The Computational Techniques Developed to Analyze DNA Gel Images

The analysis of gel electrophoresis images is very crucial for molecular biologists to comprehend and interpret their experimental results. Thus, enhancing current mathematical methods and developing new accurate ones is very important and challenging task for bioinformaticians. For example, enhancing the commonly used mathematical method in gel analysis known as "Fitting method estimation" and proposing a new efficient method entitled "Ruler estimation" for preprocessing a given image and detecting lanes and bands automatically. Both mathematical methods implemented in our newly developed software. Three mathematical models namely, linear, quadratic and cubic fitting are tested for the accuracy of detecting the bands and lanes in the gel image to determine the best fitting model. A friendly user interface is developed for this new program using MATLB GUI to extract useful bimolecular information accurately and automatically. The new software has the ability to manually add or delete any band(s) and estimate the size of any unknown band(s) on the gel. Moreover, the similarity and (dis)similarity between lanes "samples" are estimated based on comparing the numbers and sizes of bands to generate a phylogram tree

Recent advances in computational techniques

The determination of very precise orbits and geodynamic parameters from laser tracking data requires the continual development and improvement of the software systems and computational techniques. Computational accuracies at the few centimeter level are presently required to match the performance of the present day laser ranging systems and altimeters and in the next few years the accuracies are expected to increase further. The major error sources in orbit determination are briefly discussed and the present and future modeling activities needed to meet the accuracy requirements of the next few years are described

Computational Techniques

This chapter introduces fundamental computational approaches and ideas to energy materials. These can be divided into two main streams: one dealing with the motion of atoms or ions described at a simplified level of theory and another focusing on electrons. The modeling framework, which covers both streams, is outlined. The atomistic simulation techniques discussed in the chapter are concerned with describing the energy landscape of individual atoms or ions, where classical mechanics can be usefully employed as the first successful approximation. Multiscale approaches could be the method of choice if one is interested in large molecules, inhomogeneous solids, complex environments or geometrical arrangements, systems that are far away from equilibrium or have particularly long evolution times. One of the principal objectives of atomistic simulations is to derive an accurate and coherent approach to the prediction of defect structure, energetics and properties. Two of the most widely employed methods are outlined. This edition first published 2013 © 2013 John Wiley & Sons, Ltd

Computational techniques for flows with finite-rate condensation

A computational method to simulate the inviscid two-dimensional flow of a two-phase fluid was developed. This computational technique treats the gas phase and each of a prescribed number of particle sizes as separate fluids which are allowed to interact with one another. Thus, each particle-size class is allowed to move through the fluid at its own velocity at each point in the flow field. Mass, momentum, and energy are exchanged between each particle class and the gas phase. It is assumed that the particles do not collide with one another, so that there is no inter-particle exchange of momentum and energy. However, the particles are allowed to grow, and therefore, they may change from one size class to another. Appropriate rates of mass, momentum, and energy exchange between the gas and particle phases and between the different particle classes were developed. A numerical method was developed for use with this equation set. Several test cases were computed and show qualitative agreement with previous calculations

Review of some classical gravitational superenergy tensors using computational techniques

We use computational algorithms recently developed by us to study completely four index divergence free quadratic in Riemann tensor polynomials in GR. Some results are new and some other reproduce and/or correct known ones. The algorithms are part of a Mathematica package called Tools of Tensor Calculus (TTC)[web address: http://baldufa.upc.es/ttc

Satellite communication performance evaluation: Computational techniques based on moments

Computational techniques that efficiently compute bit error probabilities when only moments of the various interference random variables are available are presented. The approach taken is a generalization of the well known Gauss-Quadrature rules used for numerically evaluating single or multiple integrals. In what follows, basic algorithms are developed. Some of its properties and generalizations are shown and its many potential applications are described. Some typical interference scenarios for which the results are particularly applicable include: intentional jamming, adjacent and cochannel interferences; radar pulses (RFI); multipath; and intersymbol interference. While the examples presented stress evaluation of bit error probilities in uncoded digital communication systems, the moment techniques can also be applied to the evaluation of other parameters, such as computational cutoff rate under both normal and mismatched receiver cases in coded systems. Another important application is the determination of the probability distributions of the output of a discrete time dynamical system. This type of model occurs widely in control systems, queueing systems, and synchronization systems (e.g., discrete phase locked loops)

Some computational techniques for estimating human operator describing functions

Computational procedures for improving the reliability of human operator describing functions are described. Special attention is given to the estimation of standard errors associated with mean operator gain and phase shift as computed from an ensemble of experimental trials. This analysis pertains to experiments using sum-of-sines forcing functions. Both open-loop and closed-loop measurement environments are considered

Computational Techniques for Efficient Conversion of Image Files from Area Detectors

Area detectors are used in many scientific and technological applications such as particle and radiation physics. Thanks to the recent technological developments, the radiation sources are becoming increasingly brighter and the detectors become faster and more efficient. The result is a sharp increase in the size of data collected in a typical experiment. This situation imposes a bottleneck on data processing capabilities, and could pose a real challenge to scientific research in certain areas. This article proposes a number of simple techniques to facilitate rapid and efficient extraction of data obtained from these detectors. These techniques are successfully implemented and tested in a computer program to deal with the extraction of X-ray diffraction patterns from EDF image files obtained from CCD detectors.Comment: 16 pages, 6 figure