MyHits: improvements to an interactive resource for analyzing protein sequences.

The MyHits web site (http://myhits.isb-sib.ch) is an integrated service dedicated to the analysis of protein sequences. Since its first description in 2004, both the user interface and the back end of the server were improved. A number of tools (e.g. MAFFT, Jacop, Dotlet, Jalview, ESTScan) were added or updated to improve the usability of the service. The MySQL schema and its associated API were revamped and the database engine (HitKeeper) was separated from the web interface. This paper summarizes the current status of the server, with an emphasis on the new services.

Signal search analysis server.

Signal search analysis is a general method to discover and characterize sequence motifs that are positionally correlated with a functional site (e.g. a transcription or translation start site). The method has played an instrumental role in the analysis of eukaryotic promoter elements. The signal search analysis server provides access to four different computer programs as well as to a large number of precompiled functional site collections. The programs offered allow: (i) the identification of non-random sequence regions under evolutionary constraint; (ii) the detection of consensus sequence-based motifs that are over- or under-represented at a particular distance from a functional site; (iii) the analysis of the positional distribution of a consensus sequence- or weight matrix-based sequence motif around a functional site; and (iv) the optimization of a weight matrix description of a locally over-represented sequence motif. These programs can be accessed at: http://www.isrec.isb-sib.ch/ssa/.

Annual Report of the Iowa Client Assistance Program 2006-2007

Public report covering the services provided during fiscal 2007 by the federally mandated Client Assistance Program located in the Iowa Department of Human Rights, Division of Persons with Disabilities.

HTPSELEX--a database of high-throughput SELEX libraries for transcription factor binding sites.

HTPSELEX is a public database providing access to primary and derived data from high-throughput SELEX experiments aimed at characterizing the binding specificity of transcription factors. The resource is primarily intended to serve computational biologists interested in building models of transcription factor binding sites from large sets of binding sequences. The guiding principle is to make available all information that is relevant for this purpose. For each experiment, we try to provide accurate information about the protein material used, details of the wet lab protocol, an archive of sequencing trace files, assembled clone sequences (concatemers) and complete sets of in vitro selected protein-binding tags. In addition, we offer in-house derived binding sites models. HTPSELEX also offers reasonably large SELEX libraries obtained with conventional low-throughput protocols. The FTP site contains the trace archives and database flatfiles. The web server offers user-friendly interfaces for viewing individual entries and quality-controlled download of SELEX sequence libraries according to a user-defined sequencing quality threshold. HTPSELEX is available from ftp://ftp.isrec.isb-sib.ch/pub/databases/htpselex/ and http://www.isrec.isb-sib.ch/htpselex.

The Microbe browser for comparative genomics.

The Microbe browser is a web server providing comparative microbial genomics data. It offers comprehensive, integrated data from GenBank, RefSeq, UniProt, InterPro, Gene Ontology and the Orthologs Matrix Project (OMA) database, displayed along with gene predictions from five software packages. The Microbe browser is daily updated from the source databases and includes all completely sequenced bacterial and archaeal genomes. The data are displayed in an easy-to-use, interactive website based on Ensembl software. The Microbe browser is available at http://microbe.vital-it.ch/. Programmatic access is available through the OMA application programming interface (API) at http://microbe.vital-it.ch/api.

Determination of extreme floods using a distributed hydrological model

Hydrological models developed for extreme precipitation of PMP type are difficult to calibrate because of the scarcity of available data for these events. This article presents the process and results of calibration for a distributed hydrological model at fine scale developed for the estimation of probable maximal floods in the case of a PMP. This calibration is done on two Swiss catchments for two events of summer storms. The calculation done is concentrated on the estimation of the parameters of the model, divided in two parts. The first is necessary for the computation of flow speeds while the second is required for the determination of the initial and final infiltration capacities for each terrain type. The results, validated with the Nash equation show a good correlation between the simulated and observed flows. We also apply this model on two Romanian catchments, showing the river network and estimated flow.

Location of multiple server common service centers or public facilities for minimizing general congestion and travel cost functions

We propose a model and solution methods, for locating a fixed number ofmultiple-server, congestible common service centers or congestible publicfacilities. Locations are chosen so to minimize consumers congestion (orqueuing) and travel costs, considering that all the demand must be served.Customers choose the facilities to which they travel in order to receiveservice at minimum travel and congestion cost. As a proxy for thiscriterion, total travel and waiting costs are minimized. The travel costis a general function of the origin and destination of the demand, whilethe congestion cost is a general function of the number of customers inqueue at the facilities.

Iowa Client Assistance Program Annual Report 2008

Annual report for federal fiscal year 2008 submitted to the Rehabilitation Services Administration, Office of Special Education and Rehabilitative Services, U.S. Department of Education. This report is requied to be submitted each year by December 31th for the pervious fiscal year as part of the federal grant requirements for the Client Assistance Program grantee in each state. In Iowa, the Client Assistance Program is housed in the Division of Persons with Disabilities, Department of Human Rights and provides information and referral services and advocacy services as outlined under the Rehabilitation Act of 1973, as amended.

Generación automática de cuadros de mando vía web

El proyecto consta de una aplicación web destinada a generar cuadros de mandos para distintos clientes de una manera ágil y dinámica reduciendo así los tiempos de implementación de una herramienta de estas características. Dicha aplicación será desarrollada bajo .NET para el lado del servidor y jQuery & google Maps API para el lado cliente, por lo que hace a los informes y la base de datos todo estará implementado con Microsoft SQL Server 2008 R2.

Length of activity season drives geographic variation in body size of a widely distributed lizard

Understanding the factors that drive geographic variation in life history is an important challenge in evolutionary ecology. Here, we analyze what predicts geographic variation in life-history traits of the common lizard, Zootoca vivipara, which has the globally largest distribution range of all terrestrial reptile species. Variation in body size was predicted by differences in the length of activity season, while we found no effects of environmental temperature per se. Females experiencing relatively short activity season mature at a larger size and remain larger on average than females in populations with relatively long activity seasons. Interpopulation variation in fecundity was largely explained by mean body size of females and reproductive mode, with viviparous populations having larger clutch size than oviparous populations. Finally, body size-fecundity relationship differs between viviparous and oviparous populations, with relatively lower reproductive investment for a given body size in oviparous populations. While the phylogenetic signal was weak overall, the patterns of variation showed spatial effects, perhaps reflecting genetic divergence or geographic variation in additional biotic and abiotic factors. Our findings emphasize that time constraints imposed by the environment rather than ambient temperature play a major role in shaping life histories in the common lizard. This might be attributed to the fact that lizards can attain their preferred body temperature via behavioral thermoregulation across different thermal environments. Length of activity season, defining the maximum time available for lizards to maintain optimal performance, is thus the main environmental factor constraining growth rate and annual rates of mortality. Our results suggest that this factor may partly explain variation in the extent to which different taxa follow ecogeographic rules.

Dealing with clients' diversity in test situations: Client categorisations in psychologists' accounts of their practices

Reducing a test administration to standardised procedures reflects the test designers' standpoint. However, from the practitioners' standpoint, each client is unique. How do psychologists deal with both standardised test administration and clients' diversity? To answer this question, we interviewed 17 psychologists working in three public services for children and adolescents about their assessment practices. We analysed the numerous "client categorisations" they produced in their accounts. We found that they had shared perceptions about their clients' diversity, and reported various non-standard practices that complemented standardised test administration, but also differed from them or were even forbidden. They seem to experience a dilemma between: (a) prescribed and situated practices; (b) scientific and situated reliability; (c) commutative and distributive justice. For practitioners, dealing with clients' diversity this is a practical problem, halfway between a problem-solving task and a moral dilemma.

Sistema per gestionar les incidències d'un servei d'informàtica amb una arquitectura J2EE distribuïda en tres nivells

Tant en la meva etapa d’estudiant com en la meva curta vida laboral, he participat en el desenvolupament de varies aplicacions de gestió, tant d’escriptori com web, que majoritàriament sempre estaven dividides en tres capes però en dos nivells: la base de dades i l’aplicació, que contenia tant la lògica de negoci com la vista. Des de fa temps he tingut la curiositat i la necessitat d’intentar desenvolupar una aplicació de gestió que estigui distribuïda en tres o més nivells, separant el model de dades i la lògica de negoci de la vista. Crec que el treball de fi de carrera és idoni per desenvolupar-la. L’aplicació a desenvolupar anirà destinada a la gestió d’un servei d’informàtica, que s’encarrega de resoldre les incidències, inventariar i realitzar el manteniment preventiu dels equips informàtics d’una o de varies empreses. Es crearà una aplicació que contindrà el model de dades i la lògica de negoci. També es crearan dues aplicacions clients: una aplicació d’escriptori que donarà accés a totes i cadascuna de les funcionalitats del sistema i una aplicació web que oferirà un accés lleuger i des de qualsevol ubicació a les funcionalitats d’explotació del sistema. Per últim, també es crearà una altre aplicació web que s’encarregarà de generar els llistats sol•licitats per les dues aplicacions clients. D’aquesta manera també es centralitzarà la gestió dels llistats de les aplicacions del sistema. Per desenvolupar el sistema, s’utilitzarà la plataforma J2EE de Java, i es comptarà amb l’ajuda de marcs de treball com, per exemple, Oracle ADF o JasperReports. Com a conclusió general, puc assegurar que si es distribueixen les tres capes d’un sistema en tres nivells s’obtenen beneficis en l’administració, en el manteniment, en l’escalabilitat, en la flexibilitat i en la reutilització de les aplicacions. El principal inconvenient és el possible augment de lentitud en les aplicacions clients.

AssociationViewer: a scalable and integrated software tool for visualization of large-scale variation data in genomic context.

SUMMARY: We present a tool designed for visualization of large-scale genetic and genomic data exemplified by results from genome-wide association studies. This software provides an integrated framework to facilitate the interpretation of SNP association studies in genomic context. Gene annotations can be retrieved from Ensembl, linkage disequilibrium data downloaded from HapMap and custom data imported in BED or WIG format. AssociationViewer integrates functionalities that enable the aggregation or intersection of data tracks. It implements an efficient cache system and allows the display of several, very large-scale genomic datasets. AVAILABILITY: The Java code for AssociationViewer is distributed under the GNU General Public Licence and has been tested on Microsoft Windows XP, MacOSX and GNU/Linux operating systems. It is available from the SourceForge repository. This also includes Java webstart, documentation and example datafiles.

Virtualització de servidors. Avantatges. Implantació en una PIME real

 En la societat d’avui dia, les empreses depenen en gran part dels seus recursos informàtics. La seva capacitat de supervivència i innovació en el mercat actual, on la competitivitat és cada dia més forta, passa per una infraestructura informàtica que els permeti, no només desplegar i implantar ordinadors i servidors de manera ràpida i eficient sinó que també les protegeixi contra parades del sistema informàtic, problemes amb servidors, caigudes o desastres físics de hardware.Per evitar aquests problemes informàtics susceptibles de poder parar el funcionament d’una empresa es va començar a treballar en el camp de la virtualització informàtica amb l’objectiu de poder trobar solucions a aquests problemes a la vegada que s’aprofitaven els recursos de hardware existents d’una manera més òptim a i eficient, reduint així també el cost de la infraestructura informàtica.L’objectiu principal d’aquest treball és veure en primer pla la conversió d’una empresa real amb una infraestructura informàtica del tipus un servidor físic -una funció cap a una infraestructura virtual del tipus un servidor físic -varis servidors virtual -vàries funcions. Analitzarem l’estat actual de l’empresa, servidors i funcions, adquirirem el hardware necessari i farem la conversió de tots els seus servidors cap a una nova infraestructura virtual.Faig especial atenció a les explicacions de perquè utilitzo una opció i no un altre i també procuro sempre donar vàries opcions. Igualment remarco en quadres verds observacions a tenir en compte complementàries al que estic explicant en aquell moment, i en quadres vermells temes en els que s’ha de posar especial atenció en el moment en que es fan. Finalment, un cop feta la conversió, veurem els molts avantatges que ens ha reportat aquesta tecnologia a nivell de fiabilitat, estabilitat, capacitat de tolerància a errades, capacitat de ràpid desplegament de noves màquines, capacitat de recuperació del sistema i aprofitament de recursos físics.