Compressing DNA sequence databases with coil

Background: Publicly available DNA sequence databases such as GenBank are large, and are growing at an exponential rate. The sheer volume of data being dealt with presents serious storage and data communications problems. Currently, sequence data is usually kept in large "flat files," which are then compressed using standard Lempel-Ziv (gzip) compression – an approach which rarely achieves good compression ratios. While much research has been done on compressing individual DNA sequences, surprisingly little has focused on the compression of entire databases of such sequences. In this study we introduce the sequence database compression software coil. Results: We have designed and implemented a portable software package, coil, for compressing and decompressing DNA sequence databases based on the idea of edit-tree coding. coil is geared towards achieving high compression ratios at the expense of execution time and memory usage during compression – the compression time represents a "one-off investment" whose cost is quickly amortised if the resulting compressed file is transmitted many times. Decompression requires little memory and is extremely fast. We demonstrate a 5% improvement in compression ratio over state-of-the-art general-purpose compression tools for a large GenBank database file containing Expressed Sequence Tag (EST) data. Finally, coil can efficiently encode incremental additions to a sequence database. Conclusion: coil presents a compelling alternative to conventional compression of flat files for the storage and distribution of DNA sequence databases having a narrow distribution of sequence lengths, such as EST data. Increasing compression levels for databases having a wide distribution of sequence lengths is a direction for future work

A comparison of Bayesian and Fourier methods for frequency determination in asteroseismology

Bayesian methods are becoming more widely used in asteroseismic analysis. In particular, they are being used to determine oscillation frequencies, which are also commonly found by Fourier analysis. It is important to establish whether the Bayesian methods provide an improvement on Fourier methods. We compare, using simulated data, the standard iterative sine-wave fitting method against a Markov Chain Monte Carlo (MCMC) code that has been introduced to infer purely the frequencies of oscillation modes (Brewer et al. 2007). A uniform prior probability distribution function is used for the MCMC method. We find the methods do equally well at determining the correct oscillation frequencies, although the Bayesian method is able to highlight the possibility of a misidentification due to aliasing, which can be useful. In general, we suggest that the least computationally intensive method is preferable.Comment: 11 pages, 8 figures, accepted for publication in Communications in Asterosesimolog

Biologically-inspired design: getting it wrong and getting it right

Large, complex computing systems have many similarities to biological systems, at least at a high level. They consist of a very large number of components, the interactions between which are complex and dynamic, and the overall behavior of the system is not always predictable even if the components are well understood. These similarities have led the computing community to look to biology for design inspiration. But computing systems are not biological systems. Care must be taken when applying biological designs to computing systems, and we need to avoid applying them when they are not appropriate. We review three areas in which we have used biology as an inspiration to understand and construct computing systems. The first is the epidemiology of computer viruses, in which biological models are used to predict the speed and scope of global virus spread. The second is global defenses against computer viruses, in which the mammalian immune system is the starting point for design. The third is self-assembling autonomic systems, in which the components of a system connect locally, without global control, to provide a desired global function. In each area, we look at an approach that seems very biologically motivated, but that turns out to yield poor results. Then, we look at an approach that works well, and contrast it with the prior misstep. Perhaps unsurprisingly, attempting to reason by analogy is fraught with dangers. Rather, it is critical to have a detailed, rigorous understanding of the system being constructed and the technologies being used, and to understand the differences between the biological system and the computing system, as well as their similarities.1st IFIP International Conference on Biologically Inspired Cooperative Computing - Biological Inspiration: Just a dream?Red de Universidades con Carreras en Informática (RedUNCI

Historical Poetics, Malaysian Cinema, and the Japanese Occupation

LITTLE HAS BEEN WRITTEN, especially in English, about the history of Malaysian cinema. Rather than a fully-developed study of Malaysian film, this article is really more of an introduction to the project I am undertaking, which is a study of Malaysian cinema from the "Golden Age" (the 1950s and 1960s), including especially the films of P. Ramlee, but also such genres as the crime film, fantasy film, and pontianak (vampire) film, to today's Malaysian cinema, with its own genres, outstanding filmmakers (Aziz Osman and U-Wei Haji Shaari, for example), and performers (most obviously, Sofia Jane). And this article is as much an introduction to my methodology -- historical poetics -- as it is to my subject. Therefore, this article is divided into three sections: the first deals with the need for a new way of looking at Third World cinema; the second with a general discussion of what historical..

An Alternative Way to Price Exotic Options

One of the most important aspects of financial options is how they are priced. Although there are a variety of methods for pricing basic financial options, two of the most utilized are the Binomial Option Pricing method and the Black-Scholes Formula. The Binomial Option Pricing method requires the assumption that asset prices only increase or decrease by a certain amount in a time-period. This method also requires the creation of binomial trees to track the asset and option prices. In contrast, the Black-Scholes Formula is a general formula and does not hold the assumption that stocks only go up or down by a certain amount. When looking at more complex exotic options, they are almost always priced via the Black-Scholes Formula. This is partly because the Binomial Option Pricing method is too calculation-heavy; however, through programming languages, such as R, some computations of the Binomial Option Pricing method become more feasible. Due to this, comparisons between these two pricing methods can be made for exotic options

Patterning nonisometric origami in nematic elastomer sheets

Nematic elastomers dramatically change their shape in response to diverse stimuli including light and heat. In this paper, we provide a systematic framework for the design of complex three dimensional shapes through the actuation of heterogeneously patterned nematic elastomer sheets. These sheets are composed of \textit{nonisometric origami} building blocks which, when appropriately linked together, can actuate into a diverse array of three dimensional faceted shapes. We demonstrate both theoretically and experimentally that: 1) the nonisometric origami building blocks actuate in the predicted manner, 2) the integration of multiple building blocks leads to complex multi-stable, yet predictable, shapes, 3) we can bias the actuation experimentally to obtain a desired complex shape amongst the multi-stable shapes. We then show that this experimentally realized functionality enables a rich possible design landscape for actuation using nematic elastomers. We highlight this landscape through theoretical examples, which utilize large arrays of these building blocks to realize a desired three dimensional origami shape. In combination, these results amount to an engineering design principle, which we hope will provide a template for the application of nematic elastomers to emerging technologies