Understanding microbialite morphology using a comprehensive suite of three-dimensional analysis tools.

Microbialites can have complex morphologies that preserve clues to ancient microbial ecology. However, extracting and interpreting these clues is challenging due to both the complexity of microbial structures and the difficulties of connecting morphology to microbial processes. Fenestrate microbialites from the 2521±3 Ma Gamohaan Formation, South Africa, have intricate structures composed of three distinct microbial structures: steeply dipping supports (surfaces defined by organic inclusions), more shallowly dipping supports with diffuse organic inclusions below them, and draping laminae. In polished slabs, shallowly dipping supports with diffuse organic inclusions show apparent dips from 27° to 60°, and supports without associated zones of diffuse inclusions dip 75° to 88°, which suggests a distinction between support types based on orientation. However, dips exposed in polished slabs are apparent dips, and three-dimensional analysis is required for analysis of true dips. Through the Keck Center for Active Visualization in Earth Sciences (KeckCAVES), we used locally developed software that controls a three-dimensional environment with head and hand tracking (an "immersive environment") to visualize and interpret virtual microbialite data sets. Immersive environments have not penetrated into standard scientific work processes ("workflows") due to their high costs, steep learning curves, and low productivity for users. By contrast, our suite of software tools allowed us to develop a personalized scientific workflow that provides a complete path from initial ideas to characterization of fenestrate microbialites' features. Results of three-dimensional analysis of fenestrate microbialites show that supports with inclusions dip 65° to 75°, whereas supports without inclusions dip 85° to 90°. These results demonstrate that all supports have very steep dips, and a 10° dip gap exists between supports with and without inclusions, which suggests they grew in fundamentally different ways. Results also emphasize how valuable three-dimensional analysis is when combined with a comprehensive workflow for understanding intricate structures such as fenestrate microbialites.

BuildBeta--a system for automatically constructing beta sheets.

We describe a method that can thoroughly sample a protein conformational space given the protein primary sequence of amino acids and secondary structure predictions. Specifically, we target proteins with beta-sheets because they are particularly challenging for ab initio protein structure prediction because of the complexity of sampling long-range strand pairings. Using some basic packing principles, inverse kinematics (IK), and beta-pairing scores, this method creates all possible beta-sheet arrangements including those that have the correct packing of beta-strands. It uses the IK algorithms of ProteinShop to move alpha-helices and beta-strands as rigid bodies by rotating the dihedral angles in the coil regions. Our results show that our approach produces structures that are within 4-6 A RMSD of the native one regardless of the protein size and beta-sheet topology although this number may increase if the protein has long loops or complex alpha-helical regions.

Teleimmersive environment for remote medical collaboration.

We present the work in progress on teleimmersive framework that would allow doctors to collaborate in more natural way by being immersed in the virtual space along with the medical data they could examine and discuss with remotely located colleagues. The system consists of multiple cameras, hand tracking with gesture recognition, and virtual reality system to support volume visualization and 3D interaction with medical data.

Discrete Sibson interpolation.

Natural-neighbor interpolation methods, such as Sibson's method, are well-known schemes for multivariate data fitting and reconstruction. Despite its many desirable properties, Sibson's method is computationally expensive and difficult to implement, especially when applied to higher-dimensional data. The main reason for both problems is the method's implementation based on a Voronoi diagram of all data points. We describe a discrete approach to evaluating Sibson's interpolant on a regular grid, based solely on finding nearest neighbors and rendering and blending d-dimensional spheres. Our approach does not require us to construct an explicit Voronoi diagram, is easily implemented using commodity three-dimensional graphics hardware, leads to a significant speed increase compared to traditional approaches, and generalizes easily to higher dimensions. For large scattered data sets, we achieve two-dimensional (2D) interpolation at interactive rates and 3D interpolation (3D) with computation times of a few seconds.

ProteinShop: a tool for interactive protein manipulation and steering.

We describe ProteinShop, a new visualization tool that streamlines and simplifies the process of determining optimal protein folds. ProteinShop may be used at different stages of a protein structure prediction process. First, it can create protein configurations containing secondary structures specified by the user. Second, it can interactively manipulate protein fragments to achieve desired folds by adjusting the dihedral angles of selected coil regions using an Inverse Kinematics method. Last, it serves as a visual framework to monitor and steer a protein structure prediction process that may be running on a remote machine. ProteinShop was used to create initial configurations for a protein structure prediction method developed by a team that competed in CASP5. ProteinShop's use accelerated the process of generating initial configurations, reducing the time required from days to hours. This paper describes the structure of ProteinShop and discusses its main features.