SSMBS: a web server to locate sequentially separated motifs in biological sequences

The identification of sequence (amino acids or nucleotides) motifs in a particular order in biological sequences has proved to be of interest. This paper describes a computing server, SSMBS, which can locate anddisplay the occurrences of user-defined biologically important sequence motifs (a maximum of five) present in a specific order in protein and nucleotide sequences. While the server can efficiently locate motifs specified using regular expressions, it can also find occurrences of long and complex motifs. The computation is carried out by an algorithm developed using the concepts of quantifiers in regular expressions. The web server is available to users around the clock at http://dicsoft1.physics.iisc.ernet.in/ssmbs/.

A Method to Find Sequentially Separated Motifs in Biological Sequences (SSMBS)

Sequence motifs occurring in a particular order in proteins or DNA have been proved to be of biological interest. In this paper, a new method to locate the occurrences of up to five user-defined motifs in a specified order in large proteins and in nucleotide sequence databases is proposed. It has been designed using the concept of quantifiers in regular expressions and linked lists for data storage. The application of this method includes the extraction of relevant consensus regions from biological sequences. This might be useful in clustering of protein families as well as to study the correlation between positions of motifs and their functional sites in DNA sequences.

WebGeSTer DB-a transcription terminator database

We present WebGeSTer DB, the largest database of intrinsic transcription terminators (http://pallab.serc.iisc.ernet.in/gester). The database comprises of a million terminators identified in 1060 bacterial genome sequences and 798 plasmids. Users can obtain both graphic and tabular results on putative terminators based on default or user-defined parameters. The results are arranged in different tiers to facilitate retrieval, as per the specific requirements. An interactive map has been incorporated to visualize the distribution of terminators across the whole genome. Analysis of the results, both at the whole-genome level and with respect to terminators downstream of specific genes, offers insight into the prevalence of canonical and non-canonical terminators across different phyla. The data in the database reinforce the paradigm that intrinsic termination is a conserved and efficient regulatory mechanism in bacteria. Our database is freely accessible.

Stabilized SPH-based simulations of impact dynamics using acceleration-corrected artificial viscosity

Artificial viscosity in SPH-based computations of impact dynamics is a numerical artifice that helps stabilize spurious oscillations near the shock fronts and requires certain user-defined parameters. Improper choice of these parameters may lead to spurious entropy generation within the discretized system and make it over-dissipative. This is of particular concern in impact mechanics problems wherein the transient structural response may depend sensitively on the transfer of momentum and kinetic energy due to impact. In order to address this difficulty, an acceleration correction algorithm was proposed in Shaw and Reid (''Heuristic acceleration correction algorithm for use in SPH computations in impact mechanics'', Comput. Methods Appl. Mech. Engrg., 198, 3962-3974) and further rationalized in Shaw et al. (An Optimally Corrected Form of Acceleration Correction Algorithm within SPH-based Simulations of Solid Mechanics, submitted to Comput. Methods Appl. Mech. Engrg). It was shown that the acceleration correction algorithm removes spurious high frequency oscillations in the computed response whilst retaining the stabilizing characteristics of the artificial viscosity in the presence of shocks and layers with sharp gradients. In this paper, we aim at gathering further insights into the acceleration correction algorithm by further exploring its application to problems related to impact dynamics. The numerical evidence in this work thus establishes that, together with the acceleration correction algorithm, SPH can be used as an accurate and efficient tool in dynamic, inelastic structural mechanics. (C) 2011 Elsevier Ltd. All rights reserved.

SuSeFLAV 1.2: Program for supersymmetric mass spectra with seesaw mechanism and rare lepton flavor violating decays

Accurate supersymmetric spectra are required to confront data from direct and indirect searches of supersymmetry. SuSeFLAV is a numerical tool capable of computing supersymmetric spectra precisely for various supersymmetric breaking scenarios applicable even in the presence of flavor violation. The program solves MSSM RGEs with complete 3 x 3 flavor mixing at 2-loop level and one loop finite threshold corrections to all MSSM parameters by incorporating radiative electroweak symmetry breaking conditions. The program also incorporates the Type-I seesaw mechanism with three massive right handed neutrinos at user defined mass scales and mixing. It also computes branching ratios of flavor violating processes such as l(j) -> l(i)gamma, l(j) -> 3 l(i), b -> s gamma and supersymmetric contributions to flavor conserving quantities such as (g(mu) - 2). A large choice of executables suitable for various operations of the program are provided. Program summary Program title: SuSeFLAV Catalogue identifier: AEOD_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEOD_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License No. of lines in distributed program, including test data, etc.: 76552 No. of bytes in distributed program, including test data, etc.: 582787 Distribution format: tar.gz Programming language: Fortran 95. Computer: Personal Computer, Work-Station. Operating system: Linux, Unix. Classification: 11.6. Nature of problem: Determination of masses and mixing of supersymmetric particles within the context of MSSM with conserved R-parity with and without the presence of Type-I seesaw. Inter-generational mixing is considered while calculating the mass spectrum. Supersymmetry breaking parameters are taken as inputs at a high scale specified by the mechanism of supersymmetry breaking. RG equations including full inter-generational mixing are then used to evolve these parameters up to the electroweak breaking scale. The low energy supersymmetric spectrum is calculated at the scale where successful radiative electroweak symmetry breaking occurs. At weak scale standard model fermion masses, gauge couplings are determined including the supersymmetric radiative corrections. Once the spectrum is computed, the program proceeds to various lepton flavor violating observables (e.g., BR(mu -> e gamma), BR(tau -> mu gamma) etc.) at the weak scale. Solution method: Two loop RGEs with full 3 x 3 flavor mixing for all supersymmetry breaking parameters are used to compute the low energy supersymmetric mass spectrum. An adaptive step size Runge-Kutta method is used to solve the RGEs numerically between the high scale and the electroweak breaking scale. Iterative procedure is employed to get the consistent radiative electroweak symmetry breaking condition. The masses of the supersymmetric particles are computed at 1-loop order. The third generation SM particles and the gauge couplings are evaluated at the 1-loop order including supersymmetric corrections. A further iteration of the full program is employed such that the SM masses and couplings are consistent with the supersymmetric particle spectrum. Additional comments: Several executables are presented for the user. Running time: 0.2 s on a Intel(R) Core(TM) i5 CPU 650 with 3.20 GHz. (c) 2012 Elsevier B.V. All rights reserved.

Statistical significance of episodes with general partial orders

Frequent episode discovery is one of the methods used for temporal pattern discovery in sequential data. An episode is a partially ordered set of nodes with each node associated with an event type. For more than a decade, algorithms existed for episode discovery only when the associated partial order is total (serial episode) or trivial (parallel episode). Recently, the literature has seen algorithms for discovering episodes with general partial orders. In frequent pattern mining, the threshold beyond which a pattern is inferred to be interesting is typically user-defined and arbitrary. One way of addressing this issue in the pattern mining literature has been based on the framework of statistical hypothesis testing. This paper presents a method of assessing statistical significance of episode patterns with general partial orders. A method is proposed to calculate thresholds, on the non-overlapped frequency, beyond which an episode pattern would be inferred to be statistically significant. The method is first explained for the case of injective episodes with general partial orders. An injective episode is one where event-types are not allowed to repeat. Later it is pointed out how the method can be extended to the class of all episodes. The significance threshold calculations for general partial order episodes proposed here also generalize the existing significance results for serial episodes. Through simulations studies, the usefulness of these statistical thresholds in pruning uninteresting patterns is illustrated. (C) 2014 Elsevier Inc. All rights reserved.

Making object-oriented databases more knowledgeable (From ADAM to ABEL)

Tesis leida en la Universidad de Aberdeen. 178 p.

SAQUA - sistema baseado em software livre para análise do comportamento da qualidade das águas fluviais: aplicado à bacia do rio Paraíba do Sul.

Nesta dissertação foi desenvolvido o sistema SAQUA (Sistema para Análise da Qualidade das Águas Fluviais), que permite o acompanhamento dos dados de séries históricas de parâmetros físico-químicos para análise da qualidade de águas fluviais. A alimentação do sistema SAQUA se dá a partir do arquivo tipo texto gerado no Hidroweb, sistema de banco de dados hidrológicos da ANA (Agência Nacional de Águas), disponibilizado na internet. O SAQUA constitui uma interface que permite a análise espaço-temporal de parâmetros de qualidade da água específicos definidos pelo usuário. A interface foi construída utilizando o servidor de mapas Mapserver, as linguagens HTML e PHP, além de consultas SQL e o uso do servidor Web Apache. A utilização de uma linguagem dinâmica como o PHP permitiu usar recursos internos do Mapserver por meio de funções que interagem de forma mais flexível com códigos presentes e futuros, além de interagir com o código HTML. O Sistema apresenta como resultado a representação gráfica da série histórica por parâmetro e, em mapa, a localização das estações em análise também definidas pelo usuário, geralmente associadas a uma determinada região hidrográfica. Tanto na representação gráfica da série temporal quanto em mapa, são destacados a partir de código de cores a estação de monitoramento e a observação em que os limites estabelecidos na resolução CONAMA 357/05 não foi atendido. A classe de uso da resolução CONAMA que será usada na análise também pode ser definida pelo usuário. Como caso de estudo e demonstração das funções do SAQUA foi escolhida a bacia hidrográfica do rio Paraíba do Sul, localizada na região hidrográfica Atlântico Sudeste do Brasil. A aplicação do sistema demonstrou ótimos resultados e o potencial da ferramenta computacional como apoio ao planejamento e à gestão dos recursos hídricos. Ressalta-se ainda, que todo o sistema foi desenvolvido a partir de softwares disponibilizados segundo a licença GPL de software livre, ou seja, sem custo na aquisição de licenças, demonstrando o potencial da aplicação destas ferramentas no campo dos recursos hídricos.

Modelagem automática de sistemas fuzzy utilizando otimização por enxame de partículas.

Esta dissertaçãoo investiga a utilização de Particle Swarm Optimization (PSO) para a obtenção automática de sistemas fuzzy do tipo Mamdani, tendo como insumo apenas as definições das variáveis do problema, seus domínios e a função objetivo. Neste trabalho utilizam-se algumas técnicas conhecidas na tentativa de minimizar a obtenção de sistemas fuzzy que não sejam coerentes. As principais técnicas usadas são o método de Wang e Mendell, chamado de WM, para auxiliar na obtenção de regras, e os conceitos de clusterização para obtenção das funções de pertinência. Na função de avaliação proposta, considera-se não somente a acurácia do sistema fuzzy, através da medida do erro, mas também a sua interpretabilidade, através da medida da compacidade, que consiste da quantidade de regras e funções membro, da distinguibilidade, que permite evitar que as funções membro não se confundam, e da completude, que permite avaliar que as funções membro abranjam o máximo do domínio. O propósito deste trabalho consiste no desenvolvimento de um algoritmo baseado em PSO, cuja função de avaliação congregue todos esses objetivos. Com parâmetros bem definidos, o algoritmo pode ser utilizado em diversos tipos de problemas sem qualquer alteração, tornando totalmente automática a obtenção de sistemas fuzzy. Com este intuito, o algoritmo proposto é testado utilizando alguns problemas pré-selecionados, que foram classificados em dois grupos, com base no tipo de função: contínua ou discreta. Nos testes com funções contínuas, são utilizados sistemas tridimensionais, com duas variáveis de entrada e uma de saída, enquanto nos testes com funções discretas são utilizados problemas de classificação, sendo um com quatro variáveis e outro com seis variáveis de entrada. Os resultados gerados pelo algoritmo proposto são comparados com aqueles obtidos em outros trabalhos.

Invasionsoft: a web-enabled tool for invasive species colonization predictions

Predicting and averting the spread of invasive species is a core focus of resource managers in all ecosystems. Patterns of invasion are difficult to forecast, compounded by a lack of user-friendly species distribution model (SDM) tools to help managers focus control efforts. This paper presents a web-based cellular automata hybrid modeling tool developed to study the invasion pattern of lionfish (Pterois volitans/miles) in the western Atlantic and is a natural extension our previous lionfish study. Our goal is to make publically available this hybrid SDM tool and demonstrate both a test case (P. volitans/miles) and a use case (Caulerpa taxifolia). The software derived from the model, titled Invasionsoft, is unique in its ability to examine multiple default or user-defined parameters, their relation to invasion patterns, and is presented in a rich web browser-based GUI with integrated results viewer. The beta version is not species-specific and includes a default parameter set that is tailored to the marine habitat. Invasionsoft is provided as copyright protected freeware at http://www.invasionsoft.com.

Analysis of multivariable Smith predictors using MATLAB Containers

Containers are structured m-files which allow `data' and `methods' to be stored persistently. Containers have a user-defined class structure, so that one can have several Containers of the same class, all structurally similar, and there is a mechanism for interaction with Containers in the style of database transactions. The use of MATLAB Containers to analyze multivariable Smith predictors is discussed.

The oxidation of CH2O in the intermediate temperature range (943-995 K)

New atmospheric pressure flow reactor data on the oxidation of formaldehyde in the temperature range 943-995 K and over equivalence ratios from 0.013 to 36.7 are reported and discussed. A detailed mechanism assembled from previously published results produced acceptable agreement with the experimental data for the fuel-lean conditions, but failed to predict results for oxidative pyrolysis. Analysis or the very fuel-lean conditions, but failed to modelling results are principally sensitive to CH2O+HO2→HCO+H2O2 (6) and H2O2 +M→OH+OH+M (33). Whereas the specific rate of each reaction cannot be independently determined, it is found that the product k33.k6 is a well defined function of temperature: (3.4±3.0).1028 exp(-(26,800±400)/T). Inadequacies in the mechanism which may be responsible for the disagreement under fuel-rich conditions are discussed. © 1991 Combustion Institute.

Modelling and validation of wet steam flow in a low pressure steam turbine

Results of numerical investigations of the wet steam flow in a three stage low pressure steam turbine test rig are presented. The test rig is a scale model of a modern steam turbine design and provides flow measurements over a range of operating conditions which are used for detailed comparisons with the numerical results. For the numerical analysis a modern CFD code with user defined models for specific wet steam modelling is used. The effect of different theoretical models for nucleation and droplet growth are examined. It is shown that heterogeneous condensation is highly dependent on steam quality and, in this model turbine with high quality steam, a homogeneous theory appears to be the best choice. The homogeneous theory gives good agreement between the test rig traverse measurements and the numerical results. The differences in the droplet size distribution of the three stage turbine are shown for different loads and modelling assumptions. The different droplet growth models can influence the droplet size by a factor of two. An estimate of the influence of unsteady effects is made by means of an unsteady two-dimensional simulation. The unsteady modelling leads to a shift of nucleation into the next blade row. For the investigated three stage turbine the influence due to wake chopping on the condensation process is weak but to confirm this conclusion further investigations are needed in complete three dimensions and on turbines with more stages. Copyright © 2011 by ASME.

基于网络直角坐标机器人视觉伺服系统研究

为了实现定位抓取任务,提出基于网络的直角坐标机器人视觉控制系统。针对机器人运动控制的非线性与强耦合特性,采用神经网络控制器,构建了图像偏差与运动控制量之间的对应关系。通过对图像增强、边缘提取、特征提取等图像处理方法的综合分析,提出了一套优化组合图像处理法。在计算机网络环境下,采用自定义协议实现图像处理器与运动控制器协调控制,并将远程监控应用到机器人控制中。实验结果表明,该系统能够在视野范围内自动实现定位抓取动作。

XP. A Common Lisp Pretty Printing System

XP provides efficient and flexible support for pretty printing in Common Lisp. Its single greatest advantage is that it allows the full benefits of pretty printing to be obtained when printing data structures, as well as when printing program code. XP is efficient, because it is based on a linear time algorithm that uses only a small fixed amount of storage. XP is flexible, because users can control the exact form of the output via a set of special format directives. XP can operate on arbitrary data structures, because facilities are provided for specifying pretty printing methods for any type of object. XP also modifies the way abbreviation based on length, nesting depth, and circularity is supported so that they automatically apply to user-defined functions that perform output ??g., print functions for structures. In addition, a new abbreviation mechanism is introduced that can be used to limit the total numbers of lines printed.