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.

A global view of economic growth

This paper integrates in a unified and tractable framework some of the key insights of the field of international trade and economic growth. It examines a sequence of theoretical models that share a common description of technology and preferences but differ on their assumptions about trade frictions. By comparing the predictions of these models against each other, it is possible to identify a variety of channels through which trade affects the evolution of world income and its geographical distribution. By comparing the predictions of these models against the data, it is also possible to construct coherent explanations of income differences and long-run trends in economic growth.

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.

Policy making in divided government. A pivotal actors model with party discipline

This article presents a formal model of policy decision-making in an institutional framework of separation of powers in which the main actors are pivotal political parties with voting discipline. The basic model previously developed from pivotal politics theory for the analysis of the United States lawmaking is here modified to account for policy outcomes and institutional performances in other presidential regimes, especially in Latin America. Legislators' party indiscipline at voting and multi-partism appear as favorable conditions to reduce the size of the equilibrium set containing collectively inefficient outcomes, while a two-party system with strong party discipline is most prone to produce 'gridlock', that is, stability of socially inefficient policies. The article provides a framework for analysis which can induce significant revisions of empirical data, especially regarding the effects of situations of (newly defined) unified and divided government, different decision rules, the number of parties and their discipline. These implications should be testable and may inspire future analytical and empirical work.

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.

On the throughput-WIP trade-off in queueing systems, diminishing returns and the threshold property: A linear programming approach

We present a new unifying framework for investigating throughput-WIP(Work-in-Process) optimal control problems in queueing systems,based on reformulating them as linear programming (LP) problems withspecial structure: We show that if a throughput-WIP performance pairin a stochastic system satisfies the Threshold Property we introducein this paper, then we can reformulate the problem of optimizing alinear objective of throughput-WIP performance as a (semi-infinite)LP problem over a polygon with special structure (a thresholdpolygon). The strong structural properties of such polygones explainthe optimality of threshold policies for optimizing linearperformance objectives: their vertices correspond to the performancepairs of threshold policies. We analyze in this framework theversatile input-output queueing intensity control model introduced byChen and Yao (1990), obtaining a variety of new results, including (a)an exact reformulation of the control problem as an LP problem over athreshold polygon; (b) an analytical characterization of the Min WIPfunction (giving the minimum WIP level required to attain a targetthroughput level); (c) an LP Value Decomposition Theorem that relatesthe objective value under an arbitrary policy with that of a giventhreshold policy (thus revealing the LP interpretation of Chen andYao's optimality conditions); (d) diminishing returns and invarianceproperties of throughput-WIP performance, which underlie thresholdoptimality; (e) a unified treatment of the time-discounted andtime-average cases.

Technological change and the wealth of nations

We discuss a unified theory of directed technological change and technologyadoption that can shed light on the causes of persistent productivity differencesacross countries. In our model, new technologies are designed in advanced countries and diffuse endogenously to less developed countries. Our framework is richenough to highlight three broad reasons for productivity differences: inappropriatetechnologies, policy-induced barriers to technology adoption, and within-countrymisallocations across sectors due to policy distortions. We also discuss the effectsof two aspects of globalization, trade in goods and migration, on the wealth ofnations through their impact on the direction of technical progress. By doing so,we illustrate some of the equalizing and unequalizing forces of globalization.

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.

Does human capital stimulate investment in physical capital?: Evidence from a cost system framework

The direct effect of human capital on economic growth has been widely analysed in the economic literature. This paper, however, focuses on its indirect effect as a stimulus for private investment in physical capital. The methodological framework used is the duality theory, estimating a cost system aggregated with human capital. Empirical evidence is given for Spain for the period 1980-2000. We provide evidence on the indirect effect of human capital in making private capital investment more attractive. Among the main explanations forthis process, we observe that higher worker skill levels enable higher returns to be extracted from investment in physical capital.