Exploiting sparseness in de novo genome assembly

Background: The very large memory requirements for the construction of assembly graphs for de novo genome assembly limit current algorithms to super-computing environments. Methods: In this paper, we demonstrate that constructing a sparse assembly graph which stores only a small fraction of the observed k- mers as nodes and the links between these nodes allows the de novo assembly of even moderately-sized genomes (~500 M) on a typical laptop computer. Results: We implement this sparse graph concept in a proof-of-principle software package, SparseAssembler, utilizing a new sparse k- mer graph structure evolved from the de Bruijn graph. We test our SparseAssembler with both simulated and real data, achieving ~90% memory savings and retaining high assembly accuracy, without sacrificing speed in comparison to existing de novo assemblers

Insect Navigation and Communication in Flight and Migration: A Potential Model for Joining and Collision Avoidance in MAVs and Mobile Robots Fleet Control

The human being should be awarded the championship of navigation on the planet, on the virtues that they not only have invented and manufactured the compass, GPS, aircraft, vessel, spacecraft, but also have demonstrated exceptional non-instrumental navigation skills.12 The Austronesian expansion from the Asian mainland into the Pacific performed by the Pacific navigators, who eventually populated the most remote islands of the Pacific about 4000 years ago, is a vivid example (Wehner 1998). However, animals, especially flying birds and insects are strong contenders. Monarch butterflies can migrate up to 2000 miles from their reproductive sites in the eastern US and Canada to their over-wintering sites in the forests of Mexico, and it is postulated that they may possess a biological equivalent of a low-resolution GPS system that is based on the magnetic field of the earth. In fact, even the long-legged ants (Cataglyphis fortis) in the Saharan desert use the dead-reckoning navigation strategy, which is attributed to the Polynesians, but the ants apparently have acquired the capability much earlier, given the relative short evolutionary history of humans. In this article, we briefly review the state-of-the-art research on insect navigation and communication used in flight and communication, with the objective to inspire cross-disciplinary studies in aerospace engineering, biology and computer science

Mulian audience area

The Fifth CSIIRW '2009, April 13-15, Oak Ridge National Lab, Oak Ridge, Tennessee, USA. Includes a powerpoint presentation.The study of the First Passage Time (FPT) problem (also known as first passage problem, FPP) started more than a century ago, but its diverse applications in science and engineering mostly emerged in the last two to three decades. Assuming that X(t) is a one-dimensional stochastic process, the First Passage Time is defined as the time (T) when X(t) first crosses a threshold. Engineering reliability is obviously a suitable application domain, and indeed applications such as optimal dam design in hydrology and analysis of structural failure in civil and mechanical engineering are typical examples. Although we envision that the FPT problem has great potential in network and software reliability, it should be more useful for network security and survivability because the approaches developed for the FPT problem are mostly analytical. The assumption for this inference is that in reliability analysis, experimental or historical data are often more readily available, which makes statistical approaches such as survival analysis more convenient and likely more realistic. In contrast, data is generally more difficult to obtain in security and survivability analyses, and analytical approaches can be leveraged to play more important roles. Furthermore, security and survivability often have to deal with malicious actions that may be driven by sophisticated cognition and behavioral processes, which are highly variable over time and very difficult to detect with short term data. If the behavior of an intruder can be characterized with some stochastic process such as Brownian motion, then the FPT approach may be applied to find the closedform solution of the probability density function (PDF) of the first passage time, which can be the time when the system breaks down or when the hacker is successful in compromising a network. In addition, the solutions to FPT depend on boundary and initial conditions of the corresponding partial differential equations, and they also describe the evolution of PDF over time. This may suggest that it is possible to model the behavior changes of an intruder over time and circumstances. Another advantage of FPT analysis is that it may help solve some non-Markov stochastic process problems in reliability analysis and survival analysis. In this article, we first briefly introduce the FPT problem with Brownian motion as an example, and then suggest its potential applications in software reliability and network security

Developing an EUV multilayer adaptive mirror: the first results

The growing interest in the study of the extreme ultraviolet (EUV) radiation-matter interaction is feeding up the development of new technologies able to overcame some current technological limits. Adaptive optics is an established technology already widely used for wavefront correction in many applications such as astronomical telescopes, laser communications, high power laser systems, microscopy and high resolution imaging systems. Although this technology is already exploited in the EUV and X-ray range, its usage is only feasible in systems with a grazing incidence configuration. On the other hand, the development of a EUV normal incidence adaptive optics can open new interesting possibilities in many different fields ranging from free electron laser and synchrotron applications up to EUV photolithography. In this work we report the preliminary results achieved in the developing of a normal incidence EUV multilayered adaptive mirror tuned at 30.4nm. The proper functioning and potential applications of such device have been demonstrated by using a High order Harmonics Generation (HHG) source