Members of the Global Open Science Hardware (GOSH) community believe that scientific progress is being held back by high equipment costs, proprietary designs, and suffocating intellectual property restrictions. However, a new report, crowdsourced from over 100 contributors in 30 countries, suggests that open-source hardware, digital fabrication, and collaborative research tools can provide academics and citizen scientists alike with a promising new solution.
The community gathered in Santiago for GOSH 2017, to discuss strategies on how open scientific technologies can be made accessible to all levels of society, particularly researchers in developing countries and communities wanting to gather and analyse data about their environment. The event, organised by Dr Max Liboiron, an environmental scientist from the Memorial University of Newfoundland, resulted in the completion of a “Roadmap for making Open Science Hardware ubiquitous by 2025.”
The GOSH Roadmap includes detailed guidelines for providing global access to scientific hardware that can be fabricated using open-source designs, rather than ordered from a catalogue. “Reproducibility is a hallmark of good science, and Open Science Hardware allows for greater reproducibility,” explains GOSH’s community manifesto, which was co-authored by Dr Liboiron and Greg Austic, in consensus with attendees from the first GOSH event in 2016 at CERN in Geneva.
GOSH defines Open Science Hardware as any piece of hardware used for scientific investigation that can be obtained, assembled, used, studied, modified, shared, and sold by anyone. This includes standard lab equipment, as well as auxiliary items such as sensors, biological reagents, and electronic components.
Dr Liboiron believes that many scientific endeavours are being held back by lack of access to the tools/materials required for even routine experimental techniques, which severely limits the ability of groups to engage in the scientific process.
Even with access to existing proprietary solutions, customising hardware to meet the needs of individual experimental setups is challenging, which can restrict the implementation of experimental designs and push back scientific progress. “The fact that a lot of modern scientific equipment is a consumer product that is patented, not supplied with full design information, and difficult to repair also blocks creativity and customisation,” Dr Liboiron explains.
Open Science Hardware can increase access to tools by lowering financial barriers to participation in research, and by providing flexibility for hardware customisation. The GOSH community hopes these efforts will help democratise scientific practice by increasing the diversity of people with the tools required to perform research for knowledge discovery, education, innovation, and civic action. Also, decentralised production chains, enabled by digital fabrication methods, could create markets where it is difficult to import scientific instruments.
For example, Prof. Tom Baden (University of Sussex) and colleagues published plans for FlyPi, a 3D-printable fluorescence microscope. He estimates that FlyPi costs around five times less than comparable models. “All of our designs are available on GitHub, and we also put the best ones on Thingiverse and Open-Labware.net so they are freely accessible to anyone who wishes to use them.”
The GOSH Roadmap’s purpose is to create a focused plan for addressing the primary barrier to Open Science Hardware achieving its full potential: communities that use and develop open hardware are diverse groups, often separated by geographical and disciplinary borders. This separation limits their ability to collaborate and collectively support Open Science Hardware as a single cohesive community.
The road to 2025
Despite this, many developers of open hardware for science are highly active when it comes to sharing designs and information online, but poor documentation means that many Open Science Hardware projects never go far beyond the research lab or small community that initiated them, which significantly limits their potential use and impact.
GOSH has identified three critical activities that will enable achievement of their ambitious goal by 2025. These include ensuring that information about Open Science Hardware is accessible to a broad audience, securing support from existing institutions, such as colleges and universities, and expanding the existing community. Also, the introduction of documentation standards and quality control guidelines will help ensure that projects are shared appropriately.
GOSH members will move forward with plans for scaling both the community and the reach of open hardware distribution, at GOSH 2018 in Shenzhen, China. Find out more at: hsmag.cc/luSFbQ.
Trawling the depths
esearchers believe that of the 5.25 trillion pieces of marine plastic in the world’s oceans today, 92% are microplastics less than 5 mm in size. These tiny plastic particles can easily be ingested by marine life as small as plankton, and studies have shown that they are capable of absorbing up to a million times more chemicals than their surrounding waters. Scientists are becoming increasingly concerned that widespread ingestion of these microplastics is causing toxicants that accumulate in animals to magnify up the food chain, causing a potential threat to human health.
In response, Dr Max Liboiron created Open Science Hardware project ‘BabyLegs’ as an inexpensive means to trawl for floating marine microplastics using nylon tights, soda pop bottles, and other readily accessible materials. Dr Liboiron designed the simple sampling system to mimic the $3500 Manta Trawl, a commercial net used by marine researchers to sample the surface of the ocean. “In essence, BabyLegs looks like a little person or jellyfish, and during presentations and field research, we treat the technology like a doll because it encourages people to approach us, talk to us, and share images of the technology,” she explains. “The goal of the project is to be as accessible as possible so that people in Canada’s remote northern communities can monitor plastics in their fishing and hunting areas.”
The province of Newfoundland and Labrador has over 18 000 miles of rugged coastline, which is about twice as much as the entire United Kingdom. Many of those living outside of St. John’s, the province’s major city, do not have a regular income and lack year-round access to external supplies. This causes them to depend heavily, and even at times exclusively, on the ocean for survival.
“Rural, low-income, and Aboriginal communities rarely have control over the type of scientific questions that are asked about their areas,” says Dr Liboiron. “Our goal is to increase the ability of underserved communities to identify, redress, remediate, and create awareness and accountability around environmental concerns.”
Babylegs at sea
In March 2015, BabyLegs was first used in a raw sewage outflow from a rural community in Newfoundland, Canada. “We caught microplastic fibres from kitchen scrubbers and fibreglass strands from cigarette filters,” explains Dr Liboiron. “In Newfoundland, where I live and work, there is almost no information on the state of marine plastics, even though the province’s cultures and livelihoods are focused on the ocean.”
Dr Liboiron stresses that the data gathered by BabyLegs is qualitative rather than quantitative, meaning that you can identify types of plastics, as well as a general ratio of plastic types in your sample, but you cannot estimate the total amount of plastics in any given area. This is because as the flow of water picks up speed, the holes in the tights expand, enabling some of the smallest microplastics already collected to escape.
This type of research in Northern Canada is very tough. Most beach survey protocols – where volunteers and scientists count plastics that wash up on beaches – assume warm, sandy beaches. Currently, there are no established protocols on how to gather and study ocean plastics in an often frozen and rocky setting, like Newfoundland. “Plastics less than 5 mm in size, the most plentiful of marine plastics, disappear between rocks, making it seem as though our main type of plastic pollution is large fishing gear,” says Dr Liboiron.
To overcome this problem, a group of Dr Liboiron’s students, including Cian Kavanagh, Colin Grenning, and Nicolas Brouard-Ayres, began designing a “plastic eating device for rocky ocean coasts”, to catch microplastics that would otherwise disappear between rocks before a sample could be taken. Should an unsuspecting beachcomber stumble across the device, P.E.D.R.O.C. (as it’s affectionately known) includes a flag that describes what the technology is being used for and how passers-by can make their own. Although still in development, the P.E.D.R.O.C. 2.0 prototype was successful in detecting marine microplastics and surviving a short period of deployment on Topsail Beach, Newfoundland, an area of extreme kinetic wave energy.
Another notable project from CLEAR is the ‘Ice Cream Scoop’, an educational tool to help children learn about the marine environment by allowing them to see the presence of plastics in the ocean first hand. Additionally, there is the ‘Plastic Entanglement Trap’, a static ocean plastic monitoring device, which can be anchored in the water near a shoreline, where plastics are commonly found.
If you want to start gathering your data or contribute to one of these projects, there are many ways you can get started. A list of open-source tools and protocols to guide you through creating your studies on marine plastic pollution is available from the Civic Laboratory for Environmental Action Research website at: hsmag.cc/eoqUPe.
FlyPi Modular Microscopy System
Prof. Tom Baden, a neuroscientist at the University of Sussex, worked with André Maia Chagas of the University of Tübingen to develop the FlyPi, a 3D-printable open-source microscopy system. The FlyPi is based on a Raspberry Pi 3, Arduino Nano microcontroller, high-definition camera, and a range of off-the-shelf electronic components. All of the mechanical parts of their device are 3D-printed and allow for modular placement of additional components, including holders for Petri dishes and microscope slides. In its simplest form, the FlyPi can be assembled for well under £100. This remarkably low price means that the FlyPi can be used by under-funded labs across the world, for classroom teaching in schools, and by enthusiasts interested in participating in citizen science.
All-in-one biology lab
Tom explains that the average assembly time for the FlyPi, including the complete software setup, usually takes around two to three hours. However, those without previous soldering experience should expect it to take up to five hours. “FlyPi is not our only creation; we have actually built several pieces of equipment – pipettes, micromanipulators, and “even a pico-injector,” he says. “But some form of microscope is at the core of most biomedical labs and, as such, it’s an obvious starting point.”
According to Tom, the ever falling price of high-performance charge-coupled device (CCD) chips and optical components means that a functional neuroscience laboratory, capable of delivering high-quality research data can be built from scratch for magnitudes less than the cost required to purchase a single commercial scientific instrument. “If you break the lens out of a cheap laser pointer and tape it over a mobile phone camera, you already have a pretty powerful microscope in your pocket,” Tom explains.
While developing the FlyPi, Tom and André discovered that a popular 12 mm adjustable-focus camera module for the Raspberry Pi could already be used as an effective microscope by screwing the objective lens all the way out and aligning the optics to bring nearby objects into focus on the CCD chip. “We stumbled across this when using the camera system in an attempt to film some fruit flies in the lab, so we just integrated the feature into our microscope design,” says Tom.
And although the FlyPi doesn’t match the image clarity of most commercial microscopes, it definitely outperforms its rivals in regards to flexibility. “If you want to, you can point the camera at a tree, zoom out, and do a time-lapse over several days. Or, you can zoom all the way in, point it at a blood smear, and count macrophages,” Tom explains. When coupled with coloured sheets of plastic commonly used for theatre lighting, the system also allows for some forms of fluorescence microscopy, which can be used for tasks such as spotting parasites in tissue samples, or identifying different types of white blood cells.
To survey to what extent the FlyPi may be beneficial in a classroom scenario, Tom and André ran a series of multi-day workshops at universities in sub-Saharan Africa. In one workshop, 3D-printed parts, custom PCBs, and off-the-shelf electronics were provided to students that were then guided through the entire process of assembly and installation. Although these students had no previous experience with electronics or soldering, all of them were able to successfully assemble a working FlyPi. Assembling, using, and maintaining Open Science Hardware like the FlyPi can help students and citizen scientists expand their confidence, ideally inspiring them to build and modify other pieces of equipment themselves, which in a teaching scenario, as Tom quite rightly points out, is perhaps the most significant benefit of all.
The current version of the FlyPi only scratches the surface of possible applications, and a recent community-driven modification to the 3D-printed frame repositioned the camera and focus motor below a closed stage, resulting in a substantially more robust design, which is far better suited to classroom teaching. Other community-driven modifications include a version where all the 3D-printed parts have been replaced by LEGO bricks, as well as several forks geared towards optimising the code, 3D models, and expanding the electronic control circuits to include additional modules.
Tom and André have also set up a centralised public repository for anyone to access their Open Science Hardware projects: Open-Labware.net. This repository includes the Openspritzer, an open-source ‘Picospritzer’ that reportedly performs just as well as four-figure commercial models, and the Spikeling, a low-cost hardware implementation of a spiking neuron for neuroscience teaching and outreach. “We think it is very important that neuroscientific training and research is opened up to larger numbers of students and junior scientists around the world,” says Tom.