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CAVE usage in Research spreads to Microbiology
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CAVE usage in Research spreads to Microbiology

A new CAVE-type installation has been installed in India, for use by the mircobiology research and technology centre IMTECH. Virtalis, the manufacturer of the specific CAVE-variant technology used; the ActiveWall system, have been extremely keen to promote this major VR installation. Great news as it is for them, it is of course even better news for the increasing push to see highly immersive VR interfaces made increasingly pervasive in higher learning.


IMTECH Ph.D. students visualizing DNA/protein interaction site of the tetR protein on the new installation

 

This particular installation uses Virtalis' proprietary interface software for PyMOL, an open-source, user-sponsored, molecular visualization system. The interface software is so that PyMOL data can be interacted with in native 3D as any VR system demands, rather than the 2D or 2.5D at best, of a desktop computer interface. It is a C1 variety installation, meaning only a single wall comprises the display system, as opposed to say, a C6, in which all four walls, ceiling and floor comprise the system.

Srikrishna Subramanian, principal scientist at IMTECH, explained: “When the ActiveWall and the VR Enabler for PyMOL were installed, their application as a high-end visualisation platform for macromolecular biodata was clear. Once the integrated system was up and running, people were awe-struck by the stunning visual impact of being able to look at their structural data on a large screen where they could interact with it in real-time. The utility of this system is such that researchers can use it to interactively visualise biological macromolecules at an atomic level, allowing detailed structural analysis. In addition to serving as an exceptional research environment, our ActiveWall can be used as a teaching tool to highlight the importance of macromolecules to students and research collaborators from other related research areas.”

Obviously, the installation doesn't have to be Virtalis' to create that effect. Any of the major CAVE and GeoWall type interfaces would have the exact same effect. However, every installation of this type done successfully, raises the profile of this type of highly useful research and display tool among the next generation of researchers.

The system specifics are pretty much standard for all of this type of environment: Any user movement inside the space occupied by the system is tracked in real-time. Like most modern CAVEs, ActiveWall can handle large parties with no problem, tracking individual users independently of one another for control purposes.

For display purposes, either an average of all positions is considered, or a single lead user is chosen by means of a control wand. This user's mmovements then become critical, as their head movement, eye movent and direction of orientation control how the system displays visual data. As they move, the display moves with them, compensating for natural movements by altering the perspective of the visuals displayed, to try and make the experience feel as natural and realistic as possible.

For example, as you crouch down, ActiveWall decreases the angle on the image, moving things so your perspective is closer to the 'floor'. As you stand up, the angle widens, naturally altering the display to mimic rising higher above it. Control users of different heights will likewise have the display automatically set for them so as to be most natural for the perspective they are used to interacting with the world around them, from. All other users of the system are of course, pulled along for the ride. CAVE installations are always single-user display deals.

The control wand has other functions beyond just designating the control user, of course. Like it's distant precursor, the Wanda, the ActiveWall wand is the user's navigation tool; allowing them to fly through the virtual environment displayed, to select and manipulate data, start and stop phy6sics and chemical simulation overlays.

A more haptic control system is possible with these types of installations, but was not used in this case, owing to the current cost and fragility of dataglove units. A wand interface style was deemed sufficient for this particular installation.


An IMTECH Ph.D. scholar visualizing the interaction of the antibiotic tetracycline with the repressor protein tetR that confers antibiotic resistance in bacteria. The tetracycline molecule is shown as ball-and-sticks and coloured yellow and the side chain atoms from the tetR protein that interact with the tetracycline are coloured cyan.

 

Subramanian added: “Our lab specialises in developing new computational approaches to study protein structures by carrying out evolutionary analysis and the classification of protein families/folds. We have been using PyMOL for our research for quite some time now. Complete VR-integration of the open source PyMOL software was a very important factor in choosing Virtalis, as PyMOL is the only visualisation tool most of our students use, owing to its intuitive GUI and strong command-line scripting abilities. The first impression users have of the ActiveWall with its VR-enabled PyMOL is always a big WOW! We now have an easy to use, interactive platform on which we can visualise molecules of interest in 3D.”

IMTECH is currently using its installation to visualise biological macromolecules (especially proteins) in 3D in order to study the interaction of these molecules with one another and with other biological moieties. The system is also deployed in a teaching course on protein structures, as it helps students to visualise macromolecular interactions, such as, protein-DNA interaction, in specific contexts like multiple-drug resistance.

Subramanian concluded: “ActiveWall makes group discussions more interactive, because the minute details of a particular protein or macromolecule are much clearer in 3D on a large screen. We now have a better appreciation of how a protein’s function is modulated by atomic level interactions and the audience can see these macromolecules in rich interactive detail. The hand tracking system gives power to modulate a structure as and when needed during the course of a discussion and to visualise from multiple viewpoints.”

References

Press Release: VR Helps Microbiology R&D

PyMOL

VR for PyMOL

Local References

VR Interfaces: Star CAVE

VR Interfaces: Wanda

Staff Comments

 


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