The automation and evaluation of nested clade phylogeographic analysis

Nested clade phylogeographic analysis (NCPA) is a popular method for reconstructing the demographic history of spatially distributed populations from genetic data. Although some parts of the analysis are automated, there is no unique and widely followed algorithm for doing this in its entirety, beginning with the data, and ending with the inferences drawn from the data. This article describes a method that automates NCPA, thereby providing a framework for replicating analyses in an objective way. To do so, a number of decisions need to be made so that the automated implementation is representative of previous analyses. We review how the NCPA procedure has evolved since its inception and conclude that there is scope for some variability in the manual application of NCPA. We apply the automated software to three published datasets previously analyzed manually and replicate many details of the manual analyses, suggesting that the current algorithm is representative of how a typical user will perform NCPA. We simulate a large number of replicate datasets for geographically distributed, but entirely random-mating, populations. These are then analyzed using the automated NCPA algorithm. Results indicate that NCPA tends to give a high frequency of false positives. In our simulations we observe that 14% of the clades give a conclusive inference that a demographic event has occurred, and that 75% of the datasets have at least one clade that gives such an inference. This is mainly due to the generation of multiple statistics per clade, of which only one is required to be significant to apply the inference key. We survey the inferences that have been made in recent publications and show that the most commonly inferred processes (restricted gene flow with isolation by distance and contiguous range expansion) are those that are commonly inferred in our simulations. However, published datasets typically yield a richer set of inferences with NCPA than obtained in our random-mating simulations, and further testing of NCPA with models of structured populations is necessary to examine its accuracy.

The automation of nested clade phylogeographic analysis

ANeCA is a fully automated implementation of Nested Clade Phylogeographic Analysis. This was originally developed by Templeton and colleagues, and has been used to infer, from the pattern of gene sequence polymorphisms in a geographically structured population, the historical demographic processes that have shaped its evolution. Until now it has been necessary to perform large parts of the procedure manually. We provide a program that will take data in Nexus sequential format, and directly output a set of inferences. The software also includes TCS v1.18 and GeoDis v2.2 as part of automation.

Integrative workflow-embedded support for process automation and management

This paper presents the on-going research performed in order to integrate process automation and process management support in the context of media production. This has been addressed on the basis of a holistic approach to software engineering applied to media production modelling to ensure design correctness, completeness and effectiveness. The focus of the research and development has been to enhance the metadata management throughout the process in a similar fashion to that achieved in Decision Support Systems (DSS) to facilitate well-grounded business decisions. The paper sets out the aims and objectives and the methodology deployed. The paper describes the solution in some detail and sets out some preliminary conclusions and the planned future work.

HR-semantics roadmap: the semantic challenges and opportunities in the Human Resources domain

Purpose: This document identifies the challenges and opportunities in applying the ontology technology in the Human Resources domain. Target users: A reference for both the HR and the ontology communities. Also, to be used as a roadmap for the OOA itself, within the HR domain. Background: During the discussion panel at the OOA kick-off workshop, which was attended by more than 50 HR and ontology experts, the need for this roadmap was realized. It was obvious that the current understanding of the problem of semantics in HR is fragmented and only partial solutions exist. People from both the HR and the ontology communities speak different languages, have different understandings, and are not aware of existing solutions.

Bio-inspired ant colony optimization based clustering algorithm with mobile sinks for applications in consumer home automation networks

With the fast development of wireless communications, ZigBee and semiconductor devices, home automation networks have recently become very popular. Since typical consumer products deployed in home automation networks are often powered by tiny and limited batteries, one of the most challenging research issues is concerning energy reduction and the balancing of energy consumption across the network in order to prolong the home network lifetime for consumer devices. The introduction of clustering and sink mobility techniques into home automation networks have been shown to be an efficient way to improve the network performance and have received significant research attention. Taking inspiration from nature, this paper proposes an Ant Colony Optimization (ACO) based clustering algorithm specifically with mobile sink support for home automation networks. In this work, the network is divided into several clusters and cluster heads are selected within each cluster. Then, a mobile sink communicates with each cluster head to collect data directly through short range communications. The ACO algorithm has been utilized in this work in order to find the optimal mobility trajectory for the mobile sink. Extensive simulation results from this research show that the proposed algorithm significantly improves home network performance when using mobile sinks in terms of energy consumption and network lifetime as compared to other routing algorithms currently deployed for home automation networks.

XHA: eXtensible Hyper-Automation

O objetivo geral desta dissertação é estudar as possibilidades de flexibilização da função de saída do Sistema Hyper-Automaton além das rígidas possibilidades utilizadas atualmente com a utilização direta do HTML, objetivando eliminar as limitações como execução de aplicações proprietárias, caracteres incompatíveis entre browsers, excesso de tráfego na rede, padronizar aplicações, incrementar recursos didáticos, melhorar o suporte a aplicações multimídia atuais e futuras, facilitar a manutenção, implementação e reuso, alterar o layout de saída no browser de maneira dinâmica, explorar outros recursos de links, estabelecer padrões de organização do material instrucional criado pelo professor e muitas outras. Tal sistema anteriormente desenvolvido e funcionando adequadamente, é baseado no formalismo de Autômatos Finitos com Saída como modelo estrutural para organização de hiperdocumentos instrucionais, em especial em cursos na Web, tornando o material hipermídia independente do controle da aplicação. O Sistema Hyper-Automaton, tornou-se portanto, um sistema semi-automatizado para suporte a cursos na Web. Com o desdobramento da pesquisa, esta procurou ir mais além e descreveu possibilidades de não só estudar os aspectos possíveis de formatação de saída do sistema, mas reestruturá-lo totalmente sobre uma linguagem de markup padrão, buscando atualizá-lo tecnologicamente definindo outras possibilidades para que significativos trabalhos futuros possam de maneira mais clara serem alcançados. Dessa maneira, esta dissertação centra-se no estudo da aplicação de formas de flexibilização do Sistema Hyper-Automaton, tanto na parte da estruturação de documentos que são conteúdos instrucionais armazenados, bem como, na forma desse material tornar-se-á disponível através de navegadores WWW compatíveis com as tecnologias propostas, possibilitando o incremento substancial de funcionalidades necessárias para cursos onde a Web é o principal meio. Esta pesquisa dá prosseguimento a dois trabalhos anteriormente concluídos no PPGC e do Curso de Bacharelado em Ciência da Computação da UFRGS no ano de 2000, na seqüência, Hyper-Automaton: Hipertextos e Cursos na Web Utilizando Autômatos Finitos com Saída, dissertação de mestrado de Júlio Henrique de A. P. Machado e Hyper-Automaton: Implementação e Uso, trabalho de diplomação de Leonardo Penczek.