A Graph-Theoretical Approach to the Selection of the Minimum Tiling Path from a Physical Map

The problem of computing the minimum tiling path (MTP) from a set of clones arranged in a physical map is a cornerstone of hierarchical (clone-by-clone) genome sequencing projects. We formulate this problem in a graph theoretical framework, and then solve by a combination of minimum hitting set and minimum spanning tree algorithms. The tool implementing this strategy, called FMTP, shows improved performance compared to the widely used software FPC. When we execute FMTP and FPC on the same physical map, the MTP produced by FMTP covers a higher portion of the genome, and uses a smaller number of clones. For instance, on the rice genome the MTP produced by our tool would reduce by about 11 percent the cost of a clone-by-clone sequencing project. Source code, benchmark data sets, and documentation of FMTP are freely available at \u3ehttp://code.google.com/p/fingerprint-based-minimal-tiling-path/ under MIT license

A multi-view approach to cDNA micro-array analysis

The official published version can be obtained from the link below.Microarray has emerged as a powerful technology that enables biologists to study thousands of genes simultaneously, therefore, to obtain a better understanding of the gene interaction and regulation mechanisms. This paper is concerned with improving the processes involved in the analysis of microarray image data. The main focus is to clarify an image's feature space in an unsupervised manner. In this paper, the Image Transformation Engine (ITE), combined with different filters, is investigated. The proposed methods are applied to a set of real-world cDNA images. The MatCNN toolbox is used during the segmentation process. Quantitative comparisons between different filters are carried out. It is shown that the CLD filter is the best one to be applied with the ITE.This work was supported in part by the Engineering and Physical Sciences Research Council (EPSRC) of the UK under Grant GR/S27658/01, the National Science Foundation of China under Innovative Grant 70621001, Chinese Academy of Sciences under Innovative Group Overseas Partnership Grant, the BHP Billiton Cooperation of Australia Grant, the International Science and Technology Cooperation Project of China under Grant 2009DFA32050 and the Alexander von Humboldt Foundation of Germany

The Whole is Greater than the Sum of the Parts: Optimizing the Joint Science Return from LSST, Euclid and WFIRST

The focus of this report is on the opportunities enabled by the combination of LSST, Euclid and WFIRST, the optical surveys that will be an essential part of the next decade's astronomy. The sum of these surveys has the potential to be significantly greater than the contributions of the individual parts. As is detailed in this report, the combination of these surveys should give us multi-wavelength high-resolution images of galaxies and broadband data covering much of the stellar energy spectrum. These stellar and galactic data have the potential of yielding new insights into topics ranging from the formation history of the Milky Way to the mass of the neutrino. However, enabling the astronomy community to fully exploit this multi-instrument data set is a challenging technical task: for much of the science, we will need to combine the photometry across multiple wavelengths with varying spectral and spatial resolution. We identify some of the key science enabled by the combined surveys and the key technical challenges in achieving the synergies.Comment: Whitepaper developed at June 2014 U. Penn Workshop; 28 pages, 3 figure

Linear-scaling algorithm for rapid computation of inelastic transitions in the presence of multiple electron scattering

Strong multiple scattering of the probe in scanning transmission electron microscopy (STEM) means image simulations are usually required for quantitative interpretation and analysis of elemental maps produced by electron energy-loss spectroscopy (EELS). These simulations require a full quantum-mechanical treatment of multiple scattering of the electron beam, both before and after a core-level inelastic transition. Current algorithms scale quadratically and can take up to a week to calculate on desktop machines even for simple crystal unit cells and do not scale well to the nanoscale heterogeneous systems that are often of interest to materials science researchers. We introduce an algorithm with linear scaling that typically results in an order of magnitude reduction in computation time for these calculations without introducing additional error and discuss approximations that further improve computational scaling for larger-scale objects with modest penalties in calculation error. We demonstrate these speedups by calculating the atomic resolution STEM-EELS map using the L-edge transition of Fe, for a nanoparticle 80 Å in diameter, in 16 hours, a calculation that would have taken at least 80 days using a conventional multislice approach

The Iray Light Transport Simulation and Rendering System

While ray tracing has become increasingly common and path tracing is well understood by now, a major challenge lies in crafting an easy-to-use and efficient system implementing these technologies. Following a purely physically-based paradigm while still allowing for artistic workflows, the Iray light transport simulation and rendering system allows for rendering complex scenes by the push of a button and thus makes accurate light transport simulation widely available. In this document we discuss the challenges and implementation choices that follow from our primary design decisions, demonstrating that such a rendering system can be made a practical, scalable, and efficient real-world application that has been adopted by various companies across many fields and is in use by many industry professionals today