Updated February 4, 2020
Sampling molecular conformations and dynamics in a multiuser virtual reality framework.
O'Connor M, Deeks HM, Dawn E, Metatla O, Roudaut A, Sutton M, Thomas LM, Glowacki BR, Sage R, Tew P, Wonnacott M, Bates P, Mulholland AJ, Glowacki DR.
Sci Adv. 2018 Jun 29;4(6)
Molecular Visualization on the Holodeck.
Goddard TD, Brilliant AA, Skillman TL, Vergenz S, Tyrwhitt-Drake J, Meng EC, Ferrin TE.
J Mol Biol. 2018 Jun 28. pii: S0022-2836(18)30696-X
ConfocalVR: Immersive Visualization Applied to Confocal Microscopy.
Stefani C, Lacy-Hulbert A, Skillman T.
J Mol Biol. 2018 Jun 24. pii: S0022-2836(18)30664-8.
Drug binding sites Matt Jacobson lab Weekly group meetings using VR to analyze ligand binding using ChimeraX. Contact Wilian Cortopassi Coelho. |
p97 inhibitors Michelle Arkin lab Inhibitors of p97 involved in protein recycling and possibly neurodegnerative disease. Virtual reality demonstration for UCSF Campaign. |
Antibiotic resistance Danica Fujimori lab Mechanism of post-translational methylation of a ribosome nucleotide causing antibiotic resistance. Shown in VR for Byer's award reception. |
Cell motility 3D light microscopy Dyche Mullins lab ChimeraX VR displays 3D microscopy time series. Neutrophils crawling through collagen filaments. |
Calcium signaling in neurons Bo Huang lab Dan Xie observes calcium signaling in 8000 zebrafish neurons using 3d light-sheet microscopy time series. Demonstrated in VR for Byer's award lecture using ChimeraX VR. |
Neurodegeneration in zebrafish Steve Finkbeiner lab Neurodegeneration in zebrafish in 3d light microscopy time series from Jeremy Linsley at Glastone Institute shown with ConfocalVR. |
DNA origami virtual lab
Shawn Douglas lab Interview with Shawn on the Foo Show about his VR nano-machine lab simulation. |
Brain disorder treatment Adam Gazzaley lab Neuroscape. |
ChimeraX VR Tom Ferrin lab The ChimeraX visualization package can display atomic structures and microscopy data with the vr command. A tutorial explores mutations in a scorpion toxin. |
Collaborative structure viewing Tom Ferrin lab ChimeraX VR meeting command allows multiperson viewing of structures and microscopy data. |
ConfocalVR Tom Skillman and Caroline Stefani at Benaroya Research Insitute ConfocalVR displays multichannel 3D light microscopy data. |
Protein Databank VR viewer Tom Skillman at Benaroya Research Institute AltPDB collaborative viewing of Protein Databank molecular structures. |
Nanome from Nanome, Inc. Nanome allows display and analysis of molecular structures of proteins including multiperson collaborative sessions. |
syGlass from IstoVizio, Inc. syGlass displays volumetric and microscopy data, designed for VR. |
Molecular Zoo Alan Brilliant in Tom Ferrin lab Molecular Zoo is a biomolecule education VR program that lets children handle fully flexible molecules of life: water, aspirin, saturated fat, carbon dioxide, caffeine, ATP. |
Peroxiredoxin Fish Tank David Doak at Norwich University of the Arts Nick Young and Bianca Haux at the Centre for eResearch at the University of Auckland Juliet Gerrard and Michael Barnett from the University of Auckland School of Biological Sciences Fishtank is a STEM education application showing the pH dependent formation of protein dimers, rings and tubes of an antioxidant enzyme. Currently (Sept 2018) only Unity source code releases are available at Github, but a binary release for Windows is coming. |
Protein Backbone Explorer David Doak at Norwich University of the Arts Work in progress: interactive polypeptide backbone viewer for teaching using Unity and Oculus SDK. Currently (Sept 2018) only Unity source code releases are available at Github, but a binary release for Windows is coming. |
Nano Simbox iMD Interactive Scientific Nano Simbox iMD allows exploring flexible molecules with molecular dynamics computed in real-time on a server. It has four scenarios, handling Buckminster fullerene, threading methane through a carbon nanotube, changing the screw-sense of an organic helicene molecule, and tying a knot in a 17 amino acid peptide. Developed by Interactive Scientific in collaboration with the Glowacki lab at University of Bristol, and described in this article. |
Water VR Jonas Boström and Magnus Norrby Water VR shows water in gas, liquid and solid phases for teaching chemisty, specifically aimed at 7th grade students. Developed by EduChemVR. |
Shared VR equipment Tom Ferrin lab An HTC Vive virtual reality headset for viewing your molecular structures or microscopy data is available at the Visualization Vault in Genentech Hall at UCSF Mission Bay. Contact Tom Goddard. |
We use Windows 10 Home on our VR computers. We use primarily SteamVR to interface to all headsets. Wikipedia headset comparison. VRcompare headset comparison.
We have extensive experience with the GPUs noted below and have also been experimenting with others, so this list may be a bit out of date:
Virtual Reality in the San Francisco Public Libraries - pre-proposal to setup VR systems for informal STEM education in the 27 branches of the San Francisco public library. Full proposal due November 17, 2018.
Analysis of Molecules and Cells in Virtual Reality - Setup research VR systems in 5 UCSF labs for cryoEM structure refinement, 3D light microscopy, and multi-person VR collaborations. Funded Aug 1, 2018 for 1 year.
Exploring Drug Binding using Molecular Dynamics and Virtual Reality - proposal by Tom Goddard, Wilian Cortopassi Coelho, Matt Jacobson, Michael Grabe, Tristan Croll, and Tom Ferrin to study mutations effecting drug binding sites. Funded. January 2018.
Virtual Reality Molecular Playground - proposal for STEM education VR application to familiarize students with biomolecules. Not funded. January 2017.
Steven Abbott - Developer of many WebVR apps related to solvation.
Marc Baaden (Institut de Biologie Physico-Chimique) - Developer of UnityMol library for representing molecules in the Unity3D game engine.
Alan Brilliant (UCSC) - Developer of Molecular Zoo biomolecule education application.
Wilian Cortopassi Coelho (UCSF) - Studies drug-receptor interactions using VR in Matt Jacobson's lab. Publishing 3 drug studies in July 2018 using VR analysis.
Gareth Denyer (University of Sydney) - Developed Peppy protein structure teaching app with David Doak. Teaches structural biology at the Sydney Immersive learning laboratory.
David Doak (Norwich University of the Arts) - Developed peroxiredoxin fishtank STEM application and is working on a protein backbone explorer app.
Shawn Douglas (UCSF) - Developed VR lab simulation for DNA origami research.
Tom Ferrin (UCSF) - Provides shared HTC Vive VR equipment in the Visualization Vault.
Nicolas Floquet (U Montepellier) - Manages the MUSE-VR education facility in the Institut des Biomolécules Max Mousseron.
Christopher Fortney (NIH) - Manages the Virtual Reality Consulting Service at the NIH library.
Zack Gainsforth (Space Sciences Lab) - VR of electron microscopy of cometary dust.
Tom Goddard (UCSF) - ChimeraX VR developer.
Matt Jacobson (UCSF) - Analyzes drug binding, weekly use of VR in group meetings.
Meghan McCarthy (NIH) - Using ChimeraX VR with radiologists at NIH.
Dyche Mullins (UCSF) - VR visualization 3D light microscopy of crawling neutrophil cells.
Mike Schmid (Stanford-SLAC CryoEM Center) - VR visualization of EM tomography of bacteria, and atomic resolution virus capsids.
Tom Skillman (Immersive Science) - Founder of Immersive Science, developing VR science applications ConfocalVR for light microscopy, AltPDB for collaborative molecular structure viewing, and FCS-VR for flow cytometry analysis.
Caroline Stefani (Benaroya Research Institute) - Developer of ConfocalVR for light microscopy, working with Tom Skillman.
James Tyrwhitt-Drake - Developer of speech recognition command input from ChimeraX. Worked with Meghan McCarthy at NIH on virtual reality applications.
Sampling molecular conformations and dynamics in a multiuser virtual reality framework.
O'Connor M, Deeks HM, Dawn E, Metatla O, Roudaut A, Sutton M, Thomas LM, Glowacki BR, Sage R, Tew P, Wonnacott M, Bates P, Mulholland AJ, Glowacki DR.
Sci Adv. 2018 Jun 29;4(6)
Molecular Visualization on the Holodeck.
Goddard TD, Brilliant AA, Skillman TL, Vergenz S, Tyrwhitt-Drake J, Meng EC, Ferrin TE.
J Mol Biol. 2018 Jun 28. pii: S0022-2836(18)30696-X
ConfocalVR: Immersive Visualization Applied to Confocal Microscopy.
Stefani C, Lacy-Hulbert A, Skillman T.
J Mol Biol. 2018 Jun 24. pii: S0022-2836(18)30664-8.
Towards Commodity, Web-Based Augmented Reality Applications for Research and Education in Chemistry and Structural Biology.
Luciano A. Abriata
arXiv:1806.08332
Virtual-reality applications give science a new dimension.
Matthews D.
Nature. 2018 May;557(7703):127-128. doi: 10.1038/d41586-018-04997-2.
Journey to the centre of the cell: Virtual reality immersion into scientific data.
Johnston APR, Rae J, Ariotti N, Bailey B, Lilja A, Webb R, Ferguson C, Maher S, Davis TP, Webb RI, McGhee J, Parton RG.
Traffic. 2018 Feb;19(2):105-110. doi: 10.1111/tra.12538. Epub 2017 Nov 21.
Tom Goddard / UCSF / goddard@cgl.ucsf.edu