CSynth: scientific visualisation in VR
My Goldsmiths colleagues Peter Todd, Stephen Todd, Frederic Fol Leymarie and William Latham, together with collaborators at the University of Oxford, the Francis Crick Institute and London Geometry, have recently published a paper about a scientific visualisation system called CSynth.
VR visualisation
CSynth is a tool for visualising Chromatin, a protein closely associated with DNA, which is an important molecular building block of life and implicated in many diseases including diabetes and cancer.
Traditional tools for visualising molecular data have been 2D, but molecules are 3D. 2D visualisation can make it hard to understand the 3D structure, particularly for the very complex organic molecules that are the basis of life. 3D visualisations are better but they can still be hard to make out on a 2D screen.
This is where VR can bring real benefits. It allows you to step into the world of the molecule. You can look at it in 3D from all directions, even inside it. Most importantly you can observe the 3D structure of a molecule in the same way we observe 3D objects at human scale, not from a single viewpoint, but by moving around them, looking from different directions, moving closer to look at fine detail and even picking them up to turn them in our hands.
We use our movements to control how we see things and it is this relationship between movement and vision that allows us to understand our world and particularly its 3D structure. These relationships are called sensorimotor contingencies and the power of VR is that we can use the same sensorimotor contingencies that we have learned in the real world.
Because VR scientific visualisation tools like CSynth have the same sensorimotor contingencies as the real world, for the first time, they allow scientists to see tiny objects like molecules in the same way we see ordinary human scale objects.
Interaction
The other major benefit of CSynth is that it is interactive. Part of that interactivity is about viewing the molecule from different directions as I’ve described, but it is also about manipulating the molecules.
CSynth supports a range of different ways of viewing a molecule each of which contains different information. Scientists can switch between them to better understand the structure. They can also load different datasets and compare them.
The software also has a mathematical model of the forces that act within a molecule. This means that scientists can manipulate properties of the molecules to see how they will affect their configurations and the physics model will give accurate results. This kind of hypothesis testing and exploration is key to scientific work and a tool like CSynth allows it to happen much more quickly and easily.
The future of science?
CSynth makes it easier for scientists to investigate and understand the structure and properties fo molecules. By allowing scientists to interact with data and to view it in ways that are as close as possible to how we see and interact with the world in our daily lives, it has the potential to allow them to understand scientific data with some of the ease with which we understand the human scale world around us. This could help them find crucial insights more quickly, and maybe lead to scientific insights that would not have been possible otherwise.
VR visualisation is an exciting new frontier in many areas of science, not just biochemistry but areas as diverse as physics, neuroscience, economics and archaeology. In fact, I could see VR visualisation being important way beyond that. VR journalism is normally associated with story telling and “stepping into somebody else’s shoes”, but it is emerging at the same time as the trend of Data Journalism. Maybe in the future we will be able to make our own decisions about the data that is shaping the news by interacting with VR visualisations.
Another interesting aspect of this work is that it is an art science collaboration. It originated in Mutator, William Latham and Stephen Todd’s pioneering computational art work that used evolutionary algorithms to create striking 3D visual forms. But having created art work based on biological models, they realised that they could apply their knowledge to understanding real biological systems. They worked with computer scientists and biologists to develop software that would eventually become CSynth.
I must say I am very proud to be working at Goldsmiths with colleagues that are doing such groundbreaking interdisciplinary work.
If you are interested in finding out more about CSynth (I have focused on the VR side, but there is a lot more to say about the biology), you could read this article on the Goldsmiths web site:
The original paper is available here:
This is part of a blog I have started to support learners on our Virtual Reality MOOC, if you want to learn more about VR, that is a good place to start. If you want to go into more depth, you might be interested in our Masters in Virtual and Augmented Reality at Goldsmiths’ University of London.
