Haves and have nots must find a better way: The case for open scientific hardware

SPIRO - the automated Petri plate imaging platform designed by biologists, for biologists

Phenotyping of model organisms grown on Petri plates is often carried out manually, despite the procedures being time-consuming and laborious. The main reason for this is the limited availability of automated phenotyping facilities, whereas constructing a custom automated solution can be a daunting task for biologists. Here, we describe SPIRO, the Smart Plate Imaging Robot, an automated platform that acquires time-lapse photographs of up to four vertically oriented Petri plates in a single experiment, corresponding to 192 seedlings for a typical root growth assay and up to 2500 seeds for a germination assay. SPIRO is catered specifically to biologists' needs, requiring no engineering or programming expertise for assembly and operation. Its small footprint is optimized for standard incubators, the inbuilt green LED enables imaging under dark conditions, and remote control provides access to the data without interfering with sample growth. SPIRO's excellent image quality is suitable for automated image processing, which we demonstrate on the example of seed germination and root growth assays. Furthermore, the robot can be easily customized for specific uses, as all information about SPIRO is released under open-source licenses. Importantly, uninterrupted imaging allows considerably more precise assessment of seed germination parameters and root growth rates compared with manual assays. Moreover, SPIRO enables previously technically challenging assays such as phenotyping in the dark. We illustrate the benefits of SPIRO in proof-of-concept experiments which yielded a novel insight on the interplay between autophagy, nitrogen sensing, and photoblastic response.

The Duckbot: A system for automated imaging and manipulation of duckweed

Laboratory automation can boost precision and reproducibility of science workflows. However, current laboratory automation systems are difficult to modify for custom applications. Automating new experiment workflows therefore requires development of one-off research platforms, a process which requires significant time, resources, and experience. In this work, we investigate systems to lower the threshold to automation for plant biologists. Our approach establishes a direct connection with a generic motion platform to support experiment development and execution from a computational notebook environment. Specifically, we investigate the use of the open-source tool-changing motion platform Jubilee controlled using Jupyter notebooks. We present the Duckbot, a machine customized for automating laboratory research workflows with duckweed, a common multicellular plant. The Duckbot comprises (1) a set of end-effectors relevant for plant biology, (2) software modules which provide flexible control of these tools, and (3) computational notebooks which make use of these tools to automate duckweed experiments. We demonstrate the Duckbot's functionality by automating a particular laboratory research workflow, namely, duckweed growth assays. The Duckbot supports setting up sample plates with duckweed and growth media, gathering image data, and conducting relevant data analysis. We discuss the opportunities and limitations for developing custom laboratory automation with this platform and provide instructions on usage and customization.

Antropo: An open-source platform to increase the anthropomorphism of the Franka Emika collaborative robot arm

Robot-to-human communication is important for mutual understanding during human-robot collaboration. Most of the current collaborative robots (cobots) are designed with low levels of anthropomorphism. Therefore, the ability of cobots to express human-like communication is limited. In this work, we present an open-source platform named Antropo to increase the level of anthropomorphism of Franka Emika-a widely used collaborative robot arm. The Antropo platform includes three modules: a camera module for expressing eye gaze, a light module for visual feedback, and a sound module for acoustic feedback. These modules can be rapidly prototyped through 3D printers, laser-cutters, and off-the-shelf components available at a low cost. The Antropo platform can be easily installed on the Franka Emika robot. The added communication channels can be synchronised with the robot's motions to enhance mutual understanding. All hardware CAD design files and software files are released. The platform can be used to study human-like behaviours of cobots and the effects of these behaviours on different aspects of human-robot collaboration. We demonstrate the Antropo platform in an assembly task in which the Franka Emika robot expresses various human-like communicative behaviours via the added communication channels. We also present two industrial applications in which the Antropo platform was customised for the Universal Robots UR16e.

Open source framework for a Broadly Expandable and Reconfigurable data acquisition and automation device (BREAD)

Though open source data acquisition (DAQ) systems have been published, closed source proprietary systems are the standard despite often being prohibitively expensive. High costs, however, limit access to high-quality DAQ in low-resource settings. In many cases the functions executed by the closed source and proprietary DAQ cards could be carried out by an open source alternative; however, as desired function count increases, the simplicity of integrating the designs decreases substantially. Although the global library of open source electronic designs is expanding rapidly, and there is clear evidence they can reduce costs for scientists one device at a time, they are generally made to carry a function well, but are often not capable of scaling up or easily being integrated with other designs. Just as other open source projects have found success by having modular frameworks and clearly documented specifications, a framework to unify and enable interoperation of these open source electronics systems would be greatly beneficial to the scientific community. To meet these needs and ensure greater accessibility to high-quality electronics sensing and DAQ systems, this article shares and tests a news framework where new open source electronics can be developed and have plug-and-play functionality. The Broadly Reconfigurable and Expandable Automation Device (BREAD), consists of a basic set of guidelines and requirements to which others can contribute. Here 7 slices (boards) are provided, demonstrated, and validated: 1) Amplified Analog Input, 2) Audio Analysis / Fourier Transform, 3) +/- 10A Current Sensor, 4) 4-Channel Relay Controller 5) 4 Channel Stepper Motor Controller, 6) 4 Channel Type-K Thermocouple Reader and 7) 2 Channel USB Port. Implementing systems using BREAD rather than closed source and proprietary alternatives can result in cost savings of up to 93%.

AC/off-grid photovoltaic powered open-source ball mill

Ball milling is used for comminution by rotating a drum to grind materials using balls with specific diameters. Ball milling advantages include the potential for high capacity, predicted fineness in a specific amount of time, reliability, safety, and simplicity, but has disadvantages of high weight, energy consumption and costs, which limit accessibility. To overcome these limitations this study applies the free and open source hardware approach coupled to distributed digital manufacturing to fabricate a ball mill with a simple, customizable design that can be used in a wide range of scientific applications and circumstances including those without access to reliable grid electricity. The highly-customizable design reduces the cost to <US$130 for an AC powered version and <US$315 for a switchable power that enables off-grid operation with a solar module and battery. Using a solar photovoltaic energy source not only improves the power reliability, but also makes it easier to move the ball mill for use in field environments. The open source ball mill is capable of reducing silicon particle sizes from the millimeter scale down to the nanometer scale.

Development and Sharing of Open Science Hardware: Lessons Learned from Wikimedia Fellowships

The promise of open hardware as a branch of open science is a sustainable change of research instrumentation towards more openly documented and licensed designs. Methods, code, and data are already valued by journal editors and peer-reviews to judge if a study's result can be replicated with the information provided in a manuscript. The open hardware movement seeks to include laboratory tools and research instrumentation into the same category. Availability of and access to open hardware equipment are set to democratize professional lab work and field studies as well as enhance the transferability of methods to civic science settings. Here, we report four case studies from the first five years of the Wikimedia Program "Free Knowledge", an open science fellowship funded by Wikimedia Germany and partners. The project developers discuss and evaluate the impact related to key aspects typically attributed with open hardware: costs, availability, adaptability, community and educational value. The open hardware projects covered in this review span from natural sciences to life sciences to education.

Development and implementation of a significantly low-cost 3D bioprinter using recycled scrap material

The field of 3D bioengineering proposes to effectively contribute to the manufacture of artificial multicellular organ/tissues and the understanding of complex cellular mechanisms. In this regard, 3D cell cultures comprise a promising bioengineering possibility for the alternative treatment of organ function loss, potentially improving patient life expectancies. Patients with end-stage disease, for example, could benefit from treatment until organ transplantation or even undergo organ function restoration. Currently, 3D bioprinters can produce tissues such as trachea cartilage or artificial skin. Most low-cost 3D bioprinters are built from fused deposition modeling 3D printer frames modified for the deposition of biologically compatible material, ranging between $13.000,00 and $300.000,00. Furthermore, the cost of consumables should also be considered as they, can range from $3,85 and $100.000,00 per gram, making biomaterials expensive, hindering bioprinting access. In this context, our report describes the first prototype of a significantly low-cost 3D bioprinter built from recycled scrap metal and off-the-shelf electronics. We demonstrate the functionalized process and methodology proof of concept and aim to test it in different biological tissue scaffolds in the future, using affordable materials and open-source methodologies, thus democratizing the state of the art of this technology.

PiSpy: An affordable, accessible, and flexible imaging platform for the automated observation of organismal biology and behavior

A great deal of understanding can be gleaned from direct observation of organismal growth, development, and behavior. However, direct observation can be time consuming and influence the organism through unintentional stimuli. Additionally, video capturing equipment can often be prohibitively expensive, difficult to modify to one's specific needs, and may come with unnecessary features. Here, we describe PiSpy, a low-cost, automated video acquisition platform that uses a Raspberry Pi computer and camera to record video or images at specified time intervals or when externally triggered. All settings and controls, such as programmable light cycling, are accessible to users with no programming experience through an easy-to-use graphical user interface. Importantly, the entire PiSpy system can be assembled for less than $100 using laser-cut and 3D-printed components. We demonstrate the broad applications and flexibility of PiSpy across a range of model and non-model organisms. Designs, instructions, and code can be accessed through an online repository, where a global community of PiSpy users can also contribute their own unique customizations and help grow the community of open-source research solutions.

A review on low-cost microscopes for Open Science

This article presents a review after an exhaustive search that yielded 23 works carried out in the last decade for the availability of optical microscopes with open hardware as a low-cost alternative to commercial systems. These works were developed with the aim of covering needs within several areas such as: Bio Sciences research in institutions with limited resources, diagnosis of diseases and health screenings in large populations in developing countries, and training in educational contexts with a need for high availability of equipment and low replacement cost. The analysis of the selected works allows us to classify the analyzed solutions into two main categories, for which their essential characteristics are enumerated: portable field microscopes and multipurpose automated microscopes. Moreover, this work includes a discussion on the degree of maturity of the solutions in terms of the adoption of practices aligned with the development of Open Science. RESEARCH HIGHLIGHTS: Concise review on low-cost microscopes for developing Open Science, exposing the role of smartphone-based microscopy. The work classifies microscopes in two main categories: (1) portable field microscopes, and (2) multipurpose automated microscopes.

Design of a low-cost mobile multispectral albedometer with geopositioning and absolute orientation

Albedo is the percentage of radiation that a given surface reflects. Its study is important to evaluate thermal effects in buildings, generation capacity with bifacial panels, among others. In this work, the design and validation of a low-cost mobile albedometer is presented, which measures the reflection in 8 spectral bands in the visible, additionally the system is equipped with a Global Navigation Satellite System (GNSS) receiver, to reference its position and an Inertial Measurement Unit (IMU) to know its absolute orientation, make corrections in real time or detect errors. The purpose of designing the mobile device is to measure a larger area and, since it is georeferenced, it is to feed GIS tools that allow designers to use the information.

Professors want to share: preliminary survey results on establishing open-source-endowed professorships

This study proposes a novel policy to provide incentives for open science: to offer open-source (OS)-endowed professorships. To hold an open-source-endowed chair, in addition to demonstrated excellence in their field, professors would need to agree to (1) ensuring all of their writing is distributed via open access in some way and (2) releasing all of their intellectual property in the public domain or under appropriate open-source licenses. The results of this survey study of university professors in the U.S. show that a super majority (86.7%) of faculty respondents indicated willingness to accept an OS-endowed professorship, while only 13.3% of respondents would not be willing to accept the terms of an OS-endowed professorship. The terms of accepting an OS-endowed professorship that were the most popular among respondents were increased salary, annual discretionary budget, as a term of tenure and annual RA or TA lines. More than a quarter of responding professors declared that no additional compensation would be needed for them to accept the terms of an OS-endowed professorship. The results demonstrate a clear willingness of academics to expand open access to science, which would hasten scientific progress while also making science more just and inclusive. It is clear that science funders have a large opportunity to move towards open science by offering open–source-endowed chairs.

Open-Source Hardware May Address the Shortage in Medical Devices for Patients with Low-Income and Chronic Respiratory Diseases in Low-Resource Countries

Respiratory diseases pose an increasing socio-economic burden worldwide given their high prevalence and their elevated morbidity and mortality. Medical devices play an important role in managing acute and chronic respiratory failure, including diagnosis, monitoring, and providing artificial ventilation. Current commercially available respiratory devices are very effective but, given their cost, are unaffordable for most patients in low- and middle-income countries (LMICs). Herein, we focus on a relatively new design option—the open-source hardware approach—that, if implemented, will contribute to providing low-cost respiratory medical devices for many patients in LMICs, particularly those without full medical insurance coverage. Open source reflects a set of approaches to conceive and distribute the comprehensive technical information required for building devices. The open-source approach enables free and unrestricted use of the know-how to replicate and manufacture the device or modify its design for improvements or adaptation to different clinical settings or personalized treatments. We describe recent examples of open-source devices for diagnosis/monitoring (measuring inspiratory/expiratory pressures or flow and volume in mechanical ventilators) and for therapy (non-invasive ventilators for adults and continuous positive airway pressure support for infants) that enable building simple, low-cost (hence, affordable), and high-performance solutions for patients in LMICs. Finally, we argue that the common practice of approving clinical trials by the local hospital ethics board can be expanded to ensure patient safety by reviewing, inspecting, and approving open hardware for medical application to maximize the innovation and deployment rate of medical technologies.

Open Source Solutions in Experimental Design: An Introduction to the Symposium

The Open Science movement has increased dramatically in popularity with deserved calls to action around transparency, access to resources, and inclusion in our field. However, its practical applications within experimental design have been slow to uptake, with researchers unsure where to even start with the dizzying array of open source hardware and software solutions available. The perceived time investment and unknown cost, especially in implementing open source hardware, has stagnated the implementation of inexpensive experimental solutions, but we sought to increase awareness to lower the barrier to participation in this space. While there are countless technical and financial advantages to integrating open source solutions into every biologist's experimental design, we put an emphasis on the "people" part of the equation in our symposium. This symposium championed innovative experimental designs by early career SICB researchers across all fields of biology, from plants to animals, in the lab or in the field, or even virtually engaging with the public and students. The open science movement operates within community norms that champion transparency, continuous development, and collaboration. These values are congruent with the priorities of reducing barriers to participation in science, and we hope our symposium's collection of open source solutions encourages readers to adopt these or other innovative designs into their own experimentation.

Leveraging Intellectual Property to Prevent Nuclear War

Although international law forbids nuclear attacks, only nine states have mutually assured destruction available to prevent direct attacks against themselves, while non-nuclear states have few substantive options to deter a nuclear attack. This study analyzes the economic impacts of a theoretical international agreement that eliminates patent rights for any nuclear aggressor (i.e., free global compulsory licensing of all intellectual property (IP) for a nuclear aggressor). The results found that all but one of the nuclear states would have a significant economic disincentive to start a nuclear attack if the proposal was put into force. Payback times ranged from 1.2 to 40 years, where the entire GDP of a nuclear aggressor would be needed to offset the loss for aggression, indicate such a mechanism as a whole would be an effective nuclear deterrent. This method would not be universally effective without ensuring all nuclear states are members of the international economy and IP processes. With the growth of open-source products and reduced value of patents, this mechanism does have a limited effectiveness time. Currently it appears to be a policy trajectory worthy of future work that can enhance safety from nuclear threat without causing harm to countries of goodwill.

An Automated Scanning Transmission Electron Microscope Guided by Sparse Data Analytics

Artificial intelligence (AI) promises to reshape scientific inquiry and enable breakthrough discoveries in areas such as energy storage, quantum computing, and biomedicine. Scanning transmission electron microscopy (STEM), a cornerstone of the study of chemical and materials systems, stands to benefit greatly from AI-driven automation. However, present barriers to low-level instrument control, as well as generalizable and interpretable feature detection, make truly automated microscopy impractical. Here, we discuss the design of a closed-loop instrument control platform guided by emerging sparse data analytics. We hypothesize that a centralized controller, informed by machine learning combining limited a priori knowledge and task-based discrimination, could drive on-the-fly experimental decision-making. This platform may unlock practical, automated analysis of a variety of material features, enabling new high-throughput and statistical studies.

Bypassing shortages of personal protective equipment in low-income settings using local production and open source tools

Free and open-source hardware, 3D printing and the use of locally sourced materials are valuable tools for local problem solving. This Community Page describes how PPE supply chain problems could be bypassed using open science in a Nigerian community.

Strategic Investment in Open Hardware for National Security

Free and open-source hardware (FOSH) development has been shown to increase innovation and reduce economic costs. This article reviews the opportunity to use FOSH as a sanction to undercut imports and exports from a target criminal country. A formal methodology is presented for selecting strategic national investments in FOSH development to improve both national security and global safety. In this methodology, first the target country that is threatening national security or safety is identified. Next, the top imports from the target country as well as potentially other importing countries (allies) are quantified. Hardware is identified that could undercut imports/exports from the target country. Finally, methods to support the FOSH development are enumerated to support production in a commons-based peer production strategy. To demonstrate how this theoretical method works in practice, it is applied as a case study to a current criminal military aggressor nation, who is also a fossil-fuel exporter. The results show that there are numerous existing FOSH and opportunities to develop new FOSH for energy conservation and renewable energy to reduce fossil-fuel-energy demand. Widespread deployment would reduce the concomitant pollution, human health impacts, and environmental desecration as well as cut financing of military operations.

Institutionalizing Open Science in Africa: Limitations and Prospects

The advancement of scientific research and raising the next-generation scientists in Africa depend largely on science access. The COVID-19 pandemic has caused discussions around open science (OS) to reemerge globally, especially in resource-poor settings like Africa, where the practice of OS is low. The authors highlighted the elements, benefits, and existing initiatives of OS in Africa. More importantly, the article critically appraised the challenges, opportunities, and future considerations of OS in Africa. Addressing challenges of funding and leadership at different levels of educational, research, and government parastatals may be pivotal in charting a new course for OS in Africa. This review serves as an advocacy strategy and an informative guide to policymaking and institutionalization of OS in Africa.

Design and implementation of 3-D printed radiation shields for environmental sensors

The measurement of outdoor environmental and climatic variables is needed for many applications such as precision agriculture, environmental pollution monitoring, and the study of ecosystems. Some sensors deployed for these purposes such as temperature, relative humidity, atmospheric pressure, and carbon dioxide sensors require protection from climate factors to avoid bias. Radiation shields hold and protect sensors to avoid this bias, but commercial systems are limited, often expensive, and difficult to implement in low-cost contexts or large deployments for collaborative sensing. To overcome these challenges, this work presents an open source, easily adapted and customized design of a radiation shield. The device can be fabricated with inexpensive off-the-shelf parts and 3-D printed components and can be adapted to protect and isolate different types of sensors. Two material approaches are tested here: polylactic acid (PLA), the most common 3-D printing filament, and acrylonitrile styrene acrylate (ASA), which is known to offer better resistance against UV radiation, greater hardness, and generally higher resistance to degradation. To validate the designs, the two prototypes were installed on a custom outdoor meteorological system and temperature and humidity measurements were made in several locations for one month and compared against a proprietary system and a system with no shield. The 3-D printed materials were also both tested multiple times for one month for UV stability of their mechanical properties, their optical transmission and deformation under outdoor high-heat conditions. The results showed that ASA is the preferred material for this design and that the open source radiation shield could match the performance of proprietary systems. The open source system can be constructed for about nine US dollars, which enables mass development of flexible weather stations for monitoring needed in smart agriculture.

Open-source, Python-based, hardware and software for controlling behavioural neuroscience experiments

Laboratory behavioural tasks are an essential research tool. As questions asked of behaviour and brain activity become more sophisticated, the ability to specify and run richly structured tasks becomes more important. An increasing focus on reproducibility also necessitates accurate communication of task logic to other researchers. To these ends, we developed pyControl, a system of open-source hardware and software for controlling behavioural experiments comprising a simple yet flexible Python-based syntax for specifying tasks as extended state machines, hardware modules for building behavioural setups, and a graphical user interface designed for efficiently running high-throughput experiments on many setups in parallel, all with extensive online documentation. These tools make it quicker, easier, and cheaper to implement rich behavioural tasks at scale. As important, pyControl facilitates communication and reproducibility of behavioural experiments through a highly readable task definition syntax and self-documenting features. Here, we outline the system's design and rationale, present validation experiments characterising system performance, and demonstrate example applications in freely moving and head-fixed mouse behaviour.

Frugal Science Powered by Curiosity

More than 60 years ago, Richard Feynman gave a lecture titled "There's Plenty of Room at the Bottom: An Invitation to Enter a New Field of Physics", where he called on others to join the then-nascent field of nanotechnology. In a similar spirit, we wish to invite chemists, biologists, physicists, bioengineers, educators, high school students, and inventors of all backgrounds to join us in the emerging field of frugal science. In this Review, we define frugal science and use six case studies to describe the broad applications of frugal science, from synthetic biology to disease diagnostics. We conclude by establishing an argument for curiosity-driven research through frugal science to enable broader access in chemical and bioengineering research and drive innovation.

MicroHikari3D: an automated DIY digital microscopy platform with deep learning capabilities

A microscope is an essential tool in biosciences and production quality laboratories for unveiling the secrets of microworlds. This paper describes the development of MicroHikari3D, an affordable DIY optical microscopy platform with automated sample positioning, autofocus and several illumination modalities to provide a high-quality flexible microscopy tool for labs with a short budget. This proposed optical microscope design aims to achieve high customization capabilities to allow whole 2D slide imaging and observation of 3D live specimens. The MicroHikari3D motion control system is based on the entry level 3D printer kit Tronxy X1 controlled from a server running in a Raspberry Pi 4. The server provides services to a client mobile app for video/image acquisition, processing, and a high level classification task by applying deep learning models.

Loop-Mediated Isothermal Amplification Detection of SARS-CoV-2 and Myriad Other Applications

As the second year of the COVID-19 pandemic begins, it remains clear that a massive increase in the ability to test for SARS-CoV-2 infections in a myriad of settings is critical to controlling the pandemic and to preparing for future outbreaks. The current gold standard for molecular diagnostics is the polymerase chain reaction (PCR), but the extraordinary and unmet demand for testing in a variety of environments means that both complementary and supplementary testing solutions are still needed. This review highlights the role that loop-mediated isothermal amplification (LAMP) has had in filling this global testing need, providing a faster and easier means of testing, and what it can do for future applications, pathogens, and the preparation for future outbreaks. This review describes the current state of the art for research of LAMP-based SARS-CoV-2 testing, as well as its implications for other pathogens and testing. The authors represent the global LAMP (gLAMP) Consortium, an international research collective, which has regularly met to share their experiences on LAMP deployment and best practices; sections are devoted to all aspects of LAMP testing, including preanalytic sample processing, target amplification, and amplicon detection, then the hardware and software required for deployment are discussed, and finally, a summary of the current regulatory landscape is provided. Included as well are a series of first-person accounts of LAMP method development and deployment. The final discussion section provides the reader with a distillation of the most validated testing methods and their paths to implementation. This review also aims to provide practical information and insight for a range of audiences: for a research audience, to help accelerate research through sharing of best practices; for an implementation audience, to help get testing up and running quickly; and for a public health, clinical, and policy audience, to help convey the breadth of the effect that LAMP methods have to offer.

Utilizing Advanced Technology to Facilitate Diagnosis of Rare Retinal Disorders: A Case of Bietti Crystalline Dystrophy

SIGNIFICANCE

Optometrists, as primary eye care providers, encounter patients with rare ocular disease such as Bietti crystalline dystrophy from time to time. Using advanced technologies, which are also useful in managing common ocular conditions, to facilitate a prompt diagnosis is highly recommended.

PURPOSE

This report describes a patient with clinically diagnosed Bietti crystalline dystrophy with findings on funduscopy, multimodal imaging, and visual electrophysiology.

CASE REPORT

A 41-year-old Chinese woman who had subjectively progressing dimmed vision (especially in the left eye) for 9 months was referred to our clinic to test for retinitis pigmentosa. Best-corrected visual acuities were 6/6 and 6/7.6 in the right and left eyes, respectively. Funduscopy revealed multiple crystalline deposits on the posterior pole in both eyes. The 30-2 perimetry displayed bi-inferotemporal scotoma (left > right eye). Scotopic flash electroretinogram (ERG) yielded a normal result, whereas photopic ERG was slightly attenuated. Electro-oculogram showed an abnormal adaptation time course of the retinal pigmented epithelium (RPE). Multifocal ERG revealed a decreased central retinal response, but paracentral responses were relatively better preserved. Optical coherence tomography showed multiple patches of RPE atrophy, with disruption of the left ellipsoid zone. Outer retinal tubulations, hyperreflective dots on RPE-Bruch's membrane interface, and intraretinal bright spots were also identified.

CONCLUSIONS

Rare ocular diseases like Bietti crystalline dystrophy can be encountered by optometrists. This case report shows the ophthalmic findings of a rare chorioretinal dystrophy and provides insight on how to better use advanced equipment in an optometric practice to facilitate prompt diagnoses.

Examining cultural structures and functions in biology

Scientific culture and structure organize biological sciences in many ways. We make choices concerning the systems and questions we study. Our research then amplifies these choices into factors that influence the directions of future research by shaping our hypotheses, data analyses, interpretation, publication venues, and dissemination via other methods. But our choices are shaped by more than objective curiosity-we are influenced by cultural paradigms reinforced by societal upbringing and scientific indoctrination during training. This extends to the systems and data that we consider to be ethically obtainable or available for study, and who is considered qualified to do research, ask questions, and communicate about research. It is also influenced by the profitability of concepts like open-access-a system designed to improve equity, but which enacts gatekeeping in unintended but foreseeable ways. Creating truly integrative biology programs will require more than intentionally developing departments or institutes that allow overlapping expertise in two or more subfields of biology. Interdisciplinary work requires the expertise of large and diverse teams of scientists working together-this is impossible without an authentic commitment to addressing, not denying, racism when practiced by individuals, institutions, and cultural aspects of academic science. We have identified starting points for remedying how our field has discouraged and caused harm, but we acknowledge there is a long path forward. This path must be paved with field-wide solutions and institutional buy-in: our solutions must match the scale of the problem. Together, we can integrate-not reintegrate-the nuances of biology into our field.

Two decades of neuroscience publication trends in Africa

Neuroscience research in Africa remains sparse. Devising new policies to boost Africa's neuroscience landscape is imperative, but these must be based on accurate data on research outputs which is largely lacking. Such data must reflect the heterogeneity of research environments across the continent's 54 countries. Here, we analyse neuroscience publications affiliated with African institutions between 1996 and 2017. Of 12,326 PubMed indexed publications, 5,219 show clear evidence that the work was performed in Africa and led by African-based researchers - on average ~5 per country and year. From here, we extract information on journals and citations, funding, international coauthorships and techniques used. For reference, we also extract the same metrics from 220 randomly selected publications each from the UK, USA, Australia, Japan and Brazil. Our dataset provides insights into the current state of African neuroscience research in a global context.

In COM we trust: Feasibility of USB-based event marking

Modern experimental research often relies on the synchronization of different events prior to data analysis. One way of achieving synchronization involves marking distinct events with electrical pulses (event markers or “TTL pulses”), which are continuously recorded with research hardware, and can later be temporally aligned. Traditionally, this event marking was often performed using the parallel port in standard personal computers. However, the parallel port is disappearing from the landscape of computer hardware, being replaced by a serial (COM) port, namely the USB port. To find an adequate replacement for the parallel port, we evaluated four microcontroller units (MCUs) and the LabJack U3, an often-used USB data acquisition device, in terms of their latency and jitter for sending event markers in a simulated experiment on both Windows and Linux. Our results show that all four MCUs were comparable to the parallel port in terms of both latency and jitter, and consistently achieved latencies under 1 ms. With some caveats, the LabJack U3 can also achieve comparable latencies. In addition to the collected data, we share extensive documentation on how to build and use MCUs for event marking, including code examples. MCUs are a cost-effective, flexible, and performant replacement for the disappearing parallel port, enabling event marking and synchronization of data streams.

A new open-source hardware device to measure vertical sperm motility and concentration

Sperm motility and concentration are commonly evaluated parameters in semen analysis. Those parameters are assessed objectively with commercial instrumentation such as computer-assisted sperm analysis systems (CASA) and hemocytometer. In CASA systems, sperm motility is assessed in the horizontal plane imposed by the stage of the microscope. Thus, there is lack of measurement of the vertical velocity of sperm. The female reproductive tract is a tridimensional space which the sperm traverse to reach the ovum, and there is a need for instruments measuring parameters more relevant to this real-world situation. In this report we describe the design, construction and use of an open-source hardware (OSH) device for evaluation of the vertical velocity of sperm, called UPSPERM. This device was also used to measure sperm concentration, and agreement with hemocytometer was evaluated. Bland-Altman analysis shows good agreement between these two methods of sperm counting. As a first application of UPSPERM, we evaluated the changes in boar sperm motility at distinct pH values between 7.0 and 8.0. The UPSPERM results showed that the vertical velocity of sperm was highest at pH 7.6 and 7.8. We propose that our UPSPERM offers a reliable and affordable option for obtaining measurements of vertical velocity and sperm concentration.

Low-cost and open-source strategies for chemical separations

In recent years, a trend toward utilizing open access resources for laboratory research has begun. Open-source design strategies for scientific hardware rely upon the use of widely available parts, especially those that can be directly printed using additive manufacturing techniques and electronic components that can be connected to low-cost microcontrollers. Open-source software eliminates the need for expensive commercial licenses and provides the opportunity to design programs for specific needs. In this review, the impact of the "open-source movement" within the field of chemical separations is described, primarily through a comprehensive look at research in this area over the past five years. Topics that are covered include general laboratory equipment, sample preparation techniques, separations-based analysis, detection strategies, electronic system control, and software for data processing. Remaining hurdles and possible opportunities for further adoption of open-source approaches in the context of these separations-related topics are also discussed.

HoloBlade: an open-hardware spatial light modulator driver platform for holographic displays

Spatial light modulators (SLMs) are key research tools in several contemporary applied optics research domains. In this paper, we present the argument that an open platform for interacting with SLMs would dramatically increase their accessibility to researchers. We introduce HoloBlade, an open-hardware implementation of an SLM driver-stack, and provide a detailed exposition of HoloBlade's architecture, key components, and detailed design. An optical verification rig is constructed to demonstrate that HoloBlade can provide Fourier imaging capability in a 4f system. Finally, we discuss HoloBlade's future development roadmap and the opportunities that it presents as a research tool for applied optics.

Building a biofoundry

A biofoundry provides automation and analytics infrastructure to support the engineering of biological systems. It allows scientists to perform synthetic biology and aligned experimentation on a high-throughput scale, massively increasing the solution space that can be examined for any given problem or question. However, establishing a biofoundry is a challenging undertaking, with numerous technical and operational considerations that must be addressed. Using collated learnings, here we outline several considerations that should be addressed prior to and during establishment. These include drivers for establishment, institutional models, funding and revenue models, personnel, hardware and software, data management, interoperability, client engagement and biosecurity issues. The high cost of establishment and operation means that developing a long-term business model for biofoundry sustainability in the context of funding frameworks, actual and potential client base, and costing structure is critical. Moreover, since biofoundries are leading a conceptual shift in experimental design for bioengineering, sustained outreach and engagement with the research community are needed to grow the client base. Recognition of the significant, long-term financial investment required and an understanding of the complexities of operationalization is critical for a sustainable biofoundry venture. To ensure state-of-the-art technology is integrated into planning, extensive engagement with existing facilities and community groups, such as the Global Biofoundries Alliance, is recommended.

Machine learning for metabolic engineering: A review

Machine learning provides researchers a unique opportunity to make metabolic engineering more predictable. In this review, we offer an introduction to this discipline in terms that are relatable to metabolic engineers, as well as providing in-depth illustrative examples leveraging omics data and improving production. We also include practical advice for the practitioner in terms of data management, algorithm libraries, computational resources, and important non-technical issues. A variety of applications ranging from pathway construction and optimization, to genetic editing optimization, cell factory testing, and production scale-up are discussed. Moreover, the promising relationship between machine learning and mechanistic models is thoroughly reviewed. Finally, the future perspectives and most promising directions for this combination of disciplines are examined.

SiCTeC: An inexpensive, easily assembled Peltier device for rapid temperature shifting during single-cell imaging

Single-cell imaging, combined with recent advances in image analysis and microfluidic technologies, have enabled fundamental discoveries of cellular responses to chemical perturbations that are often obscured by traditional liquid-culture experiments. Temperature is an environmental variable well known to impact growth and to elicit specific stress responses at extreme values; it is often used as a genetic tool to interrogate essential genes. However, the dynamic effects of temperature shifts have remained mostly unstudied at the single-cell level, due largely to engineering challenges related to sample stability, heatsink considerations, and temperature measurement and feedback. Additionally, the few commercially available temperature-control platforms are costly. Here, we report an inexpensive (<$110) and modular Single-Cell Temperature Controller (SiCTeC) device for microbial imaging-based on straightforward modifications of the typical slide-sample-coverslip approach to microbial imaging-that controls temperature using a ring-shaped Peltier module and microcontroller feedback. Through stable and precise (±0.15°C) temperature control, SiCTeC achieves reproducible and fast (1-2 min) temperature transitions with programmable waveforms between room temperature and 45°C with an air objective. At the device's maximum temperature of 89°C, SiCTeC revealed that Escherichia coli cells progressively shrink and lose cellular contents. During oscillations between 30°C and 37°C, cells rapidly adapted their response to temperature upshifts. Furthermore, SiCTeC enabled the discovery of rapid morphological changes and enhanced sensitivity to substrate stiffness during upshifts to nonpermissive temperatures in temperature-sensitive mutants of cell-wall synthesis enzymes. Overall, the simplicity and affordability of SiCTeC empowers future studies of the temperature dependence of single-cell physiology.

Partially RepRapable automated open source bag valve mask-based ventilator

This study describes the development of a simple and easy-to-build portable automated bag valve mask (BVM) compression system, which, during acute shortages and supply chain disruptions can serve as a temporary emergency ventilator. The resuscitation system is based on the Arduino controller with a real-time operating system installed on a largely RepRap 3-D printable parametric component-based structure. The cost of the materials for the system is under $170, which makes it affordable for replication by makers around the world. The device provides a controlled breathing mode with tidal volumes from 100 to 800 mL, breathing rates from 5 to 40 breaths/minute, and inspiratory-to-expiratory ratio from 1:1 to 1:4. The system is designed for reliability and scalability of measurement circuits through the use of the serial peripheral interface and has the ability to connect additional hardware due to the object-oriented algorithmic approach. Experimental results after testing on an artificial lung for peak inspiratory pressure (PIP), respiratory rate (RR), positive end-expiratory pressure (PEEP), tidal volume, proximal pressure, and lung pressure demonstrate repeatability and accuracy exceeding human capabilities in BVM-based manual ventilation. Future work is necessary to further develop and test the system to make it acceptable for deployment outside of emergencies such as with COVID-19 pandemic in clinical environments, however, the nature of the design is such that desired features are relatively easy to add using protocols and parametric design files provided.

Partially RepRapable automated open source bag valve mask-based ventilator

This study describes the development of a simple and easy-to-build portable automated bag valve mask (BVM) compression system, which, during acute shortages and supply chain disruptions can serve as a temporary emergency ventilator. The resuscitation system is based on the Arduino controller with a real-time operating system installed on a largely RepRap 3-D printable parametric component-based structure. The cost of the materials for the system is under $170, which makes it affordable for replication by makers around the world. The device provides a controlled breathing mode with tidal volumes from 100 to 800 mL, breathing rates from 5 to 40 breaths/minute, and inspiratory-to-expiratory ratio from 1:1 to 1:4. The system is designed for reliability and scalability of measurement circuits through the use of the serial peripheral interface and has the ability to connect additional hardware due to the object-oriented algorithmic approach. Experimental results after testing on an artificial lung for peak inspiratory pressure (PIP), respiratory rate (RR), positive end-expiratory pressure (PEEP), tidal volume, proximal pressure, and lung pressure demonstrate repeatability and accuracy exceeding human capabilities in BVM-based manual ventilation. Future work is necessary to further develop and test the system to make it acceptable for deployment outside of emergencies such as with COVID-19 pandemic in clinical environments, however, the nature of the design is such that desired features are relatively easy to add using protocols and parametric design files provided.

In situ characterisation and manipulation of biological systems with Chi.Bio

The precision and repeatability of in vivo biological studies is predicated upon methods for isolating a targeted subsystem from external sources of noise and variability. However, in many experimental frameworks, this is made challenging by nonstatic environments during host cell growth, as well as variability introduced by manual sampling and measurement protocols. To address these challenges, we developed Chi.Bio, a parallelised open-source platform that represents a new experimental paradigm in which all measurement and control actions can be applied to a bulk culture in situ. In addition to continuous-culturing capabilities, it incorporates tunable light outputs, spectrometry, and advanced automation features. We demonstrate its application to studies of cell growth and biofilm formation, automated in silico control of optogenetic systems, and readout of multiple orthogonal fluorescent proteins in situ. By integrating precise measurement and actuation hardware into a single low-cost platform, Chi.Bio facilitates novel experimental methods for synthetic, systems, and evolutionary biology and broadens access to cutting-edge research capabilities.

Open-Source Grinding Machine for Compression Screw Manufacturing

Some of the most promising distributed recycling and additive manufacturing (DRAM) technical systems use fused particle fabrication (FPF) or fused granular fabrication (FGF), where compression screws force post-consumer waste plastic through a heated nozzle for direct 3D printing. To assist the technical evolution of these systems, this study provided the details of an invention for a low-cost, easily replicable open-source grinding machine for compression screw manufacturing. The system itself can be largely fabricated using FPF/FGF following the self-replicating rapid prototyper (RepRap) methodology. This grinding machine can be made from a cordless cut-off grinder and < $155 in parts. The new invention is demonstrated to be able to cut custom screws with variable (i) channel depths, (ii) screw diameters, (iii) screw lengths, (iv) pitches, (v) abrasive disk thicknesses, (vi) handedness of the screws, (vii) and materials (three types of steel tested: 1045 steel, 1144 steel, and 416 stainless steel). The results show that the device is more than capable of replicating commercial screws as well as providing makers with a much greater flexibility to make custom screws. This invention enables the DRAM toolchain to become even more self-sufficient, which assists the goals of the circular economy.

Impact of 3D printed medical equipment on the management of the Covid19 pandemic

Very high mortality rates of coronavirus pandemic (COVID-19) are observed around the world due to lack of medical equipment. The increased need for medical devices and personal protective equipment (PPE) has kept several healthcare professionals at risk. Fortunately, 3D printing technology allows to overcome the lack of medical supplies. This study highlights the impact of 3D printing on the combat against COVID19, and its importance in the medical product supply chain. Indeed, the existing medical equipment fabricated by 3D printing technology and its role in the management of Covid19 pandemic is presented. Moreover, the last works are examined to know whether the models of the medical equipment are free of use and whether useful informations are presented (eg, available design data and setup guidelines).

Distributed Manufacturing of Open Source Medical Hardware for Pandemics

Distributed digital manufacturing offers a solution to medical supply and technology shortages during pandemics. To prepare for the next pandemic, this study reviews the state-of-the-art of open hardware designs needed in a COVID-19-like pandemic. It evaluates the readiness of the top twenty technologies requested by the Government of India. The results show that the majority of the actual medical products have some open source development, however, only 15% of the supporting technologies required to produce them are freely available. The results show there is still considerable research needed to provide open source paths for the development of all the medical hardware needed during pandemics. Five core areas of future research are discussed, which include (i) technical development of a wide-range of open source solutions for all medical supplies and devices, (ii) policies that protect the productivity of laboratories, makerspaces, and fabrication facilities during a pandemic, as well as (iii) streamlining the regulatory process, (iv) developing Good-Samaritan laws to protect makers and designers of open medical hardware, as well as to compel those with knowledge that will save lives to share it, and (v) requiring all citizen-funded research to be released with free and open source licenses.

Robotic microscopy for everyone: the OpenFlexure microscope

Optical microscopes are an essential tool for both the detection of disease in clinics, and for scientific analysis. However, in much of the world access to high-performance microscopy is limited by both the upfront cost and maintenance cost of the equipment. Here we present an open-source, 3D-printed, and fully-automated laboratory microscope, with motorised sample positioning and focus control. The microscope is highly customisable, with a number of options readily available including trans- and epi- illumination, polarisation contrast imaging, and epi-florescence imaging. The OpenFlexure microscope has been designed to enable low-volume manufacturing and maintenance by local personnel, vastly increasing accessibility. We have produced over 100 microscopes in Tanzania and Kenya for educational, scientific, and clinical applications, demonstrating that local manufacturing can be a viable alternative to international supply chains that can often be costly, slow, and unreliable.

Leveraging open hardware to alleviate the burden of COVID-19 on global health systems

With the current rapid spread of COVID-19, global health systems are increasingly overburdened by the sheer number of people that need diagnosis, isolation and treatment. Shortcomings are evident across the board, from staffing, facilities for rapid and reliable testing to availability of hospital beds and key medical-grade equipment. The scale and breadth of the problem calls for an equally substantive response not only from frontline workers such as medical staff and scientists, but from skilled members of the public who have the time, facilities and knowledge to meaningfully contribute to a consolidated global response. Here, we summarise community-driven approaches based on Free and Open Source scientific and medical Hardware (FOSH) as well as personal protective equipment (PPE) currently being developed and deployed to support the global response for COVID-19 prevention, patient treatment and diagnostics.

A review of open source ventilators for COVID-19 and future pandemics

Coronavirus Disease 2019 (COVID-19) threatens to overwhelm our medical infrastructure at the regional level causing spikes in mortality rates because of shortages of critical equipment, like ventilators. Fortunately, with the recent development and widespread deployment of small-scale manufacturing technologies like RepRap-class 3-D printers and open source microcontrollers, mass distributed manufacturing of ventilators has the potential to overcome medical supply shortages. In this study, after providing a background on ventilators, the academic literature is reviewed to find the existing and already openly-published, vetted designs for ventilators systems. These articles are analyzed to determine if the designs are open source both in spirit (license) as well as practical details (e.g. possessing accessible design source files, bill of materials, assembly instructions, wiring diagrams, firmware and software as well as operation and calibration instructions). Next, the existing Internet and gray literature are reviewed for open source ventilator projects and designs. The results of this review found that the tested and peer-reviewed systems lacked complete documentation and the open systems that were documented were either at the very early stages of design (sometimes without even a prototype) and were essentially only basically tested (if at all). With the considerably larger motivation of an ongoing pandemic, it is assumed these projects will garner greater attention and resources to make significant progress to reach a functional and easily-replicated system. There is a large amount of future work needed to move open source ventilators up to the level considered scientific-grade equipment, and even further work needed to reach medical-grade hardware. Future work is needed to achieve the potential of this approach by developing policies, updating regulations, and securing funding mechanisms for the development and testing of open source ventilators for both the current COVID19 pandemic as well as for future pandemics and for everyday use in low-resource settings.

A review of open source ventilators for COVID-19 and future pandemics

Coronavirus Disease 2019 (COVID-19) threatens to overwhelm our medical infrastructure at the regional level causing spikes in mortality rates because of shortages of critical equipment, like ventilators. Fortunately, with the recent development and widespread deployment of small-scale manufacturing technologies like RepRap-class 3-D printers and open source microcontrollers, mass distributed manufacturing of ventilators has the potential to overcome medical supply shortages. In this study, after providing a background on ventilators, the academic literature is reviewed to find the existing and already openly-published, vetted designs for ventilators systems. These articles are analyzed to determine if the designs are open source both in spirit (license) as well as practical details (e.g. possessing accessible design source files, bill of materials, assembly instructions, wiring diagrams, firmware and software as well as operation and calibration instructions). Next, the existing Internet and gray literature are reviewed for open source ventilator projects and designs. The results of this review found that the tested and peer-reviewed systems lacked complete documentation and the open systems that were documented were either at the very early stages of design (sometimes without even a prototype) and were essentially only basically tested (if at all). With the considerably larger motivation of an ongoing pandemic, it is assumed these projects will garner greater attention and resources to make significant progress to reach a functional and easily-replicated system. There is a large amount of future work needed to move open source ventilators up to the level considered scientific-grade equipment, and even further work needed to reach medical-grade hardware. Future work is needed to achieve the potential of this approach by developing policies, updating regulations, and securing funding mechanisms for the development and testing of open source ventilators for both the current COVID19 pandemic as well as for future pandemics and for everyday use in low-resource settings.

ElectroPen: An ultra-low-cost, electricity-free, portable electroporator

Electroporation is a basic yet powerful method for delivering small molecules (RNA, DNA, drugs) across cell membranes by application of an electrical field. It is used for many diverse applications, from genetically engineering cells to drug- and DNA-based vaccine delivery. Despite this broad utility, the high cost of electroporators can keep this approach out of reach for many budget-conscious laboratories. To address this need, we develop a simple, inexpensive, and handheld electroporator inspired by and derived from a common household piezoelectric stove lighter. The proposed "ElectroPen" device can cost as little as 23 cents (US dollars) to manufacture, is portable (weighs 13 g and requires no electricity), can be easily fabricated using 3D printing, and delivers repeatable exponentially decaying pulses of about 2,000 V in 5 ms. We provide a proof-of-concept demonstration by genetically transforming plasmids into Escherichia coli cells, showing transformation efficiency comparable to commercial devices, but at a fraction of the cost. We also demonstrate the potential for rapid dissemination of this approach, with multiple research groups across the globe validating the ease of construction and functionality of our device, supporting the potential for democratization of science through frugal tools. Thus, the simplicity, accessibility, and affordability of our device holds potential for making modern synthetic biology accessible in high school, community, and resource-poor laboratories.

This Community Page article describes an ultra-low–cost (23-cent) 3D-printed electroporator, inspired by a common barbecue lighter, designed to enable broader access to synthetic biology in high-school, community, and budget-conscious laboratories.

Parametric CAD modeling for open source scientific hardware: Comparing OpenSCAD and FreeCAD Python scripts

Open source hardware for scientific equipment needs to provide source files and enough documentation to allow the study, replication and modification of the design. In addition, parametric modeling is encouraged in order to facilitate customization for other experiments. Parametric design using a solid modeling programming language allows customization and provides a source file for the design. OpenSCAD is the most widely used scripting tool for parametric modeling of open source labware. However, OpenSCAD lacks the ability to export to standard parametric formats; thus, the parametric dimensional information of the model is lost. This is an important deficiency because it is key to share the design in the most accessible formats with no information loss. In this work we analyze OpenSCAD and compare it with FreeCAD Python scripts. We have created a parametric open source hardware design to compare these tools. Our findings show that although Python for FreeCAD is more arduous to learn, its advantages counterbalance the initial difficulties. The main benefits are being able to export to standard parametric models; using Python language with its libraries; and the ability to use and integrate the models in its graphical interface. Thus, making it more appropriate to design open source hardware for scientific equipment.

Principles of open source bioinstrumentation applied to the poseidon syringe pump system

The poseidon syringe pump and microscope system is an open source alternative to commercial systems. It costs less than $400 and can be assembled in under an hour using the instructions and source files available at https://pachterlab.github.io/poseidon . We describe the poseidon system and use it to illustrate design principles that can facilitate the adoption and development of open source bioinstruments. The principles are functionality, robustness, safety, simplicity, modularity, benchmarking, and documentation.