Dynamic simulation of regulatory networks using SQUAD.

BACKGROUND: The ambition of most molecular biologists is the understanding of the intricate network of molecular interactions that control biological systems. As scientists uncover the components and the connectivity of these networks, it becomes possible to study their dynamical behavior as a whole and discover what is the specific role of each of their components. Since the behavior of a network is by no means intuitive, it becomes necessary to use computational models to understand its behavior and to be able to make predictions about it. Unfortunately, most current computational models describe small networks due to the scarcity of kinetic data available. To overcome this problem, we previously published a methodology to convert a signaling network into a dynamical system, even in the total absence of kinetic information. In this paper we present a software implementation of such methodology. RESULTS: We developed SQUAD, a software for the dynamic simulation of signaling networks using the standardized qualitative dynamical systems approach. SQUAD converts the network into a discrete dynamical system, and it uses a binary decision diagram algorithm to identify all the steady states of the system. Then, the software creates a continuous dynamical system and localizes its steady states which are located near the steady states of the discrete system. The software permits to make simulations on the continuous system, allowing for the modification of several parameters. Importantly, SQUAD includes a framework for perturbing networks in a manner similar to what is performed in experimental laboratory protocols, for example by activating receptors or knocking out molecular components. Using this software we have been able to successfully reproduce the behavior of the regulatory network implicated in T-helper cell differentiation. CONCLUSION: The simulation of regulatory networks aims at predicting the behavior of a whole system when subject to stimuli, such as drugs, or determine the role of specific components within the network. The predictions can then be used to interpret and/or drive laboratory experiments. SQUAD provides a user-friendly graphical interface, accessible to both computational and experimental biologists for the fast qualitative simulation of large regulatory networks for which kinetic data is not necessarily available.

Nursing Needs Assessment Tool User Guide 2006 (PDF 207 KB)

The user guide describes how to undertake an assessment using the nursing needs assessment tool.

Aplicació per la creació de classes interactives de Ciclo Indoor

Es tracta d'un projecte evolutiu que permetrà crear una aplicació que serveixi de suport gràfic per a les classes de Ciclo Indoor i que a més a més permetrà al professor preparar-les en pocs minuts. També tindrà un apartat dedicat a gestionar als usuaris del sistema mitjançant una connexió a una base de dades que també ha sigut dissenyada i desenvolupada en aquest projecte.

LiveUpdate : gestor de descargas

La función principal de LiveUpdate será la de descargar actualizaciones mediante un servidor remoto permitiendo tener un control integral de todas las descargas disponibles. El desarrollo del proyecto estará marcado por la tecnología en la que se basa, Windows Presentation Foundation (WPF) para la creación de interfaces gráficas enriquecidas, y el lenguaje en que se sustenta, C#. La metodología utilizada estará caracterizada por el modelo Modelo‐Vista‐VistaModelo (MVVM) y los estándares corporativos que Mitsubishi aplica en su software. Finalmente, el sistema también dispondrá de soporte multiidioma pudiendo visualizar idiomas con caracteres no latinos como el ruso (cirílico) o el japonés (katakana, hiragana).

Generación de interfaces para aplicaciones por línea de comandos

Generación dinámica de interfaces web basadas en ficheros descriptivos XML para el control de la parametrización compleja y ejecución de programas por línea de comandos. La necesidad surge con la aplicación mlcoalsim, utilizada por investigadores de la UAB, cuya parametrización requiere la edición manual de un fichero de texto la sintaxis del cual es complicada y pesada. Con la generación de interfaces web se pretende ayudar a los usuarios en la correcta parametrización y ejecución de aplicaciones como mlcoalsim.

MyHits: a new interactive resource for protein annotation and domain identification.

The MyHits web server (http://myhits.isb-sib.ch) is a new integrated service dedicated to the annotation of protein sequences and to the analysis of their domains and signatures. Guest users can use the system anonymously, with full access to (i) standard bioinformatics programs (e.g. PSI-BLAST, ClustalW, T-Coffee, Jalview); (ii) a large number of protein sequence databases, including standard (Swiss-Prot, TrEMBL) and locally developed databases (splice variants); (iii) databases of protein motifs (Prosite, Interpro); (iv) a precomputed list of matches ('hits') between the sequence and motif databases. All databases are updated on a weekly basis and the hit list is kept up to date incrementally. The MyHits server also includes a new collection of tools to generate graphical representations of pairwise and multiple sequence alignments including their annotated features. Free registration enables users to upload their own sequences and motifs to private databases. These are then made available through the same web interface and the same set of analytical tools. Registered users can manage their own sequences and annotations using only web tools and freeze their data in their private database for publication purposes.

DCU per a la configurabilitat d'una estació de treball clínic

Gairebé un 50% dels metges de la sanitat catalana realitzen actualment les seves tasques assistencials en entorns SAP. Donada la naturalesa de la seva feina, és fàcil afirmar que les aplicacions que utilitzen habitualment haurien d'haver estat desenvolupades centrant l'atenció en l'usuari i el context en què aquest realitza la seva feina. Però degut a diversos motius organitzatius, això no ha estat així. Aquest projecte pretén demostrar el valor afegit que pot aportar el Disseny Centrat en l'Usuari en el desenvolupament d'aplicacions assistencials en l'àmbit SAP Sanitat. S'ha realitzat una investigació prèvia de les necessitats reals dels usuaris, un anàlisi del context d'ús i dels diferents perfils de usuari, s'ha desenvolupat un prototip amb la nova tecnologia que aporta SAP per al desenvolupament de interfícies tipus web integrades en el sistema (SAP Webdynpro for ABAP), i finalment s'ha realitzat la corresponent avaluació heurística i el test de usuaris. S'ha arribat principalment a tres conclusions: en primer lloc, ha sorprès la bona disposició dels usuaris metges per a participar en aquesta mena de projectes; en segon lloc, ha quedat demostrada la importància de l'anàlisi del context, així com la rellevància que el dissenyador estigui quan més a prop millor de l'usuari final; i finalment, cal destacar que la tecnologia emprada ha limitat qualitativament diverses opcions de disseny.

ARCHITECTING USER-CENTRIC PRIVACY-AS-A-SET-OF-SERVICES: DIGITAL IDENTITY RELATED PRIVACY FRAMEWORK

AbstractDigitalization gives to the Internet the power by allowing several virtual representations of reality, including that of identity. We leave an increasingly digital footprint in cyberspace and this situation puts our identity at high risks. Privacy is a right and fundamental social value that could play a key role as a medium to secure digital identities. Identity functionality is increasingly delivered as sets of services, rather than monolithic applications. So, an identity layer in which identity and privacy management services are loosely coupled, publicly hosted and available to on-demand calls could be more realistic and an acceptable situation. Identity and privacy should be interoperable and distributed through the adoption of service-orientation and implementation based on open standards (technical interoperability). Ihe objective of this project is to provide a way to implement interoperable user-centric digital identity-related privacy to respond to the need of distributed nature of federated identity systems. It is recognized that technical initiatives, emerging standards and protocols are not enough to guarantee resolution for the concerns surrounding a multi-facets and complex issue of identity and privacy. For this reason they should be apprehended within a global perspective through an integrated and a multidisciplinary approach. The approach dictates that privacy law, policies, regulations and technologies are to be crafted together from the start, rather than attaching it to digital identity after the fact. Thus, we draw Digital Identity-Related Privacy (DigldeRP) requirements from global, domestic and business-specific privacy policies. The requirements take shape of business interoperability. We suggest a layered implementation framework (DigldeRP framework) in accordance to model-driven architecture (MDA) approach that would help organizations' security team to turn business interoperability into technical interoperability in the form of a set of services that could accommodate Service-Oriented Architecture (SOA): Privacy-as-a-set-of- services (PaaSS) system. DigldeRP Framework will serve as a basis for vital understanding between business management and technical managers on digital identity related privacy initiatives. The layered DigldeRP framework presents five practical layers as an ordered sequence as a basis of DigldeRP project roadmap, however, in practice, there is an iterative process to assure that each layer supports effectively and enforces requirements of the adjacent ones. Each layer is composed by a set of blocks, which determine a roadmap that security team could follow to successfully implement PaaSS. Several blocks' descriptions are based on OMG SoaML modeling language and BPMN processes description. We identified, designed and implemented seven services that form PaaSS and described their consumption. PaaSS Java QEE project), WSDL, and XSD codes are given and explained.

The Eukaryotic Promoter Database EPD: the impact of in silico primer extension.

The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, experimentally defined by a transcription start site (TSS). There may be multiple promoter entries for a single gene. The underlying experimental evidence comes from journal articles and, starting from release 73, from 5' ESTs of full-length cDNA clones used for so-called in silico primer extension. Access to promoter sequences is provided by pointers to TSS positions in nucleotide sequence entries. The annotation part of an EPD entry includes a description of the type and source of the initiation site mapping data, links to other biological databases and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis. Web-based interfaces have been developed that enable the user to view EPD entries in different formats, to select and extract promoter sequences according to a variety of criteria and to navigate to related databases exploiting different cross-references. Tools for analysing sequence motifs around TSSs defined in EPD are provided by the signal search analysis server. EPD can be accessed at http://www.epd. isb-sib.ch.

Uso de tecnologías abiertas (Processing) en el desarrollo de interfaces avanzadas de visualización y acceso de datos : Estudio del caso Organic.Edunet

El artículo muestra, a través del estudio del caso del buscador semántico del portal Organic.Edunet, cómo el uso de tecnologías cerradas en la creación de interfaces avanzadas de visualización de datos impide su desarrollo y evolución. En el artículo se mostrará también cómo, combinado con técnicas para la medición y valoración de la usabilidad de las aplicaciones, el uso de tecnologías abiertas permite detectar los problemas del interface, proponer soluciones o alternativas, e implementarlas rápidamente.

Open to the users' needs : combining user-centered design, standards and open source software

This case study introduces our continuous work to enhance the virtual classroom in order to provide faculty and students with an environment open to their needs, compliant with learning standards and, therefore compatible with other e-learning environments, and based on open source software. The result is a modulable, sustainable and interoperable learning environment that can be adapted to different teaching and learning situations by incorporating the LMS integrated tools as well as wikis, blogs, forums and Moodle activities among others.

Virtual Library Services for a Virtual University : User-Oriented Virtual Sites in an Open Library

La llegada de las tecnologías de la información, y su uso cada vez mayor y generalizado que se está haciendo de ellas, ha permitido para que una nueva situación aparezca que, a su vez, ha originado - de hecho, que ha precipitado - una serie de cambios de gran importancia en todos los niveles, pero especialmente en los niveles sociales, económicos y culturales. Este nueva escena ha tenido una gran influencia en el entorno pedagógico. De hecho, la aparición de nuevos modelos educativos como resultado de este cambio ha estado sucediendo de una manera continuada e ininterrumpida durante la década pasada. Estos cambios recientes en los sistemas actuales de enseñanza y de aprendizaje han significado un aumento y un cambio en el tipo de demandas hechas desde las bibliotecas y los centros de documentación.

Biofilm formation at the solid-liquid and air-liquid interfaces by Acinetobacter species

The members of the genus Acinetobacter are Gram-negative cocobacilli that are frequently found in the environment but also in the hospital setting where they have been associated with outbreaks of nosocomial infections. Among them, Acinetobacter baumannii has emerged as the most common pathogenic species involved in hospital-acquired infections. One reason for this emergence may be its persistence in the hospital wards, in particular in the intensive care unit; this persistence could be partially explained by the capacity of these microorganisms to form biofilm. Therefore, our main objective was to study the prevalence of the two main types of biofilm formed by the most relevant Acinetobacter species, comparing biofilm formation between the different species. Findings: Biofilm formation at the air-liquid and solid-liquid interfaces was investigated in different Acinetobacter spp. and it appeared to be generally more important at 25°C than at 37°C. The biofilm formation at the solid-liquid interface by the members of the ACB-complex was at least 3 times higher than the other species (80-91% versus 5-24%). In addition, only the isolates belonging to this complex were able to form biofilm at the air-liquid interface; between 9% and 36% of the tested isolates formed this type of pellicle. Finally, within the ACB-complex, the biofilm formed at the air-liquid interface was almost 4 times higher for A. baumannii and Acinetobacter G13TU than for Acinetobacter G3 (36%, 27% & 9% respectively). Conclusions: Overall, this study has shown the capacity of the Acinetobacter spp to form two different types of biofilm: solid-liquid and air-liquid interfaces. This ability was generally higher at 25°C which might contribute to their persistence in the inanimate hospital environment. Our work has also demonstrated for the first time the ability of the members of the ACB-complex to form biofilm at the air-liquid interface, a feature that was not observed in other Acinetobacter species.

TNF-alpha blockers in inflammatory bowel diseases: practical consensus recommendations and a user's guide.

More than seventy years after their initial characterisation, the aetiology of inflammatory bowel diseases remains elusive. A recent review evaluating the incidence trends of the last 25 years concluded that an increasing incidence has been observed almost worldwide. A north-south gradient is still found in Europe. Genetic associations are variably reproduced worldwide and indicate a strong impact of environmental factors. Tumour necrosis factor alpha (TNF-alpha) has been shown to play a critical role in the pathogenesis of inflammatory bowel disease (IBD). TNF-alpha blockers are biological agents that specifically target this key cytokine in the inflammatory process and have become a mainstay in the therapy of inflammatory bowel diseases. This paper reviews the necessary investigations before using such agents, the use of such agents in pregnancy and lactation, the role of co-immunosuppression, how to monitor efficacy and safety, dose-adaptation, and the decision as to when to switch to another TNF-alpha blocker. Finally it gives recommendations for special situations. Currently there are three TNF-alpha blockers available for clinical use in IBD in Switzerland: infliximab (Remicade), adalimumab (Humira) and certolizumab pegol (Cimzia). Infliximab is a chimeric monoclonal antibody composed of a human IgG1 constant region and a murine variable region and is administered intravenously. Adalimumab is a humanised monoclonal antibody, with both human IgG1 constant and variable regions. Certolizumab pegol is a pegylated, humanised monoclonal anti-TNF fragment antigen binding fragment. Both adalimumab and certolizumab pegol are administered by subcutaneous injection. The efficacy and safety of TNF-alpha blockers in Crohn's disease has been reviewed. The authors conclude that the three above-mentioned agents are effective in luminal Crohn's disease. In fistulizing Crohn's disease, TNF-alpha blockers other than infliximab require additional investigation.