PhD Studentship (ALBERT CDT)
The Smart Lab: Integrating Low-Cost, Open-Source Hardware and Software for ALBERT
Applications closed
Applications for this position are now closed. See our current opportunities.
Overview
Research labs are full of hardware and software: sensors and systems all working to deliver high-quality results. But critically, these systems operate as data islands, with little oversight or integration. This includes complex multi-hardware experiments, semi- or non-autonomous robotic systems, environmental, energy and safety-critical monitoring. Effective, meaningful (and above all) safe integration of these systems, is essential to take full advantage of the benefits of lab autonomy. Within the ALBERT programme, you will be investigating the autonomous integration of these systems, to create a cohesive, whole-lab approach, delivering impactful time-, cost- and energy-saving benefits to end users.
The problem
Research labs face practical and financial constraints that prohibit high levels of systems integration. This results in over-reliance on human labour for simple tasks, potential for high equipment downtime and energy wastage, and hinders the development of interventions that might resolve these issues. Lab instrumentation may be bespoke, comprised of many individual components, where no standards for integration exist. Commercial lab monitoring systems (or experimental control software) are often proprietary, lack data sovereignty, and dependent on ongoing subscriptions. This is both financially unsustainable, and often places reliance on cloud-based servers that, at a moment’s notice, can render perfectly functional hardware into e-waste.
What is needed
A cost-effective, reliable, vendor-agnostic framework for hardware and software that can integrate the lab environment, to deliver lab-specific insight, guidance and assistance. This system should itself be capable of interacting with other autonomous and non-autonomous systems, and be simple enough to interface with, so that it is accessible to researchers across disciplines.
The solution
You will be studying the interdisciplinary lab environment and leveraging existing open-source frameworks to produce your own solution to this challenge. The open-source community has already integrated many different types of systems and devices – but only in the home automation space. Software such as Home Assistant; frameworks such as Node-RED and ESPhome; and protocols such as MQTT, have been deployed to create complex, integrated home monitoring and automation systems. These are based on low-cost microcontrollers and single-board computers (e.g. ESP32 and Raspberry Pi platforms), and at their core are highly modular and open. You will build upon these systems, to both facilitate hardware and software integration, while adding a layer of autonomy that guides end users through helpful interventions.
In this project, you will:
- study the needs of laboratory autonomy across multiple highly-interdisciplinary laboratories, and by engaging with existing human-interaction expertise within the ALBERT cohort,
- develop an open hardware platform capable of integrating with a variety of laboratory-based equipment, using existing frameworks as a starting point,
- integrate these devices with both Home Assistant and eLabFTW (an open-source electronic laboratory notebook) and develop meaningful interventions,
- develop guidance and documentation to enable your work to be accessible to non-automation specialist researchers,
- publish and promote your findings and code for both the academic and open-source communities,
- explore the opportunity to commercialise your work, using open-source-centric business models.
The team
You’ll be supervised by the cross-disciplinary team of Dr Stuart Higgins (School of Physics, Engineering and Technology), Professor Alison Parkin (Department of Chemistry) and Dr Chris Spicer (Department of Chemistry). You will be based in Stuart’s lab, and at the heart of a new, generously-funded, interdisciplinary research team, focused on the development of bioelectronic devices for the study of bioelectricity (the fundamental role of electricity in the regulation of all living things). Our research spans physics, chemistry, biology, material science, and electronic engineering. By design we work across many different types of lab environment (cleanrooms, engineering-, biology-, material characterisation- and imaging-labs).
Our challenges
You’ll have the chance to co-develop new autonomous and integrated lab setups, and be exposed to a wide-variety of practical challenges, including: integrating robotic aspirate-dispensing patterning systems with environmental monitoring and control, longitudinal bioelectronic and environmental cell culture sensing and stimulation, high-throughput microscopy (both instrument integration and data handling), while incorporating our Electronic Laboratory Notebook system via its open API. Through Prof. Parkin and Dr. Spicer you will understand how to design solutions that impact chemistry-heavy lab environments, and tackle other practical challenges, such as adaptive glovebox control and alerting. Alongside this, you will have scope to tackle common challenges, applicable across the university, such as the effective monitoring and control of refrigeration systems for the preservation expensive reagents or biological samples. And have the opportunity to implement systems that make significant cost and energy savings.
Beyond the lab
We are committed to best practice in academic research and will support your professional development throughout your studies. Stuart is an award-winning supervisor, with a background in bioelectronics and open-source research data management.1 Joining the team, you will have the opportunity to engage in award-winning science communication and public engagement, and have the opportunity to develop confident and effective communication skills to work with scientists from many disciplines.
You will be
A computer scientist, electronic engineer, physicist or open-source enthusiast, looking for a well-defined problem to apply and develop your skills. You will be comfortable working with microcontrollers, single-board computers, and various languages (e.g. python, C++), and ideally have experience with developing autonomous systems. You don’t need to have previously worked in physics/chemistry/biology labs, but be happy to do so in order to environments develop understanding and implement integrations. We are looking for a candidate with strong self-motivation and an appetite for new knowledge and skills.
By the end of this studentship
You will have developed a highly desirable skillset in developing hardware and software for interdisciplinary biotechnology research environments, along highly transferrable professional skills, applicable to both academic and industrial careers. You will have a portfolio of open-source work, to exploit further with the team in a commercial context, or to use as the basis for a career in software/hardware development.
Want to know more? Contact Stuart for an informal conversation.
Funding notes
Funding notes (text provided by the University of York)
We have fully funded projects available for the September 2024 start. Fully funded for up to 3.5 years by the EPSRC/University and covers (i) a tax-free annual stipend at the standard Research Council rate (£18,622 for 2024-25), (ii) tuition fees, (iii) funding for consumables. Candidates of any nationality are welcome to apply and up to 30% of DTP studentships may be awarded to exceptional international students.
How to Apply (text provided by the University of York)
Applicants must apply via the University’s online application system at https://www.york.ac.uk/study/postgraduate-research/apply/. Please read the application guidance first so that you understand the various steps in the application process. To apply, please select the PhD in Electronic Engineering for September 2024 entry.
On the postgraduate application form, please select 'CDT Autonomous Robotic Systems for Lab Experiments' as your source of funding. You do not need to provide a research proposal, just enter the name of the project you wish to apply for.
Apply now
Applications closed
Applications for this position are now closed. See our current opportunities.
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Higgins SG, Nogiwa-Valdez AA, Stevens MM, Considerations for Implementing Electronic Laboratory Notebooks in an Academic Research Environment, 2022, Nature Protocols, DOI: 10.1038/s41596-021-00645-8 ↩