Scalable global alignment for multiple biological networks

<p>Abstract</p> <p>Background</p> <p>Advances in high-throughput technology has led to an increased amount of available data on protein-protein interaction (PPI) data. Detecting and extracting functional modules that are common across multiple networks is an important step towards understanding the role of functional modules and how they have evolved across species. A global protein-protein interaction network alignment algorithm attempts to find such functional orthologs across multiple networks.</p> <p>Results</p> <p>In this article, we propose a scalable global network alignment algorithm based on clustering methods and graph matching techniques in order to detect conserved interactions while simultaneously attempting to maximize the sequence similarity of nodes involved in the alignment. We present an algorithm for multiple alignments, in which several PPI networks are aligned. We empirically evaluated our algorithm on three real biological datasets with 6 different species and found that our approach offers a significant benefit both in terms of quality as well as speed over the current state-of-the-art algorithms.</p> <p>Conclusion</p> <p>Computational experiments on the real datasets demonstrate that our multiple network alignment algorithm is a more efficient and effective algorithm than the state-of-the-art algorithm, IsoRankN. From a qualitative standpoint, our approach also offers a significant advantage over IsoRankN for the multiple network alignment problem.</p

Nlcviz: Tensor Visualization And Defect Detection In Nematic Liquid Crystals

Visualization and exploration of nematic liquid crystal (NLC) data is a challenging task due to the multidimensional and multivariate nature of the data. Simulation study of an NLC consists of multiple timesteps, where each timestep computes scalar, vector, and tensor parameters on a geometrical mesh. Scientists developing an understanding of liquid crystal interaction and physics require tools and techniques for effective exploration, visualization, and analysis of these data sets. Traditionally, scientists have used a combination of different tools and techniques like 2D plots, histograms, cut views, etc. for data visualization and analysis. However, such an environment does not provide the required insight into NLC datasets. This thesis addresses two areas of the study of NLC data---understanding of the tensor order field (the Q-tensor) and defect detection in this field. Tensor field understanding is enhanced by using a new glyph (NLCGlyph) based on a new design metric which is closely related to the underlying physical properties of an NLC, described using the Q-tensor. A new defect detection algorithm for 3D unstructured grids based on the orientation change of the director is developed. This method has been used successfully in detecting defects for both structured and unstructured models with varying grid complexity

Detection and visualization of anomalous structures in molecular dynamics simulation data

Figure 1: Si system with a tri-interstitial defect (dataset I1) (a) Lattice with bulk and defect (b) Salient Iso-surface with ability to distinguish between bulk and defect (c) An arbitrary slice of electron density data showing the shape of defect. In this article we explore techniques to detect and visualize features in data from molecular dynamics (MD) simulations. Although the techniques proposed are general, we focus on silicon (Si) atomic systems. The first set of methods use 3D location of atoms. Defects are detected and categorized using local operators and statistical modeling. Our second set of exploratory techniques employ electron density data. This data is visualized to glean the defects. We describe techniques to automatically detect the salient iso-values for iso-surface extraction and designing transfer functions.We compare and contrast the results obtained from both sources of data. Essentially, we find that the methods of defect (feature) detection are at least as robust as those based on the exploration of electron density for Si systems