, to make engagement in Open Source Hardware not only easier, but also more promising to the scientific community. Projects can also be cited via DOI’s, which are internationally curated short links and the standard way of referencing scientific literature. The new initiative is growing fast: Richard Bowman’s microscope from the beginning of this article can already be found. The wireless communication designs of Shuttleworth Fellow and collaborator Luca Mustafa will be released soon, just like several projects of the OpenPlant Initiative in Cambridge and a number of other scientific interest groups. Even a journal on Open Source Hardware from the Ubiquity Press will be launched and intends to use DocuBricks as the preferred documentation format. When will you join the effort to make science more open and reproducible?

Tobias Wenzel is a PhD candidate at the University of Cambridge and DocuBricks founder. This blog is a summary of a presentation given at Cafe Synthetique in November 2015.

https://uk.linkedin.com/in/wenzeltobias

http://www.winton.phy.cam.ac.uk/directory/TWenzel