Knowledge management for systems biology a general and visually driven framework applied to translational medicine

Background: To enhance our understanding of complex biological systems like diseases we need to put all of the available data into context and use this to detect relations, pattern and rules which allow predictive hypotheses to be defined. Life science has become a data rich science with information about the behaviour of millions of entities like genes, chemical compounds, diseases, cell types and organs, which are organised in many different databases and/or spread throughout the literature. Existing knowledge such as genotype - phenotype relations or signal transduction pathways must be semantically integrated and dynamically organised into structured networks that are connected with clinical and experimental data. Different approaches to this challenge exist but so far none has proven entirely satisfactory. Results: To address this challenge we previously developed a generic knowledge management framework, BioXM™, which allows the dynamic, graphic generation of domain specific knowledge representation models based on specific objects and their relations supporting annotations and ontologies. Here we demonstrate the utility of BioXM for knowledge management in systems biology as part of the EU FP6 BioBridge project on translational approaches to chronic diseases. From clinical and experimental data, text-mining results and public databases we generate a chronic obstructive pulmonary disease (COPD) knowledge base and demonstrate its use by mining specific molecular networks together with integrated clinical and experimental data. Conclusions: We generate the first semantically integrated COPD specific public knowledge base and find that for the integration of clinical and experimental data with pre-existing knowledge the configuration based set-up enabled by BioXM reduced implementation time and effort for the knowledge base compared to similar systems implemented as classical software development projects. The knowledgebase enables the retrieval of sub-networks including protein-protein interaction, pathway, gene - disease and gene - compound data which are used for subsequent data analysis, modelling and simulation. Pre-structured queries and reports enhance usability; establishing their use in everyday clinical settings requires further simplification with a browser based interface which is currently under development.

Marco metodológico para la definición de un perfil profesional en educación superior = Methodological framework for the definition of a professional profile in higher education

En el marco del Espacio Europeo de Educación Superior 1 se inscriben innumerables acciones que están desarrollando todas las universidades europeas con la intención de llegar al 2010 con un bagaje lo suficientemente importante como para afrontar este cambio con entereza y sobretodo conservando (o incrementando) la calidad de los procesos de enseñanza- aprendizaje que hasta el momento han predominado. Dentro de este amplio proceso de transformación se encuentra el diseño de los nuevos Grados que brinda la oportunidad de replantear los planes de estudios, por tanto, la organización de las asignaturas, estructura de los contenidos, metodologías y sistemas de evaluación. Toda esta reflexión debe girar, a nuestro entender, alrededor de tres núcleos que se encuentran en estado deinterdependencia: los escenarios profesionales, los perfiles profesionales y las competencias que en ellos se inscriben.Para poder plantear los nuevos Grados en coherencia con la era del EEES debe hacerse un análisis minucioso de los perfil profesionales demandados por el mercado de trabajo que, al fin y al cabo será el destino de los profesionales que se forman en nuestras universidades, es por ello, que la tarea de definir el perfil profesional a priori del diseño de los nuevos Grados resulta una máxima para garantizar la calidad de estos. En este trabajo se presenta un ejemplo de metodología a seguir para la definición de un perfil profesional en Educación Superior, concretamente, el del Ingeniero TIC mediante el Análisis Funcional.

Framework multitouch per a la creació fàcil d'aplicacions interactives

El projecte que aquí es presenta explora un nou enfocament a la interacció amb elssistemes interactius que típicament es proposen en museus. En aquests sistemes lainteracció i el feedback visual venen determinats per l’aplicació programada per l’arstista i no permet a l’usuari modificar-ne el seu comportament sinó tan sols interactuar amb les accións predefinides.L’enfocament que es planteja en aquest projecte és convertir als usuaris consumidorsd’aquests sistemes interactius en creadors i editors de les seves pròpies experiències.D’aquesta manera un sistema interactiu podrà ser modificat per l’usuari i així oferirdiferents respostes donada una mateixa entrada. Això es fa utilitzant un dispositiumultitouch com a sistema de configuració visual d’aquestes aplicacions així com un segon dispositiu com a sortida de l’aplicació visual.Aquest projecte neix de la idea de desenvolupar una eina útil i de fàcil ús per a crear aplicacions interactives, sense necessitat de tenir nocions de programació, de manera que qualsevol usuari inexpert pugui partir d’una idea i crear la seva pròpia aplicació interactiva.Així doncs, a través de diversos prototips i proves d’usabilitat es perfila una interfície de programació visual sobre una superfície tangible que sigui intuïtiva i fàcil d’utilitzar per a tot tipus d’usuaris.Per tal de dur a terme això s’ha dissenyat un sistema on s’utilitzen dos pantallesmultitouch, una amb la interfície de programació visual i l’altre amb la sortida del sistema creat. Això permet la interacció simultània entre usuaris creadors i usuaris consumidors de manera que l’experiència del consumidor pugui ser modificada en viu pel creador, segons interactuï amb la interfície de configuració.

Biana: a software framework for compiling biological interactions and analyzing networks

Background: The analysis and usage of biological data is hindered by the spread of information across multiple repositories and the difficulties posed by different nomenclature systems and storage formats. In particular, there is an important need for data unification in the study and use of protein-protein interactions. Without good integration strategies, it is difficult to analyze the whole set of available data and its properties.Results: We introduce BIANA (Biologic Interactions and Network Analysis), a tool for biological information integration and network management. BIANA is a Python framework designed to achieve two major goals: i) the integration of multiple sources of biological information, including biological entities and their relationships, and ii) the management of biological information as a network where entities are nodes and relationships are edges. Moreover, BIANA uses properties of proteins and genes to infer latent biomolecular relationships by transferring edges to entities sharing similar properties. BIANA is also provided as a plugin for Cytoscape, which allows users to visualize and interactively manage the data. A web interface to BIANA providing basic functionalities is also available. The software can be downloaded under GNU GPL license from http://sbi.imim.es/web/BIANA.php.Conclusions: BIANA's approach to data unification solves many of the nomenclature issues common to systems dealing with biological data. BIANA can easily be extended to handle new specific data repositories and new specific data types. The unification protocol allows BIANA to be a flexible tool suitable for different user requirements: non-expert users can use a suggested unification protocol while expert users can define their own specific unification rules.

Property as an economic concept: Reconciling legal and economic conceptions of property rights in a Coasean framework

Adopting a simplistic view of Coase (1960), most economic analyses of property rightsdisregard both the key advantage that legal property rights (that is, in rem rights) provide torightholders in terms of enhanced enforcement, and the difficulties they pose to acquirers interms of information asymmetry about legal title. Consequently, these analyses tend to overstatethe role of "private ordering" and disregard the two key elements of property law: first, theessential conflict between property (that is, in rem) enforcement and transaction costs; and,second, the institutional solutions created to overcome it, mainly contractual registries capable ofmaking truly impersonal (that is, asset-based) trade viable when previous relevant transactionson the same assets are not verifiable by judges. This paper fills this gap by reinterpreting bothelements within the Coasean framework and thus redrawing the institutional foundations of bothproperty and corporate contracting.

A house price index defined in the potential outcomes framework

Current methods for constructing house price indices are based on comparisons of sale prices of residential properties sold two or more times and on regression of the sale prices on the attributes of the properties and of their locations. The two methods have well recognised deficiencies, selection bias and model assumptions, respectively. We introduce a new method based on propensity score matching. The average house prices for two periods are compared by selecting pairs of properties, one sold in each period, that are as similar on a set of available attributes (covariates) as is feasible to arrange. The uncertainty associated with such matching is addressed by multiple imputation, framing the problem as involving missing values. The method is applied to aregister of transactions ofresidential properties in New Zealand and compared with the established alternatives.

A search theory of money and commerce with Neoclassical production

This paper advances a highly tractable model with search theoretic foundations for money and neoclassical growth. In the model, manufacturingand commerce are distinct and separate activities. In manufacturing,goods are efficiently produced combining capital and labor. In commerce,goods are exchanged in bilateral meetings. The model is applied to studythe effects of inßation on capital accumulation and welfare. With realisticparameters, inflation has large negative effects on welfare even though itraises capital and output. In contrast, with cash-in-advance, a deviceinformally motivated with bilateral trading, inflation depresses capitaland output and has a negligible effect on welfare.

Web professional de serveis informàtics, basat en software de codi obert

El PFC tracte de la implementació d'un web de serveis informàtics basat en software de codi obert i per tal de emprendre-ho i tirar endavant com a negoci, s'ha dut a terme un estudi de les tecnologies i un pla d'empresa, mirant de treu-re la màxima rendibilitat al web.Els serveis escollits com a model de negoci són bàsicament quatre: el disseny web, el disseny de webs e-commerce o tendes virtuals, la implementació de gestors de recursos d'empresa coneguts com ERP (de l'anglès Enterprise Resources Planning), i la implementació de gestors de relacions amb els clients coneguts com CRM (de l'anglès Customer Relationship Management).El primer capítol es una introducció, el segon capítol tracta de el software lliure, que és, quins models de negoci aporta i els tipus de llicència existents, el tercer capítol es un pla d'empresa on es detalla els serveis que oferirem i com ho gestionarem, el quart capítol tracta de les tecnologies utilitzades i el per que, i finalment unes conclusions.La web, netsolucion.com, que s'ha dissenyat amb Wordpress, implica no tan sols el haver d'estudiar i d'aprendre aquesta plataforma sinó també totes les que s'ofereixen com a serveis, que son:Gestor de Bases de Dades MySQL i PHP per al disseny web, Prestashop per al disseny de tendes virtuals, OpenERP per a la implementació dels gestors de recursos de empresa (ERP's) i els gestors de relacions amb els clients (CRM's).

Towards a database on societal impact of Mediterranean floods in the framework of the HYMEX project

The NW Mediterranean region experiences every year heavy rainfall and flash floods that occasionally produce catastrophic damages. Less frequent are floods that affect large regions. Although a large number of databases devoted exclusively to floods or considering all kind of natural hazards do exist, usually they only record catastrophic flood events. This paper deals with the new flood database that is being developed within the framework of HYMEX project. Results are focused on four regions representative of the NW sector of Mediterranean Europe: Catalonia, Spain; the Balearic Islands, Spain; Calabria, Italy; and Languedoc-Roussillon, Midi-Pyrenées and PACA, France. The common available 30-yr period starts in 1981 and ends in 2010. The paper shows the database structure and criteria, the comparison with other flood databases, some statistics on spatial and temporal distribution, and an identification of the most important events. The paper also provides a table that includes the date and affected region of all the catastrophic events identified in the regions of study, in order to make this information available for all audiences.

Patients' right to information: a review of the regulatory and ethical framework

[eng] Aim: The paper examines the current situation of recognition of patients' right to information in international standards and in the national laws of Belgium, France, Italy, Spain (and Catalonia), Switzerland and the United Kingdom.Methodology: International standards, laws and codes of ethics of physicians and librarians that are currently in force were identified and analyzed with regard to patients' right to information and the ownership of this right. The related subjects of access to clinical history, advance directives and informed consent were not taken into account.Results: All the standards, laws and codes analyzed deal with guaranteeing access to information. The codes of ethics of both physicians and librarians establish the duty to inform.Conclusions: Librarians must collaborate with physicians in the process of informing patients.

Building a Social Accounting Matrix within the ESA95 Framework: Obtaining a Dataset for Applied General Equilibrium Modelling

This research provides a description of the process followed in order to assemble a "Social Accounting Matrix" for Spain corresponding to the year 2000 (SAMSP00). As argued in the paper, this process attempts to reconcile ESA95 conventions with requirements of applied general equilibrium modelling. Particularly, problems related to the level of aggregation of net taxation data, and to the valuation system used for expressing the monetary value of input-output transactions have deserved special attention. Since the adoption of ESA95 conventions, input-output transactions have been preferably valued at basic prices, which impose additional difficulties on modellers interested in computing applied general equilibrium models. This paper addresses these difficulties by developing a procedure that allows SAM-builders to change the valuation system of input-output transactions conveniently. In addition, this procedure produces new data related to net taxation information.

Interaccion among systems of finite size in predictive relativistic mechanics I. General framework

We derive a Hamiltonian formulation for the three-dimensional formalism of predictive relativistic mechanics. This Hamiltonian structure is used to derive a set of dynamical equations describing the interaction among systems in perturbation theory.

Classical predictive electrodynamics of two charges with radiation: General framework. I.

Outgoing radiation is introduced in the framework of the classical predictive electrodynamics using LorentzDiracs equation as a subsidiary condition. In a perturbative scheme in the charges the first radiative self-terms of the accelerations, momentum and angular momentum of a two charge system without external field are calculated.

State-to-state reaction probabilities within the quantum transition state framework

Rigorous quantum dynamics calculations of reaction rates and initial state-selected reaction probabilities of polyatomic reactions can be efficiently performed within the quantum transition state concept employing flux correlation functions and wave packet propagation utilizing the multi-configurational time-dependent Hartree approach. Here, analytical formulas and a numerical scheme extending this approach to the calculation of state-to-state reaction probabilities are presented. The formulas derived facilitate the use of three different dividing surfaces: two dividing surfaces located in the product and reactant asymptotic region facilitate full state resolution while a third dividing surface placed in the transition state region can be used to define an additional flux operator. The eigenstates of the corresponding thermal flux operator then correspond to vibrational states of the activated complex. Transforming these states to reactant and product coordinates and propagating them into the respective asymptotic region, the full scattering matrix can be obtained. To illustrate the new approach, test calculations study the D + H2(ν, j) → HD(ν′, j′) + H reaction for J = 0.

Building a Social Accounting Matrix within the ESA95 Framework: Obtaining a Dataset for Applied General Equilibrium Modelling

This research provides a description of the process followed in order to assemble a "Social Accounting Matrix" for Spain corresponding to the year 2000 (SAMSP00). As argued in the paper, this process attempts to reconcile ESA95 conventions with requirements of applied general equilibrium modelling. Particularly, problems related to the level of aggregation of net taxation data, and to the valuation system used for expressing the monetary value of input-output transactions have deserved special attention. Since the adoption of ESA95 conventions, input-output transactions have been preferably valued at basic prices, which impose additional difficulties on modellers interested in computing applied general equilibrium models. This paper addresses these difficulties by developing a procedure that allows SAM-builders to change the valuation system of input-output transactions conveniently. In addition, this procedure produces new data related to net taxation information.