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Visualisation and education
Garvan and the Weizmann Institute are working together to advance the wider understanding of genomics in the community, with a focus on molecular visualisation and education initiatives.
Building on existing expertise in virtual reality and biomedical animation, immersive visualisation experiences with broad appeal are being developed through the partnership.
The animations developed for these experiences weave storytelling and the tools of cinema, art and design, anchored by authentic scientific data, to blend multi resolution data and connect with the audience.
In education, a new collaborative research project has been established, bringing together extensive educational research expertise at Weizmann with Garvan’s molecular visualisation and genomics education expertise. The team will work with teachers in Australian and Israeli middle and secondary schools, investigating how best to support the meaningful usage of 3D molecular animations by teachers in the classroom. This work will complement Garvan’s emerging programs that use authentic genomic data and real-world scenarios in teacher education.
Project 1: Molecular Animations
RNA (yellow) being copied from DNA (pink), a view inside the enzyme RNA polymerase, Kate Patterson
Molecular animations are characterised by the blending of multiple resolutions of authentic scientific data with the tools of cinema, art and design. Scientific concepts and molecules are so tiny they are smaller than the wavelength of visible light. Visualisation helps to make research less opaque for non-expert audiences but also for scientists. Authentic scientific data informs the visualisations, which means that they can aid not only the understanding of biological processes, but also can help to generate new research questions.
Heartbeats of our genome
This animation is a 360 stereoscopic animation created by Kate Patterson and designed for a Google Cardboard headset, or similar. It can also be viewed in 360 via YouTube on your mobile device or desktop. Please select the highest possible quality for the best viewing experience.
Our DNA contains the genetic information needed to make proteins, the building blocks of our bodies. This animation shows the first step in this process, with just one RNA molecule being copied from DNA. Our genome encodes hundreds of thousands of different RNA molecules but any one cell has access to only a subset of this genome library. So each cell has a unique RNA pattern, representing our genome in action. The RNA pattern in each cell can change over time, but also in disease. With single cell genomics, the unique RNA pattern in each cell can be uncovered, thousands of cells at a time which means that even the rarest, rogue cells can be identified, giving new insights into human disease.
GarvanVR is an application available for both iphone and android phones that allows users to experience molecular animations in 360 degrees. Users can select ‘view in 360’ to see the animation on their mobile screen, or ‘view in VR’ to view in 3D using a virtual reality headset such as Google Cardboard.
Instructions for assembling and using your VR viewer:
How are molecular animations created?
Molecular animations draw on authentic scientific data and detailed discussions with scientific advisors to determine the specific scientific aspects to be communicated, the overall narrative and then the script that will accompany the final animation. Various sources of scientific literature inform the content and the protein databank (PDB) is heavily utilised, which contains molecular structural data that can be directly imported into 3D animation software via the plugin Molecular Maya. A typical 3D animation is 3-5 minutes long and takes 3-6 months to create.
Description of the process:
STEP 1: Research and story development in association with scientific advisors. References include scientific literature and molecular, sctructural data.
STEP 2: Storyboard development and hand-drawn sketches to capture the key frames and messages to be conveyed by the animation.
STEP 3: Development of 3D models, animation rigs and dynamic effects in 3D animation software Autodesk Maya. Plugins required for molecular data: Molecular Maya. Look development including lights, cameras and shaders.
STEP 4: Editing together scenes, compositing using After Effects. Voice over is recorded and sound design is added during this stage.
Individual scenes are sketched in hand drawn illustrations that contribute to the storyboard, a process adapted from traditional film making and animation techniques. When finalized, the 2D storyboard is then re-created in 3D within the animation software Autodesk maya. Molecules are shaded and animation rigs are attached in order to bring the molecules to life, with dynamic effects applied that allow the structures to move in a way that is sensitive to their scientific attributes, yet engaging for the audience.
Every second of animation contains approximately 30 individual frames, each rendered out from the 3D animation software for compositing in Adobe After effects. Depending on the complexity of the scene, individual frames can take 1 - 90 minutes each to render. Individual frames are brought together and edited with appropriate scene transitions and additional cinematic effects to add atmosphere and to aid storytelling. The script is finalized and recorded in a professional studio. Sound designers are then also engaged to design an appropriate molecular soundscape and the final animation is rendered.
The following molecular animations created by Kate Patterson are narrative-driven and designed for viewing on a traditional mobile, computer, or large screen format. They have been translated into Hebrew and are being showcased at the Davidson Institute of Science Education at Weizmann, Israel.
Tagging DNA is an animation about DNA and epigenetics. It shows how DNA can be compact and hence unavailable, and open and hence available for gene transcription. It shows the methylation molecule DNMT adding a Ch3 methyl molecule onto a cytosine base of DNA. It also demonstrates the methylation pattern with respect to a DNA code.
Cancer Is Not One Disease draws on the experience of a pancreatic cancer patient. It shows that even though cancers may look the same under the microscope, they may have a very different genetic signature. It shows the protein p53 and describes how in a normal healthy cell p53 helps the cell respond to DNA damage. In cancer, p53 is mutated, allowing more and more genetic mistakes to accumulate and increasing the risk of cancer forming.
Producer, scientific storytelling and molecular assets: Dr Kate Patterson
Scientific Advisors: Professor Chris Goodnow and Professor Susan Clark
Trailer of VR Cell Explorer
Project 2: Immersive Visualisation Dome
The Garvan-Weizmann Centre for Cellular Genomics is home to a bespoke three metre immersive visualisation dome called the Cell Observatory. This structure allows small groups to interact with each other, as well as the molecular wonderland being showcased inside the dome. The dome is designed to immerse audiences inside a single cell, inside a molecular landscape which offers a more meaningful and memorable way to access complex scientific concepts and data.
Project 4: Collaborative Research – Visualisation in Education
Our research explores models to support teachers’ meaningful usage of 3D molecular animations in Australian and Israeli middle and secondary schools. It brings together the extensive educational research experience of Prof. Anat Yarden and Prof. Ron Blonder and their respective research groups at the Weizmann Institute of Science with Garvan’s genomics education expertise with Ms Bronwyn Terrill. 3D molecular animations by Garvan’s Dr Kate Patterson will form the basis of this research and focus on DNA and genomics - related concepts covered in the animations.