Laboratorio virtual de software libre para bibliotecas

La elección de un programa de gestión de bibliotecas se ve afectada muchas veces por una serie de condiciones sociales, económicas y políticas que hacen que la elección no sea la más adecuada para las necesidades, características y funciones de la biblioteca. El software libre está siendo una de las soluciones más optadas, por sus libertades de copia, modificación y distribución, además de la libertad de licencias y las posibilidades de interoperación con otras aplicaciones. Esta nueva tendencia hacia el software libre en bibliotecas se refleja también en los estudios de biblioteconomía y documentación, en los que desde diferentes asignaturas se aportan conocimientos sobre programas de automatización, de gestión de repositorios, incluso del sistema operativo Linux/GNU, entre otros. Esta combinación entre las necesidades de los centros y la tendencia al uso de software libre, es la que un grupo de profesores de la Facultat de Biblioteconomia i Documentació (Universitat de Barcelona) y estudiantes, miembros del Grup de Treball sobre Programari Lliure per als Professionals de la Informació (Cobdc), han querido aportar a la comunidad profesional, creando un laboratorio virtual para el uso de software libre de aplicación en bibliotecas.

Use of the FACTS solvation model for protein-ligand docking calculations. Application to EADock.

Protein-ligand docking has made important progress during the last decade and has become a powerful tool for drug development, opening the way to virtual high throughput screening and in silico structure-based ligand design. Despite the flattering picture that has been drawn, recent publications have shown that the docking problem is far from being solved, and that more developments are still needed to achieve high successful prediction rates and accuracy. Introducing an accurate description of the solvation effect upon binding is thought to be essential to achieve this goal. In particular, EADock uses the Generalized Born Molecular Volume 2 (GBMV2) solvent model, which has been shown to reproduce accurately the desolvation energies calculated by solving the Poisson equation. Here, the implementation of the Fast Analytical Continuum Treatment of Solvation (FACTS) as an implicit solvation model in small molecules docking calculations has been assessed using the EADock docking program. Our results strongly support the use of FACTS for docking. The success rates of EADock/FACTS and EADock/GBMV2 are similar, i.e. around 75% for local docking and 65% for blind docking. However, these results come at a much lower computational cost: FACTS is 10 times faster than GBMV2 in calculating the total electrostatic energy, and allows a speed up of EADock by a factor of 4. This study also supports the EADock development strategy relying on the CHARMM package for energy calculations, which enables straightforward implementation and testing of the latest developments in the field of Molecular Modeling.

A virtual exhibition of open source software for libraries

Frequently the choice of a library management program is conditioned by social, economic and/or political factors that result in the selection of a system that is not altogether suitable for the library’s needs, characteristics and functions. Open source software is quickly becoming a preferred solution, owing to the freedom to copy, modify and distribute it and the freedom from contracts, as well as for greater opportunities for interoperability with other applications. These new trends regarding open source software in libraries are also reflected in LIS studies, as evidenced by the different courses addressing automated programs, repositorymanagement, including the Linux/GNU operating system, among others. The combination of the needs of the centres and the new trends for open source software is the focus of a virtual laboratory for the use of open source software for library applications. It was the result of a project, whose aim was to make a useful contribution to the library community, that was carried out by a group of professors of the School of Library and Information Science of the University of Barcelona, together with a group of students, members of a Working Group on Open Source Software for Information Professionals, of the Professional Library Association of Catalonia.

3D virtual rendering before laparoscopic partial splenectomy in children.

INTRODUCTION: Partial splenectomy in children is a good surgical option for hematological diseases and focal splenic tumors because it allows the preservation of the spleen's immunological function. Furthermore, it can be performed by laparoscopy in children as it is a safe procedure, offering the benefits of a minimally invasive approach. MATERIALS AND METHODS: The software VR-render LE version 0.81 is a system that enables the visualization of bidimentional 3D images with magnification of anatomical details. We have applied this system to five cases of non-parasitic splenic cysts before laparoscopic partial splenectomy. RESULTS: The images obtained with VR rendering software permitted the preoperative reconstruction of the vascularization of the splenic hilum, allowing the surgeon safe vessel control during laparoscopic procedures. All five partial splenectomies were carried out with no complications or major blood loss. CONCLUSIONS: Laparoscopic partial splenectomy should be a first choice procedure because it is feasible, reproducible, and safe for children; furthermore, it preserves enough splenic tissue thereby preventing post-splenectomy infections. Volume rendering provides high anatomical resolution and can be useful in guiding the surgical procedure.

Measurement and simulation of anisotropy in the Infrared and Raman spectra of beta-FeSi2 single crystals

In this paper we show that the orthorhombic phase of FeSi2 (stable at room temperature) displays a sizable anisotropy in the infrared spectra, with minor effects in the Raman data too. This fact is not trivial at all, since the crystal structure corresponds to a moderate distortion of the fluorite symmetry. Our analysis is carried out on small single crystals grown by flux transport, through polarization-resolved far-infrared reflectivity and Raman measurements. Their interpretation has been obtained by means of the simulated spectra with tight-binding molecular dynamics.

SIMSAFADIM-CLASTIC: A new approach to mathematical 3D forward simulation modelling for terrigenous and carbonate marine sedimentation

Most sedimentary modelling programs developed in recent years focus on either terrigenous or carbonate marine sedimentation. Nevertheless, only a few programs have attempted to consider mixed terrigenous-carbonate sedimentation, and most of these are two-dimensional, which is a major restriction since geological processes take place in 3D. This paper presents the basic concepts of a new 3D mathematical forward simulation model for clastic sediments, which was developed from SIMSAFADIM, a previous 3D carbonate sedimentation model. The new extended model, SIMSAFADIM-CLASTIC, simulates processes of autochthonous marine carbonate production and accumulation, together with clastic transport and sedimentation in three dimensions of both carbonate and terrigenous sediments. Other models and modelling strategies may also provide realistic and efficient tools for prediction of stratigraphic architecture and facies distribution of sedimentary deposits. However, SIMSAFADIM-CLASTIC becomes an innovative model that attempts to simulate different sediment types using a process-based approach, therefore being a useful tool for 3D prediction of stratigraphic architecture and facies distribution in sedimentary basins. This model is applied to the neogene Vallès-Penedès half-graben (western Mediterranean, NE Spain) to show the capacity of the program when applied to a realistic geologic situation involving interactions between terrigenous clastics and carbonate sediments.

Critical behavior of a system with orientational and positional degrees of freedom: A Monte Carlo simulation study

The critical behavior of a system constituted by molecules with a preferred symmetry axis is studied by means of a Monte Carlo simulation of a simplified two-dimensional model. The system exhibits two phase transitions, associated with the vanishing of the positional order of the center of mass of the molecules and with the orientational order of the symmetry axis. The evolution of the order parameters and the specific heat is also studied. The transition associated with the positional degrees of freedom is found to change from a second-order to a first-order behavior when the two phase transitions are close enough, due to the coupling with the orientational degrees of freedom. This fact is qualitatively compared with similar results found in pure liquid crystals and liquid-crystal mixtures.

Monte Carlo simulation of interface alloying

An Ising-like model, with interactions ranging up to next-nearest-neighbor pairs, is used to simulate the process of interface alloying. Interactions are chosen to stabilize an intermediate "antiferromagnetic" ordered structure. The dynamics proceeds exclusively by atom-vacancy exchanges. In order to characterize the process, the time evolution of the width of the intermediate ordered region and the diffusion length is studied. Both lengths are found to follow a power-law evolution with exponents depending on the characteristic features of the model.

Modeling premartensitic effects in Ni2MnGa: A mean-field and Monte Carlo simulation study

ic first-order transition line ending in a critical point. This critical point is responsible for the existence of large premartensitic fluctuations which manifest as broad peaks in the specific heat, not always associated with a true phase transition. The main conclusion is that premartensitic effects result from the interplay between the softness of the anomalous phonon driving the modulation and the magnetoelastic coupling. In particular, the premartensitic transition occurs when such coupling is strong enough to freeze the involved mode phonon. The implication of the results in relation to the available experimental data is discussed.

Landscape structure affects dispersal in the greater white-toothed shrew: inference between genetic and simulated ecological distances

Animal dispersal in a fragmented landscape depends on the complex interaction between landscape structure and animal behavior. To better understand how individuals disperse, it is important to explicitly represent the properties of organisms and the landscape in which they move. A common approach to modelling dispersal includes representing the landscape as a grid of equal sized cells and then simulating individual movement as a correlated random walk. This approach uses a priori scale of resolution, which limits the representation of all landscape features and how different dispersal abilities are modelled. We develop a vector-based landscape model coupled with an object-oriented model for animal dispersal. In this spatially explicit dispersal model, landscape features are defined based on their geographic and thematic properties and dispersal is modelled through consideration of an organism's behavior, movement rules and searching strategies (such as visual cues). We present the model's underlying concepts, its ability to adequately represent landscape features and provide simulation of dispersal according to different dispersal abilities. We demonstrate the potential of the model by simulating two virtual species in a real Swiss landscape. This illustrates the model's ability to simulate complex dispersal processes and provides information about dispersal such as colonization probability and spatial distribution of the organism's path

Application of Visualization and Simulation Program to Improve Work Zone Safety and Mobility, January 2010

A previous study sponsored by the Smart Work Zone Deployment Initiative, “Feasibility of Visualization and Simulation Applications to Improve Work Zone Safety and Mobility,” demonstrated the feasibility of combining readily available, inexpensive software programs, such as SketchUp and Google Earth, with standard two-dimensional civil engineering design programs, such as MicroStation, to create animations of construction work zones. The animations reflect changes in work zone configurations as the project progresses, representing an opportunity to visually present complex information to drivers, construction workers, agency personnel, and the general public. The purpose of this study is to continue the work from the previous study to determine the added value and resource demands created by including more complex data, specifically traffic volume, movement, and vehicle type. This report describes the changes that were made to the simulation, including incorporating additional data and converting the simulation from a desktop application to a web application.