SwissDock, a protein-small molecule docking web service based on EADock DSS.

Most life science processes involve, at the atomic scale, recognition between two molecules. The prediction of such interactions at the molecular level, by so-called docking software, is a non-trivial task. Docking programs have a wide range of applications ranging from protein engineering to drug design. This article presents SwissDock, a web server dedicated to the docking of small molecules on target proteins. It is based on the EADock DSS engine, combined with setup scripts for curating common problems and for preparing both the target protein and the ligand input files. An efficient Ajax/HTML interface was designed and implemented so that scientists can easily submit dockings and retrieve the predicted complexes. For automated docking tasks, a programmatic SOAP interface has been set up and template programs can be downloaded in Perl, Python and PHP. The web site also provides an access to a database of manually curated complexes, based on the Ligand Protein Database. A wiki and a forum are available to the community to promote interactions between users. The SwissDock web site is available online at http://www.swissdock.ch. We believe it constitutes a step toward generalizing the use of docking tools beyond the traditional molecular modeling community.

Creació del nucli d'un servidor web

Disseny i implementació d'un nou servidor web multifil i multiplataforma en C++.

Creación del núcleo de un servidor web

L'objectiu particular és elaborar el nucli principal d'un servidor web, que tingui com a característiques: multithread, multiprocés, desenvolupament en Java, funcionament en entorns Windows, GNU Linux i heterogenis.

Sulautetun järjestelmän Web-käyttö

Diplomityössä on tutkittu sulautetun järjestelmän liittämistä Ethernet-verkkoon sekä TCP/IP-protokollapinoon kuuluvien tavallisimpien protokollien toimintaa. Työn tuloksien perusteella on suunniteltu harjoitustyö, jota voidaan käyttää sähkötekniikan osaston opetuksessa. Työssä hankittiin Atmelin sulautettu Web-serverikortti (EWS) ja STK500-kortti serverin ohjelmointiin. Serverin mukana tuli Internet-yhteyden mahdollistava TCP/IP-pinon lähdekoodi. Työssä selvitettiin TCP/IP:hen kuuluvien protokollien toimintaa teoriassa ja käytännön toteutusta EWS:n avulla. Lähdekoodiin lisättiin ominaisuudet, joiden avulla laite hakee kellonaikatiedot aikapalvelimelta time-protokollaa käyttäen ja lähettää sähköpostia määriteltyyn osoitteeseen sähköpostipalvelimen kautta. Laitetta käytettiin sekä palvelimena että asiakkaana. Työssä perehdyttiin sulautettujen järjestelmien yleisiin ominaisuuksiin ja erilaisiin verkonhallinnan apuohjelmiin. Työssä tutkittiin palvelin- ja asiakaskoneen välillä Ethernetissä kulkevaa verkkoliikennettä. Työssä minimoitiin protokollatiedostojen viemä tila prosessorin muistista ja tutkittiin Internet-yhteyden kuluttamien kellojaksojen määrää. Työssä selvitettiin tietoturva-kysymysten merkitystä ja toteutusta sulautetuissa järjestelmissä.

BioSuper: A web tool for the superimposition of biomolecules and assemblies with rotational symmetry

Background Most of the proteins in the Protein Data Bank (PDB) are oligomeric complexes consisting of two or more subunits that associate by rotational or helical symmetries. Despite the myriad of superimposition tools in the literature, we could not find any able to account for rotational symmetry and display the graphical results in the web browser. Results BioSuper is a free web server that superimposes and calculates the root mean square deviation (RMSD) of protein complexes displaying rotational symmetry. To the best of our knowledge, BioSuper is the first tool of its kind that provides immediate interactive visualization of the graphical results in the browser, biomolecule generator capabilities, different levels of atom selection, sequence-dependent and structure-based superimposition types, and is the only web tool that takes into account the equivalence of atoms in side chains displaying symmetry ambiguity. BioSuper uses ICM program functionality as a core for the superimpositions and displays the results as text, HTML tables and 3D interactive molecular objects that can be visualized in the browser or in Android and iOS platforms with a free plugin. Conclusions BioSuper is a fast and functional tool that allows for pairwise superimposition of proteins and assemblies displaying rotational symmetry. The web server was created after our own frustration when attempting to superimpose flexible oligomers. We strongly believe that its user-friendly and functional design will be of great interest for structural and computational biologists who need to superimpose oligomeric proteins (or any protein). BioSuper web server is freely available to all users at http://ablab.ucsd.edu/BioSuper webcite.

Kuorman tasaus web-palvelimissa

Web-palvelussa sivuston suorituskyky muodostaa suuren osan käyttökokemuksen mielekkyydestä. Sivuston ollessa kuormitetumpi kuin normaalisti, saattaa se toimia tavallista hitaammin. Tasaamalla yhden web-palvelimen kuormaa muille palvelimille, joko laitteisto tai ohjelmistopohjaisella kuormantasauksella, voidaan saavuttaa merkittäviä suorituskykyparannuksia koko palvelulle. Teoriaosassa selvitettiin kuormantasaukseen soveltuvien algoritmien toimintaa sekä tietokantapohjaista replikaatiota, joka välittää saamansa tiedon lähes välittömästi toiselle palvelimelle. Apachen kuormantasausmoduuliin sekä sen sisältämiin algoritmeihin luotiin myös katsaus teoriaosassa. Varsinaisessa työssä luotiin Apachen kuormantasauspalvelimen ja kahden suorituspalvelimen avulla toimiva palvelinjärjestelmä. Kuormantasaimeen asennettiin käyttöön tahmeat sessiot, joiden toimintaa selvitettiin Drupal-ohjelman avulla. Apachessa on ollut ongelmia tahmeiden sessioiden kanssa, mutta työssä huomattiin kaiken toimivan mainiosti. Kuormantasaus ja tietokantojen replikaatio toimi, kuten odotettiin.

PDBSprotEC: A web-accessible database linking PDB chains to EC numbers via SwissProt

A mapping between chains in the Protein Databank and Enzyme Classification numbers is invaluable for research into structure-function relationships. Mapping at the chain level is a non-trivial problem and we present an automatically updated Web-server, which provides this link in a queryable form and as a downloadable XML or flat file.

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/

MATIW 1451 - monitoramento e acionamento de transdutores inteligentes através da Web (Padrão IEEE 1451)

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

DiffServer: Application Level Differentiated Services for Web Servers

Web content hosting, in which a Web server stores and provides Web access to documents for different customers, is becoming increasingly common. For example, a web server can host webpages for several different companies and individuals. Traditionally, Web Service Providers (WSPs) provide all customers with the same level of performance (best-effort service). Most service differentiation has been in the pricing structure (individual vs. business rates) or the connectivity type (dial-up access vs. leased line, etc.). This report presents DiffServer, a program that implements two simple, server-side, application-level mechanisms (server-centric and client-centric) to provide different levels of web service. The results of the experiments show that there is not much overhead due to the addition of this additional layer of abstraction between the client and the Apache web server under light load conditions. Also, the average waiting time for high priority requests decreases significantly after they are assigned priorities as compared to a FIFO approach.

Gestor web de recursos geoespaciales con tecnología Openlayers

[ES] El objetivo de este Trabajo Final de Grado (TFG) es la creación de un prototipo de aplicación web para la gestión de recursos geoespaciales. Esta propuesta surgió a partir de la necesidad de disponer de una herramienta que no tuviera que ser instalada en un dispositivo, sino servida por un servidor web, permitiendo su acceso desde cualquier parte y dispositivo. El resultado fue el Gestor Web de Recursos Geoespaciales con Tecnología OpenLayers, una aplicación que combina diversas herramientas (OpenLayers, GeoServer, PostgreSQL, jQuery…) – todas ellas basadas en Software Libre – para cumplir funcionalidades como la creación de primitivas vectoriales sobre un mapa, gestión y visualización de la información asociada, edición de estilos, modificación de coordenadas, etc. siendo todas éstas funcionalidades características de un Sistema de Información Geográfica (SIG) y ofreciendo una interfaz de uso cómoda y eficaz, que abstraiga al usuario de detalles internos y complejos. El material desarrollado dispone del potencial necesario para convertirse en una solución a las necesidades de gestión de información geoespacial de la ULPGC, especialmente en el campus de Tafira, sobre el que se ha ejemplificado su uso. Además, a diferencia de las herramientas ofertadas por empresas como Google o Microsoft, esta aplicación está por completo bajo una licencia GNU GPL v3, lo que permite que se pueda indagar dentro de su código, mejorarlo y añadir funcionalidades a cualquier persona interesada.

Managing server energy and reducing operational cost for online service providers

The past decade has seen the energy consumption in servers and Internet Data Centers (IDCs) skyrocket. A recent survey estimated that the worldwide spending on servers and cooling have risen to above $30 billion and is likely to exceed spending on the new server hardware . The rapid rise in energy consumption has posted a serious threat to both energy resources and the environment, which makes green computing not only worthwhile but also necessary. This dissertation intends to tackle the challenges of both reducing the energy consumption of server systems and by reducing the cost for Online Service Providers (OSPs). Two distinct subsystems account for most of IDC’s power: the server system, which accounts for 56% of the total power consumption of an IDC, and the cooling and humidifcation systems, which accounts for about 30% of the total power consumption. The server system dominates the energy consumption of an IDC, and its power draw can vary drastically with data center utilization. In this dissertation, we propose three models to achieve energy effciency in web server clusters: an energy proportional model, an optimal server allocation and frequency adjustment strategy, and a constrained Markov model. The proposed models have combined Dynamic Voltage/Frequency Scaling (DV/FS) and Vary-On, Vary-off (VOVF) mechanisms that work together for more energy savings. Meanwhile, corresponding strategies are proposed to deal with the transition overheads. We further extend server energy management to the IDC’s costs management, helping the OSPs to conserve, manage their own electricity cost, and lower the carbon emissions. We have developed an optimal energy-aware load dispatching strategy that periodically maps more requests to the locations with lower electricity prices. A carbon emission limit is placed, and the volatility of the carbon offset market is also considered. Two energy effcient strategies are applied to the server system and the cooling system respectively. With the rapid development of cloud services, we also carry out research to reduce the server energy in cloud computing environments. In this work, we propose a new live virtual machine (VM) placement scheme that can effectively map VMs to Physical Machines (PMs) with substantial energy savings in a heterogeneous server cluster. A VM/PM mapping probability matrix is constructed, in which each VM request is assigned with a probability running on PMs. The VM/PM mapping probability matrix takes into account resource limitations, VM operation overheads, server reliability as well as energy effciency. The evolution of Internet Data Centers and the increasing demands of web services raise great challenges to improve the energy effciency of IDCs. We also express several potential areas for future research in each chapter.

Servicio Web para gestión de juego cooperativo sobre desarrollo humano

Este Proyecto Fin de Carrera (PFC) tiene como objetivos el análisis, diseño e implementación de un sistema web que permita a los usuarios familiarizarse con el Índice de Desarrollo Humano (IDH), publicado anualmente por Naciones Unidas, ofreciendo un servicio de gestión y descarga de una aplicación móvil relacionada con dicho índice. La aplicación móvil es un juego educativo basado en preguntas sobre el IDH de los países, desarrollada en paralelo con este proyecto. El servicio web implementado en este proyecto facilita tanto la descarga, administración y actualización de contenidos como la interacción entre los usuarios. El sistema está formado por un servidor web, una base de datos de usuarios y contenidos y un portal web desde el cual puede descargarse la aplicación móvil, realizar consultas sobre estadísticas de juego y conocer el IDH sin necesidad de jugar. El buscador avanzado que ha sido desarrollado para conocer el IDH permite al usuario adquirir destrezas y entrenarse por sí solo para mejorar sus resultados de juego. Los administradores del sistema tienen la capacidad de gestionar el contenido del portal, los usuarios que solicitan darse de alta y la funcionalidad ofrecida, es decir, actualización del juego, foros y noticias. La instalación del sistema implementado en un servidor web ha permitido su verificación exitosa así como la provisión del servicio de información y sensibilización sobre el IDH, actualizado mediante la información de Naciones Unidas, motivación original del proyecto. ABSTRACT This Final Year Project takes as targets the analysis, design and implementation of a web system that allows to the users to familiarize with the Human Development Index (HDI), published annually by United Nations, offering a service of management and download a mobile application associated with that index. The mobile application is an educational game based on questions on the IDH of the countries, developed in parallel with this project. The web service implemented by means of this Project facilitates download, administration and update of contents and the interaction between the users across the cooperative game. The system consists of a web server, a database of users and content and a web portal from which you can download the mobile application, perform queries on game statistics, or discover the HDI without need for play. The advanced search engine that has been developed for the HDI allows the user to purchase and train for skills to improve their game results. System administrators have the ability to manage the content of the portal, users requesting register and the functionality offered, i.e., update to the game, forums and news. The installation of the system that was implemented has allowed successful verification and the provision of an information and awareness on the HDI, updated with the information from the United Nations, original motivation of the project.

Towards a web-based progressive handwriting recognition environment for mathematical problem solving

The emergence of pen-based mobile devices such as PDAs and tablet PCs provides a new way to input mathematical expressions to computer by using handwriting which is much more natural and efficient for entering mathematics. This paper proposes a web-based handwriting mathematics system, called WebMath, for supporting mathematical problem solving. The proposed WebMath system is based on client-server architecture. It comprises four major components: a standard web server, handwriting mathematical expression editor, computation engine and web browser with Ajax-based communicator. The handwriting mathematical expression editor adopts a progressive recognition approach for dynamic recognition of handwritten mathematical expressions. The computation engine supports mathematical functions such as algebraic simplification and factorization, and integration and differentiation. The web browser provides a user-friendly interface for accessing the system using advanced Ajax-based communication. In this paper, we describe the different components of the WebMath system and its performance analysis.

SVRMHC prediction server for MHC-binding peptides

The binding between antigenic peptides (epitopes) and the MHC molecule is a key step in the cellular immune response. Accurate in silico prediction of epitope-MHC binding affinity can greatly expedite epitope screening by reducing costs and experimental effort. Recently, we demonstrated the appealing performance of SVRMHC, an SVR-based quantitative modeling method for peptide-MHC interactions, when applied to three mouse class I MHC molecules. Subsequently, we have greatly extended the construction of SVRMHC models and have established such models for more than 40 class I and class II MHC molecules. Here we present the SVRMHC web server for predicting peptide-MHC binding affinities using these models. Benchmarked percentile scores are provided for all predictions. The larger number of SVRMHC models available allowed for an updated evaluation of the performance of the SVRMHC method compared to other well- known linear modeling methods. SVRMHC is an accurate and easy-to-use prediction server for epitope-MHC binding with significant coverage of MHC molecules. We believe it will prove to be a valuable resource for T cell epitope researchers.