New citizen science project From Diamond Light Source seeks to train AI to identify virus particles
Credit: Diamond Light Source, 2019
Today sees the launch of an innovative Citizen Science Project by Diamond Light Source, the UK’s national synchrotron science facility.The project uses a crowdsourcing model to call on people of all ages around the world to help speed up the analysis of the terabytes of data that Diamond generates every day. The first task set for citizen scientists is to spend a few minutes looking at a series of screens to identify viruses. More tasks will be set for other targets over the next three years. This will help train Artificial Intelligence systems (AI) and develop new ways of segmenting data, with the aim to automate the data segmentation processes. Doing this will dramatically speed up scientists’ ability to understand their research data in a matter of days rather than the current weeks, allowing for a faster path to understanding disease structures, and perhaps speeding up pathways to drug development.
Unveiled at the American Association for the Advancement of Science in Washington DC, The Diamond “Science Scribbler – Virus Project”, is the first of its kind that members of the public can help with in such a big way. It is funded by the world’s biggest biomedical charity, the Wellcome Trust and being developed in collaboration with Zooniverse, the renowned citizen science web platform.
Professor Dave Stuart FRS, MRC Professor of Structural Biology at the University of Oxford and Life Sciences Director at Diamond Light Source explains:
“The ultimate goal is to completely automate segmentation using advances in deep learning. Such methods require significant quantities of already segmented data to train the systems we use. To build segmented data for this development, Zooniverse will offer members of the public across the globe the chance to partake in segmenting datasets to help researchers. This project aims to address these issues by providing tools to help researchers label features of interest, and to gather the data that is produced by citizen scientists in a standardised way that can be used to automate the process in the future, thereby helping fasten the analysis process from weeks to days or less.”
Diamond produces 500 terabytes of biological data a month, from high-resolution detailed atomic maps to low resolution data, which makes the current methodologies of data segmentation challenging. Data is often low contrast and blurred, and can be so large in size it becomes hugely labour-intensive to analyse.
Dave Stuart continues:
“What we are doing now is to use cryo-electron tomography to visualise virus particles from the reovirus family in very thin slices cut from frozen infected cells. Our aim is, ultimately, to understand the full life cycle, how the virus gets into the cell, replicates, assembles and finally leaves the cell. In the tomograms here we have taken a snapshot 12 hours after infection and are aiming to visualise intermediate steps in the assembly process which have not been visible before, and to then work out how virus assembly is organised in time and space within the cell.”
Reoviruses belong to a large family of viruses that infect a wide range of animals and plants. Some members of the family cause widespread disease, notably Rotaviruses, which is responsible for serious gastroenteritis across the globe. In contrast, reoviruses themselves, whilst they pervasively infect humans, they do not typically produce symptoms. Indeed, they are being trialled as possible anti-cancer agents, since they specifically replicate in many cancer cells activated for division. They are therefore a good starting point to try to understand the life-cycle of this family of viruses.
Mark Basham, Project Coordinator at Diamond Light Source, says:
“We simply need as many people as possible to view images and locate what they recognise to be virus particles. This is based on real data and exciting work already underway at Diamond looking at the reovirus. This is screen time we can all advocate and we are not making too great a claim when we say it could benefit all of mankind in terms of accelerating scientists’ analysis of their research.”
Prof Chris Lintott, Zooniverse PI at the University of Oxford, further adds; “You don’t need any specialised background, training, or expertise to participate in any of the Zooniverse projects. We make it easy for anyone interested to contribute to real academic research, on their own computer or through a mobile Application, at their own convenience. We hopeThe Diamond “Science Scribbler – Virus Project”will entice you to become a regular volunteer.”
Project Coordinator Dr Mark Basham concludes:
“Artificial Intelligence has begun to have a massive impact on the world in the last few years, from beating humans in games such as Go, to the amazing advances in self-driving cars. These dramatic developments have been aided by the availability of vast quantities of data with which AI systems can be trained with. Alongside these developments, 3D imaging of frozen cells, for example, has also developed rapidly, but as yet, very little training data is available. Researchers spend much of their time manually processing their data and this is an area where AI could be heavily used. However, for, machine learning to be possible, we need human input to guide the process and this is where members of the public can make a huge difference to our work.”
Spare 10 minutes to help drive science forward, by trying out the project here:http://www.
Diamond Light Source is the UK’s synchrotron science facility. Shaped like a huge ring, it works like a
giant microscope, harnessing the power of electrons to produce bright light that scientists can use to study anything from fossils to jet engines to viruses and vaccines. Diamond speeds up electrons to near light speeds, producing a light 10 billion times brighter than the Sun, which is then directed off into 32 laboratories known as ‘beamlines’.
At Diamond, scientists can access state-of-the-art cryo-EM facilities through the Electron Bio-Imaging Centre (eBIC), for both single particle analysis , cryo-tomography and onsite cryo-microscopes – currently being used by sciesntists to study everything, from complex virus structures, to never before seen proteins. eBIC was established at Diamond following a £15.6 million grant from the Wellcome Trust, the Medical Research Council (MRC) and the Biotechnology and Biological Sciences Research Council (BBSRC). It was the first high-end cryo-electron microscopy (cryo-EM) facility worldwide to be
embedded in a synchrotron with user operations set up to mirror the well-established synchrotron beamline model.
eBIC is a collaboration between Diamond, Birkbeck College and Oxford University. EBIC’s advanced microscopes, detectors and software, allows scientists to investigate and visualise the structure of individual cells and bio-molecules.
Each year thousands of scientists use the UK’s synchrotron and its integrated facilities (eBIC, ePSIC etc.), with 57% visiting and 43% accessing the facility remotely. Diamond’s state-of-the-art facilities and world-class people act as agents of change, addressing 21st century challenges such as disease, clean energy and food security. Diamond research supports new medicines, technologies and advances of all kinds. More than 7,000 papers have been published because of research conducted at the facility. Funded by the UK Government through the Science and Technology Facilities Council (STFC), and by the Wellcome Trust, Diamond is one of the most advanced scientific facilities in the world, and its pioneering capabilities
are helping to keep the UK at the forefront of scientific research. http://www.
The Zooniverse is the world’s largest and most popular platform for people-powered research. This
research is made possible by volunteers — hundreds of thousands of people around the world who come together to assist professional researchers. Our goal is to enable research that would not be possible, or practical, otherwise. Zooniverse research results in new discoveries, datasets useful to the wider research community, and many publications. http://www.
About Oxford University’s Division of Structural Biology:
The Division of Structural Biology (STRUBI) is part of the Nuffield Department of Clinical Medicine at the University of Oxford. STRUBI is located in the Wellcome Centre for Human Genetics and includes the Oxford Protein Production Facility (OPPF), the Oxford Particle Imaging Centre (OPIC) and the Cellular Imaging Core. The Division applies the techniques of structural biology, particularly macromolecular crystallography and electron microscopy, to the study of biomedically important processes.