The DISOPRED server for the prediction of protein disorder

Dynamically disordered regions appear to be relatively abundant in eukaryotic proteomes. The DISOPRED server allows users to submit a protein sequence, and returns a probability estimate of each residue in the sequence being disordered. The results are sent in both plain text and graphical formats, and the server can also supply predictions of secondary structure to provide further structural information.

The PSIPRED protein structure prediction server

The PSIPRED protein structure prediction server allows users to submit a protein sequence, perform a prediction of their choice and receive the results of the prediction both textually via e-mail and graphically via the web. The user may select one of three prediction methods to apply to their sequence: PSIPRED, a highly accurate secondary structure prediction method; MEMSAT 2, a new version of a widely used transmembrane topology prediction method; or GenTHREADER, a sequence profile based fold recognition method.

The ModFOLD4 server for the quality assessment of 3D protein models

Once you have generated a 3D model of a protein, how do you know whether it bears any resemblance to the actual structure? To determine the usefulness of 3D models of proteins, they must be assessed in terms of their quality by methods that predict their similarity to the native structure. The ModFOLD4 server is the latest version of our leading independent server for the estimation of both the global and local (per-residue) quality of 3D protein models. The server produces both machine readable and graphical output, providing users with intuitive visual reports on the quality of predicted protein tertiary structures. The ModFOLD4 server is freely available to all at: http://www.reading.ac.uk/bioinf/ModFOLD/.

The FunFOLD2 server for the prediction of protein-ligand interactions

The FunFOLD2 server is a new independent server that integrates our novel protein–ligand binding site and quality assessment protocols for the prediction of protein function (FN) from sequence via structure. Our guiding principles were, first, to provide a simple unified resource to make our function prediction software easily accessible to all via a simple web interface and, second, to produce integrated output for predictions that can be easily interpreted. The server provides a clean web interface so that results can be viewed on a single page and interpreted by non-experts at a glance. The output for the prediction is an image of the top predicted tertiary structure annotated to indicate putative ligand-binding site residues. The results page also includes a list of the most likely binding site residues and the types of predicted ligands and their frequencies in similar structures. The protein–ligand interactions can also be interactively visualized in 3D using the Jmol plug-in. The raw machine readable data are provided for developers, which comply with the Critical Assessment of Techniques for Protein Structure Prediction data standards for FN predictions. The FunFOLD2 webserver is freely available to all at the following web site: http://www.reading.ac.uk/bioinf/FunFOLD/FunFOLD_form_2_0.html.

Assessing the quality of modelled 3D protein structures using the ModFOLD server

Model quality assessment programs (MQAPs) aim to assess the quality of modelled 3D protein structures. The provision of quality scores, describing both global and local (per-residue) accuracy are extremely important, as without quality scores we are unable to determine the usefulness of a 3D model for further computational and experimental wet lab studies.Here, we briefly discuss protein tertiary structure prediction, along with the biennial Critical Assessment of Techniques for Protein Structure Prediction (CASP) competition and their key role in driving the field of protein model quality assessment methods (MQAPs). We also briefly discuss the top MQAPs from the previous CASP competitions. Additionally, we describe our downloadable and webserver-based model quality assessment methods: ModFOLD3, ModFOLDclust, ModFOLDclustQ, ModFOLDclust2, and IntFOLD-QA. We provide a practical step-by-step guide on using our downloadable and webserver-based tools and include examples of their application for improving tertiary structure prediction, ligand binding site residue prediction, and oligomer predictions.

IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences

IntFOLD is an independent web server that integrates our leading methods for structure and function prediction. The server provides a simple unified interface that aims to make complex protein modelling data more accessible to life scientists. The server web interface is designed to be intuitive and integrates a complex set of quantitative data, so that 3D modelling results can be viewed on a single page and interpreted by non-expert modellers at a glance. The only required input to the server is an amino acid sequence for the target protein. Here we describe major performance and user interface updates to the server, which comprises an integrated pipeline of methods for: tertiary structure prediction, global and local 3D model quality assessment, disorder prediction, structural domain prediction, function prediction and modelling of protein-ligand interactions. The server has been independently validated during numerous CASP (Critical Assessment of Techniques for Protein Structure Prediction) experiments, as well as being continuously evaluated by the CAMEO (Continuous Automated Model Evaluation) project. The IntFOLD server is available at: http://www.reading.ac.uk/bioinf/IntFOLD/

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.

Upgrading a TCABR data analysis and acquisition system for remote participation using Java, XML, RCP and modern client/server communication/authentication

The TCABR data analysis and acquisition system has been upgraded to support a joint research programme using remote participation technologies. The architecture of the new system uses Java language as programming environment. Since application parameters and hardware in a joint experiment are complex with a large variability of components, requirements and specification solutions need to be flexible and modular, independent from operating system and computer architecture. To describe and organize the information on all the components and the connections among them, systems are developed using the extensible Markup Language (XML) technology. The communication between clients and servers uses remote procedure call (RPC) based on the XML (RPC-XML technology). The integration among Java language, XML and RPC-XML technologies allows to develop easily a standard data and communication access layer between users and laboratories using common software libraries and Web application. The libraries allow data retrieval using the same methods for all user laboratories in the joint collaboration, and the Web application allows a simple graphical user interface (GUI) access. The TCABR tokamak team in collaboration with the IPFN (Instituto de Plasmas e Fusao Nuclear, Instituto Superior Tecnico, Universidade Tecnica de Lisboa) is implementing this remote participation technologies. The first version was tested at the Joint Experiment on TCABR (TCABRJE), a Host Laboratory Experiment, organized in cooperation with the IAEA (International Atomic Energy Agency) in the framework of the IAEA Coordinated Research Project (CRP) on ""Joint Research Using Small Tokamaks"". (C) 2010 Elsevier B.V. All rights reserved.

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.

Uma ferramenta de manipulação de pacotes para análise de protocolos de redes industriais baseados em TCP/IP

This work presents a packet manipulation tool developed to realize tests in industrial devices that implements TCP/IP-based communication protocols. The tool was developed in Python programming language, as a Scapy extension. This tool, named IndPM- Industrial Packet Manipulator, can realize vulnerability tests in devices of industrial networks, industrial protocol compliance tests, receive server replies and utilize the Python interpreter to build tests. The Modbus/TCP protocol was implemented as proof-of-concept. The DNP3 over TCP protocol was also implemented but tests could not be realized because of the lack of resources. The IndPM results with Modbus/TCP protocol show some implementation faults in a Programmable Logic Controller communication module frequently utilized in automation companies

e-Pontos: Uma solução embarcada de automação comercial aplicada a clubes de fidelidade baseado em tecnologia RFID e esmart card

In practically all vertical markets and in every region of the planet, loyalty marketers have adopted the tactic of recognition and reward to identify, maintain and increase the yield of their customers. Several strategies have been adopted by companies, and the most popular among them is the loyalty program, which displays a loyalty club to manage these rewards. But the problem with loyalty programs is that customer identification and transfer of loyalty points are made in a semiautomatic. Aiming at this, this paper presents a master's embedded business automation solution called e-Points. The goal of e-Points is munir clubs allegiances with fully automated tooling technology to identify customers directly at the point of sales, ensuring greater control over the loyalty of associate members. For this, we developed a hardware platform with embedded system and RFID technology to be used in PCs tenant, a smart card to accumulate points with every purchase and a web server, which will provide services of interest to retailers and customers membership to the club