Phylogeography unplugged: comparative surveys in the genomic era

In March 2012, the authors met at the National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina, USA, to discuss approaches and cooperative ventures in Indo-Pacific phylogeography. The group emerged with a series of findings: (1) Marine population structure is complex, but single locus mtDNA studies continue to provide powerful first assessment of phylogeographic patterns. (2) These patterns gain greater significance/power when resolved in a diversity of taxa. New analytical tools are emerging to address these analyses with multi-taxon approaches. (3) Genome-wide analyses are warranted if selection is indicated by surveys of standard markers. Such indicators can include discordance between genetic loci, or between genetic loci and morphology. Phylogeographic information provides a valuable context for studies of selection and adaptation. (4) Phylogeographic inferences are greatly enhanced by an understanding of the biology and ecology of study organisms. (5) Thorough, range-wide sampling of taxa is the foundation for robust phylogeographic inference. (6) Congruent geographic and taxonomic sampling by the Indo-Pacific community of scientists would facilitate better comparative analyses. The group concluded that at this stage of technology and software development, judicious rather than wholesale application of genomics appears to be the most robust course for marine phylogeographic studies. Therefore, our group intends to affirm the value of traditional (''unplugged'') approaches, such as those based on mtDNA sequencing and microsatellites, along with essential field studies, in an era with increasing emphasis on genomic approaches.

New tools for self-organised pattern formation

Position-dependent gene expression is a critical aspect of the development and behaviour of multicellular organisms. It requires a complex series of interactions to occur between different cell types in addition to intracellular signalling cascades. We used Escherichia coli to study the properties of an artificial signalling system at the interface between two expanding cell populations. We genetically engineered one population to produce a diffusible acyl-homoserine lactone (AHL) signal, and another population to respond to it. Our experiments demonstrate how such a signal can be used to reproducibly generate simple visible patterns with high accuracy in swimming agar. The producing and responding cassettes of two such signalling systems can be linked to produce a symmetric interface for bidirectional communication that can be used to visualise molecular logic. Intracellular feedback between these two cassettes would then create a framework for self-organised patterning of higher complexity. Adapting the experiments of Basu et al. (Basu et al., 2005) using cell motility, rather than a differential response to AHL concentrations as a way to define zones of response, we noted how the interaction of sender and receiver cell populations on a swimming plate could lead to complex pattern formation. Equipping highly motile strains such as E. coli MC1000 with AHL-mediated auto-inducing systems based on Vibrio fischeri luxI/luxR and Pseudomonas aeruginosa lasI/lasR cassettes would allow the amplification of a response to an AHL signal and its propagation. We designed and synthesised codon-optimised auto-inducing luxI/R and lasI/R cassettes as optimal gene expression is crucial for the generation of robust patterns. We still have to complete and test the entire genetic circuitry, although by modelling the system we were able to demonstrate its feasibility. © 2007 The Institution of Engineering and Technology.

Open Personalization: Involving Third Parties in Improving the User Experience of Websites

Traditional software development captures the user needs during the requirement analysis. The Web makes this endeavour even harder due to the difficulty to determine who these users are. In an attempt to tackle the heterogeneity of the user base, Web Personalization techniques are proposed to guide the users’ experience. In addition, Open Innovation allows organisations to look beyond their internal resources to develop new products or improve existing processes. This thesis sits in between by introducing Open Personalization as a means to incorporate actors other than webmasters in the personalization of web applications. The aim is to provide the technological basis that builds up a trusty environment for webmasters and companion actors to collaborate, i.e. "an architecture of participation". Such architecture very much depends on these actors’ profile. This work tackles three profiles (i.e. software partners, hobby programmers and end users), and proposes three "architectures of participation" tuned for each profile. Each architecture rests on different technologies: a .NET annotation library based on Inversion of Control for software partners, a Modding Interface in JavaScript for hobby programmers, and finally, a domain specific language for end-users. Proof-of-concept implementations are available for the three cases while a quantitative evaluation is conducted for the domain specific language.

In situ measurement of dissolved inorganic carbon speciation in natural waters, pH, pC02, TA, & TC02, Honolulu, Hawaii, February 16-18, 2005: workshop proceedings

The Alliance for Coastal Technology (ACT) convened a workshop on the in situ measurement of dissolved inorganic carbon species in natural waters in Honolulu, Hawaii, on February 16, 17, and 18, 2005. The workshop was designed to summarize existing technologies for measuring the abundance and speciation of dissolved inorganic carbon and to make strategic recommendations for future development and application of these technologies to coastal research and management. The workshop was not focused on any specific technology, however, most of the attention of the workshop was on in situ pC02 sensors given their recent development and use on moorings for the measurement of global carbon fluxes. In addition, the problems and limitations arising from the long-term deployment of systems designed for the measurement of pH, total dissolved inorganic carbon (DIC), and total alkalinity (TA) were discussed. Participants included researchers involved in carbon biogeochemistry, industry representatives, and coastal resource managers. The primary questions asked during the workshop were: I. What are the major impediments to transform presently used shipboard pC02 measurement systems for use on cost-eficient moorings? 2. What are the major technical hurdles for the in situ measurement of TA and DIC? 3. What specific information do we need to coordinate efforts for proof of concept' testing of existing and new technologies, inter-calibration of those technologies, better software development, and more precise knowledge quantzjjing the geochemistry of dissolved inoeanic carbon species in order to develop an observing system for dissolved inorganic carbon? Based on the discussion resulting from these three questions, the following statements were made: Statement No. 1 Cost-effective, self-contained technologies for making long-term, accurate measurements of the partial pressure of C02 gas in water already exist and at present are ready for deployment on moorings in coastal observing systems. Statement No. 2 Cost-effective, self-contained systems for the measurement of pH, TA, and DIC are still needed to both fully define the carbonate chemistry of coastal waters and the fluxes of carbon between major biogeochemical compartments (e.g., air-sea, shelf-slope, water column-sediment, etc.). (pdf contains 23 pages)

Embryogenesis of Heterobranchus longifilis (Curvier and Valenciennes, 1840)

Studies on development of H. longifilis (Curvier and Valenciennes, 1840) were conducted at a temperature of 25EC ( 1Ec) in aquaria tanks continuous development were monitored with the use of wild Heerbrugy photomacroscope and length of yolk and larva were monitored using Stereo Olympus microscope with ocular micrometer. The division into animal and vegetal poles was observed 22 minutes after activation. The first cleavage occurred 65 minutes after activation while the second division which was perpendicular to the first line of division occurred 74 minutes after activation. This was quickly followed by the third and fourth cleavage at 80th and 82nd minutes after activation respectively. Morular stage was reached at 4 hours 20 minutes with formation of optic bud at 14 hours 35 minutes. (DBO) Developing embryo hatched after 27 hours of activation at a mean length of 6.63 and mean yolk length of 2.17. Yolk size decrease at an average rate of 38.5 % till the 5th day of total absorption. Growth of larvae proceeded faster in tail-anus region than in anus-snout portion of the body. The rate of yolk absorption and larva development (survival) as monitored in this work gives important information in Research and development programme for H. longifilis larva - an important aspect of Research development and implementation of appropriate technologies in small scale fisheries

Lógica nebulosa aplicada a um sistema de detecção de intrusos em computação em nuvem.

O objetivo deste trabalho é avaliar os riscos de ocorrências de intrusos em um sistema de computação em nuvem para sistemas distribuídos utilizando lógica nebulosa. A computação em nuvem é um tema que vem sendo bastante abordado e vem alavancando discussões calorosas, tanto na comunidade acadêmica quanto em palestras profissionais. Embora essa tecnologia esteja ganhando mercado, alguns estudiosos encontram-se céticos afirmando que ainda é cedo para se tirar conclusões. Isto se deve principalmente por causa de um fator crítico, que é a segurança dos dados armazenados na nuvem. Para esta dissertação, foi elaborado um sistema distribuído escrito em Java com a finalidade de controlar um processo de desenvolvimento colaborativo de software na nuvem, o qual serviu de estudo de caso para avaliar a abordagem de detecção de intrusos proposta. Este ambiente foi construído com cinco máquinas (sendo quatro máquinas virtuais e uma máquina real). Foram criados dois sistemas de inferência nebulosos, para análise de problemas na rede de segurança implementados em Java, no ambiente distribuído. Foram realizados diversos testes com o intuito de verificar o funcionamento da aplicação, apresentando um resultado satisfatório dentro dessa metodologia.

Desenvolvimento e implementação de algoritmo para análise de dutos fabricados ou reparados com material compósito carregados com pressão interna utilizando o método dos elementos finitos.

A integridade de dutos ganha importância à medida em que o desenvolvimento da indústria expande a malha para transportar líquidos e gases num contexto de aumento das exigências ambientais. Um importante aliado para manutenção da integridade de dutos são reparos de materiais compósitos. Estes materiais apresentam baixa densidade, capacidade de direcionar resistência de acordo com as direções das solicitações, execução de reparo a frio sem necessidade de interromper produção ou grande maquinário. Este trabalho tem como objetivo desenvolver e implementar um algoritmo de elementos finitos que permita avaliar os esforços e a resistência das paredes de um tubos fabricados ou reparados com laminados de material compósito carregados com pressão interna. Entre as vantagens de desenvolver um programa tem-se: agilidade de avaliação, menor custo com licença, menores exigências computacionais, possibilidade de desenvolver o programa e o melhor entendimento da modelagem dos fenômenos. Utiliza-se como entrada do programa o diâmetro do duto, pressão interna e parâmetros do laminado. A modelagem em elementos finitos é realizada a partir da teoria clássica de laminados. Aplicando o carregamento resultante da pressão interna, determina-se os deslocamentos e são calculadas as tensões e aplicado o critério de falha de Tsai-Hill em cada camada. Estudos experimentais e numéricos encontrados na literatura foram simulados com o programa gerado e os resultados para propriedades do laminado, tensões nos dutos e pressão de ruptura apresentam concordância com os resultados da literatura.O programa ainda tem sua estrutura modificada para encontrar a pressão de falha a partir dos dados do laminado. O programa implementado permite uma avaliação rápida de resistência do reparo e possibilita avaliar rapidamente a resposta a mudanças nos parâmetros de projeto do laminado.

BarraCUDA - a fast short read sequence aligner using graphics processing units.

BACKGROUND: With the maturation of next-generation DNA sequencing (NGS) technologies, the throughput of DNA sequencing reads has soared to over 600 gigabases from a single instrument run. General purpose computing on graphics processing units (GPGPU), extracts the computing power from hundreds of parallel stream processors within graphics processing cores and provides a cost-effective and energy efficient alternative to traditional high-performance computing (HPC) clusters. In this article, we describe the implementation of BarraCUDA, a GPGPU sequence alignment software that is based on BWA, to accelerate the alignment of sequencing reads generated by these instruments to a reference DNA sequence. FINDINGS: Using the NVIDIA Compute Unified Device Architecture (CUDA) software development environment, we ported the most computational-intensive alignment component of BWA to GPU to take advantage of the massive parallelism. As a result, BarraCUDA offers a magnitude of performance boost in alignment throughput when compared to a CPU core while delivering the same level of alignment fidelity. The software is also capable of supporting multiple CUDA devices in parallel to further accelerate the alignment throughput. CONCLUSIONS: BarraCUDA is designed to take advantage of the parallelism of GPU to accelerate the alignment of millions of sequencing reads generated by NGS instruments. By doing this, we could, at least in part streamline the current bioinformatics pipeline such that the wider scientific community could benefit from the sequencing technology.BarraCUDA is currently available from http://seqbarracuda.sf.net.

基于MDA的TRISO-Model模型管理方法及应用

TRISO-Model(tridimensional integrated software development model)是为处理软件开发的复杂性和动态性而提出的三维集成软件开发方法学,其中,多维模型之间的语义一致性维护以及对模型应用中公共操作部分的重用,提出了基于一致语义进行模型管理的需求.给出了基于MDA(model driven architecture)进行模型管理的方法MDA-MMMethod(MDA based model management method),应用MDA的4层模型管理结构,基于MDA核心标准MOF(meta object facility)所提供的公共语义基础管理模型和元模型,MDA-MMMethod支持各种MDA模型操作标准实现在TRSIO-model应用中的重用.开发了相应的支持系统MDA-MMSystem(MDA based model management system),应用于SoftPM的项目实践中.与传统方法相比,模型应用的开发效率得到了显著提高,同时降低了开发成本.最后,给出了模型融合的应用实例介绍.

一种用户主导的面向领域应用软件开发新方法

提出一种应用软件开发的新方法 ,称为“用户工程”.这是一种基于构件化软件系统结构的用户主导的面向领域的应用软件开发方法 ,强调用户在应用软件开发中的主导作用 ,试图将应用软件的开发过程变成用户详细定义过程 ,而不仅仅是传统的编程过程 .它为越来越多的应用软件开发需求提供了可能有效的一个途径

面向大规模定制的软件开发模式

在领域工程、基于构件的软件工程和并行工程的基础上，提出了面向大规模定制的软件开发模式。该模式以大规模开发标准软件的效益满足用户的个性化需求。介绍了面向大规模定制的软件开发过程，面向大规模定制的软件产品族体系结构，以及面向大模型定制软件开发的产品集成过程模型。最后介绍了一种面向大规模定制的敏捷软件开发组织。

面向信息系统工程监理的软件工具IT-PM

在信息系统工程开发中引入监理机制已经成为业界的共识。监理组织以独立“第三方”身份加入项目,通过“控制、管理、协调”的手段,达到提高项目质量的目的。分析了信息系统工程监理自动化支持的研究现状,提出了面向信息系统工程监理的软件工具IT-PM。工具以信息系统工程监理的过程模型为基础,支持监理工作的流程和信息管理自动化。

模糊逻辑的采用软件开发工作量估算

软件估算是有半个世纪发展历史的计算机科学领域的一个巨大挑战，因为软件估算涉及到软件项目的成本和计划。开发人员需要能够获得基于他们自己的程序得到的包含了工作量估算的实践。软件成本估算主要估算开发软件系统所需的工作量、时间、人力资源等。一种有效的方式是在项目早期确定成本时估算工作量。软件成本主要依据项目的需求规格说明书来确定。目前，实施可靠、准确的成本估算仍是软件工程领域的一个挑战。 在项目早期阶段，许多项目属性尚未确定。此时的软件估算通常是不准确的，估算 的准确程度取决于用于估算的可靠且可用的信息的数量。在后续的项目分析和设计阶段，对项目的了解更加深入，估算不确定性减少，估算准确性提高。大部分估算模型未考虑这种不确定性，只是得到了确定的估算结果。这些模型需要改进，以得到估计范围和估算结果的发生概率。 新的方法（如：模糊逻辑）可能提供了软件工作量估算的替代方案。软件开发总是可以用一组具有一定程度模糊性的参数来表征。这就需要在模型中引入一定程度的不确定性，以使模型更接近实际。模糊逻辑在这方面很合适。应用模糊逻辑可以解决目前工作量估算模型存在的许多问题。而且，模糊逻辑已经与算法的和非算法的工作量估算模型结合，用于解决固有不确定性问题。 本文提出一种基于模糊逻辑规模的软件开发工作量估算方法。软件规模不是一个单个数字，可以看作是一个三角模糊数(triangular fuzzy number, TFN)。应用本文方法，可以通过改变约束条件对任意常数中的工作量估算结果进行优化。基于对本文方法中模糊权重的平均方差解释%(Variance Accounted For, VAF%) ， 提出了一种最优化算法。应用COCOMO 公开数据集进行了验证实验。与实际工作量估算的比较结果表明，基于偏差系数，本文提出的模型提供了较好的估算结果。 最后，提出了一种改进的基于模糊案例的推理(Fuzzy Case-Based Reasoning , FCBR)方法，该方法集成了agent 技术，可以从多个组织的分布式数据库中找到相似项目。基于该方法，可以从分布式预定义的项目成本数据库中收集软件成本数据，进而建立软件成本估算模型。该模型应用FCBR 方法，在不同软件组织的历史软件项目度量数据中找到类似项目。

predicting upgrade project defects based on enhancement requirements: an empirical study

Chinese Acad Sci, ISCAS Lab Internet Software Technologies

面向少儿多通道交互技术软件系统的研究

将研究一个面向少儿益智系统,该系统将多种益智娱乐开发包构建在城堡中,少儿通过多通道交互方式可以在城堡中随意漫游、体验、学习和娱乐。另外,通过该系统开发包,幼儿园和小学的教师及儿童自己都可以开发少儿益智游戏和学习素材供少儿使用。