Disseny i desenvolupament d’una aplicació web basada en software lliure per a la gestió d’incidències de les Vies Verdes de Girona

El present document és la memòria descriptiva dels treballs realitzats per la Laura Vergoñós Pascual durant el projecte final del Màster en Tecnologies de la Informació Geogràfica, 12a edició, durant el transcurs del conveni de col·labració entre el Departament de Geografia i el SIGTE (Servei d’Informació Geogràfica i Teledetecció). S’hi exposen la seqüència de tasques realitzades durant el desenvolupament d’una aplicació web basada en software lliure per a la gestió d’incidències de les Vies Verdes de Girona. Processos: construcció de la base de dades, disseny i anàlisi de requeriments de l’aplicació, solució de programació, resultats

Quantificació de l'error comès pels models de níxol ecològic al predir la distribució d'especies generalistes

Report for the scientific sojourn carried out at the University of California at Berkeley, from September to December 2007. Environmental niche modelling (ENM) techniques are powerful tools to predict species potential distributions. In the last ten years, a plethora of novel methodological approaches and modelling techniques have been developed. During three months, I stayed at the University of California, Berkeley, working under the supervision of Dr. David R. Vieites. The aim of our work was to quantify the error committed by these techniques, but also to test how an increase in the sample size affects the resultant predictions. Using MaxEnt software we generated distribution predictive maps, from different sample sizes, of the Eurasian quail (Coturnix coturnix) in the Iberian Peninsula. The quail is a generalist species from a climatic point of view, but an habitat specialist. The resultant distribution maps were compared with the real distribution of the species. This distribution was obtained from recent bird atlases from Spain and Portugal. Results show that ENM techniques can have important errors when predicting the species distribution of generalist species. Moreover, an increase of sample size is not necessary related with a better performance of the models. We conclude that a deep knowledge of the species’ biology and the variables affecting their distribution is crucial for an optimal modelling. The lack of this knowledge can induce to wrong conclusions.

Aplicación de la ingeniería software sobre la herramienta MATE Analyzer

MATE (Monitoring, Analysis and Tuning Environment) es un proyecto que surge en 2004 como tesis doctoral de Anna Sikora con el propósito de investigar la mejora de rendimiento de aplicaciones paralelas a través de la modificación dinámica. Nuestro proyecto supone un paso adelante en cuestiones de calidad de software y pretende dotar al proyecto MATE de una base de desarrollo sólida de cara a futuras lineas de trabajo. Para ello se hace frente a la problemática desde tres perspectivas: la creación de una metodología de desarrollo (y su aplicación sobre el proyecto existente), la implantación de un entorno de desarrollo de soporte y el desarrollo de nuevas características para favorecer la portabilidad y la usabilidad, entre otros aspectos.

Information systems for water resources management improvement in developing countries

Water resources management, as also water service provision projects in developing countries have difficulties to take adequate decisions due to scarce reliable information, and a lack of proper information managing. Some appropriate tools need to be developed in order to improve decision making to improve water management and access of the poorest, through the design of Decision Support Systems (DSS). On the one side, a DSS for developing co-operation projects on water access improvement has been developed. Such a tool has specific context constrains (structure of the system, software requirements) and needs (Logical Framework Approach monitoring, organizational-learning, accountability and evaluation) that shall be considered for its design. Key aspects for its successful implementation have appeared to be a participatory design of the system and support of the managerial positions at the inception phase. A case study in Tanzania was conducted, together with the Spanish NGO ONGAWA – Ingeniería para el Desarrollo. On the other side, DSS are required also to improve decision making on water management resources in order to achieve a sustainable development that not only improves the living conditions of the population in developing countries, but that also does not hinder opportunities of the poorest on those context. A DSS made to fulfil these requirements shall be using information from water resources modelling, as also on the environment and the social context. Through the research, a case study has been conducted in the Central Rift Valley of Ethiopia, an endhorreic basin 160 km south of Addis Ababa. There, water has been modelled using ArcSWAT, a physically based model which can assess the impact of land management practices on large complex watersheds with varying soils, land use and management conditions over long periods of time. Moreover, governance on water and environment as also the socioeconomic context have been studied.

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.

Gamma Knife, CyberKnife, TomoTherapy: gadgets or useful tools?

Purpose of reviewThis review provides information and an update on stereotactic radiosurgery (SRS) equipment, with a focus on intracranial lesions and brain neoplasms.Recent findingsGamma Knife radiosurgery represents the gold standard for intracranial radiosurgery, using a dedicated equipment, and has recently evolved with a newly designed technology, Leksell Gamma Knife Perfexion. Linear accelerator-based radiosurgery is more recent, and originally based on existing systems, either adapted or dedicated to radiosurgery. Equipment incorporating specific technologies, such as the robotic CyberKnife system, has been developed. Novel concepts in radiation therapy delivery techniques, such as intensity-modulated radiotherapy, were also developed; their integration with computed tomography imaging and helical delivery has led to the TomoTherapy system. Recent data on the management of intracranial tumors with radiosurgery illustrate the trend toward a larger use and acceptance of this therapeutic modality.SummarySRS has become an important alternative treatment for a variety of lesions. Each radiosurgery system has its advantages and limitations. The 'perfect' and ubiquitous system does not exist. The choice of a radiosurgery system may vary with the strategy and needs of specific radiosurgery programs. No center can afford to acquire every technology, and strategic choices have to be made. Institutions with large neurosurgery and radiation oncology programs usually have more than one system, allowing optimization of the management of patients with a choice of open neurosurgery, radiosurgery, and radiotherapy. Given its minimally invasive nature and increasing clinical acceptance, SRS will continue to progress and offer new advances as a therapeutic tool in neurosurgery and radiotherapy.

Maps as risk mitigation tools. Adaptation of the Swiss hazard assessment and mapping methodology to a Moroccan site: Beni Mellal

Dans le contexte climatique actuel, les régions méditerranéennes connaissent une intensification des phénomènes hydrométéorologiques extrêmes. Au Maroc, le risque lié aux inondations est devenu problématique, les communautés étant vulnérables aux événements extrêmes. En effet, le développement économique et urbain rapide et mal maîtrisé augmente l'exposition aux phénomènes extrêmes. La Direction du Développement et de la Coopération suisse (DDC) s'implique activement dans la réduction des risques naturels au Maroc. La cartographie des dangers et son intégration dans l'aménagement du territoire représentent une méthode efficace afin de réduire la vulnérabilité spatiale. Ainsi, la DDC a mandaté ce projet d'adaptation de la méthode suisse de cartographie des dangers à un cas d'étude marocain (la ville de Beni Mellal, région de Tadla-Azilal, Maroc). La méthode suisse a été adaptée aux contraintes spécifiques du terrain (environnement semi-aride, morphologie de piémont) et au contexte de transfert de connaissances (caractéristiques socio-économiques et pratiques). Une carte des phénomènes d'inondations a été produite. Elle contient les témoins morphologiques et les éléments anthropiques pertinents pour le développement et l'aggravation des inondations. La modélisation de la relation pluie-débit pour des événements de référence, et le routage des hydrogrammes de crue ainsi obtenus ont permis d'estimer quantitativement l'aléa inondation. Des données obtenues sur le terrain (estimations de débit, extension de crues connues) ont permis de vérifier les résultats des modèles. Des cartes d'intensité et de probabilité ont été obtenues. Enfin, une carte indicative du danger d'inondation a été produite sur la base de la matrice suisse du danger qui croise l'intensité et la probabilité d'occurrence d'un événement pour obtenir des degrés de danger assignables au territoire étudié. En vue de l'implémentation des cartes de danger dans les documents de l'aménagement du territoire, nous nous intéressons au fonctionnement actuel de la gestion institutionnelle du risque à Beni Mellal, en étudiant le degré d'intégration de la gestion et la manière dont les connaissances sur les risques influencent le processus de gestion. L'analyse montre que la gestion est marquée par une logique de gestion hiérarchique et la priorité des mesures de protection par rapport aux mesures passives d'aménagement du territoire. Les connaissances sur le risque restent sectorielles, souvent déconnectées. L'innovation dans le domaine de la gestion du risque résulte de collaborations horizontales entre les acteurs ou avec des sources de connaissances externes (par exemple les universités). Des recommandations méthodologiques et institutionnelles issues de cette étude ont été adressées aux gestionnaires en vue de l'implémentation des cartes de danger. Plus que des outils de réduction du risque, les cartes de danger aident à transmettre des connaissances vers le public et contribuent ainsi à établir une culture du risque. - Severe rainfall events are thought to be occurring more frequently in semi-arid areas. In Morocco, flood hazard has become an important topic, notably as rapid economic development and high urbanization rates have increased the exposure of people and assets in hazard-prone areas. The Swiss Agency for Development and Cooperation (SADC) is active in natural hazard mitigation in Morocco. As hazard mapping for urban planning is thought to be a sound tool for vulnerability reduction, the SADC has financed a project aimed at adapting the Swiss approach for hazard assessment and mapping to the case of Morocco. In a knowledge transfer context, the Swiss method was adapted to the semi-arid environment, the specific piedmont morphology and to socio-economic constraints particular to the study site. Following the Swiss guidelines, a hydro-geomorphological map was established, containing all geomorphic elements related to known past floods. Next, rainfall / runoff modeling for reference events and hydraulic routing of the obtained hydrographs were carried out in order to assess hazard quantitatively. Field-collected discharge estimations and flood extent for known floods were used to verify the model results. Flood hazard intensity and probability maps were obtained. Finally, an indicative danger map as defined within the Swiss hazard assessment terminology was calculated using the Swiss hazard matrix that convolves flood intensity with its recurrence probability in order to assign flood danger degrees to the concerned territory. Danger maps become effective, as risk mitigation tools, when implemented in urban planning. We focus on how local authorities are involved in the risk management process and how knowledge about risk impacts the management. An institutional vulnerability "map" was established based on individual interviews held with the main institutional actors in flood management. Results show that flood hazard management is defined by uneven actions and relationships, it is based on top-down decision-making patterns, and focus is maintained on active mitigation measures. The institutional actors embody sectorial, often disconnected risk knowledge pools, whose relationships are dictated by the institutional hierarchy. Results show that innovation in the risk management process emerges when actors collaborate despite the established hierarchy or when they open to outer knowledge pools (e.g. the academia). Several methodological and institutional recommendations were addressed to risk management stakeholders in view of potential map implementation to planning. Hazard assessment and mapping is essential to an integrated risk management approach: more than a mitigation tool, danger maps represent tools that allow communicating on hazards and establishing a risk culture.

Gene expression databases and data mining.

The DNA microarray technology has arguably caught the attention of the worldwide life science community and is now systematically supporting major discoveries in many fields of study. The majority of the initial technical challenges of conducting experiments are being resolved, only to be replaced with new informatics hurdles, including statistical analysis, data visualization, interpretation, and storage. Two systems of databases, one containing expression data and one containing annotation data are quickly becoming essential knowledge repositories of the research community. This present paper surveys several databases, which are considered "pillars" of research and important nodes in the network. This paper focuses on a generalized workflow scheme typical for microarray experiments using two examples related to cancer research. The workflow is used to reference appropriate databases and tools for each step in the process of array experimentation. Additionally, benefits and drawbacks of current array databases are addressed, and suggestions are made for their improvement.

Desarrollo de un softphone, implementación de una centralita basada en código libre e integración con herramienta CRM

El proyecto consiste en la creación mediante software libre de un sistema de telefonía corporativo, que ofrece la mayor parte de las funcionalidades de un sistema telefónico implantado en cualquier PYME de la actualidad y que tiene como elemento principal una centralita telefónica Asterisk, así como en el desarrollo de un softphone(teléfono software) utilizando el protocolo de señalización SIP, que explota gran parte de las funcionalidades que proporciona la centralita. Este sistema de telefonía tiene además la capacidad de integrarse con herramientas CRM a través de la importación de los contactos en el listín corporativo del softphone.

SwissDock, a protein-small molecule docking web service based on EADock DSS.

Most life science processes involve, at the atomic scale, recognition between two molecules. The prediction of such interactions at the molecular level, by so-called docking software, is a non-trivial task. Docking programs have a wide range of applications ranging from protein engineering to drug design. This article presents SwissDock, a web server dedicated to the docking of small molecules on target proteins. It is based on the EADock DSS engine, combined with setup scripts for curating common problems and for preparing both the target protein and the ligand input files. An efficient Ajax/HTML interface was designed and implemented so that scientists can easily submit dockings and retrieve the predicted complexes. For automated docking tasks, a programmatic SOAP interface has been set up and template programs can be downloaded in Perl, Python and PHP. The web site also provides an access to a database of manually curated complexes, based on the Ligand Protein Database. A wiki and a forum are available to the community to promote interactions between users. The SwissDock web site is available online at http://www.swissdock.ch. We believe it constitutes a step toward generalizing the use of docking tools beyond the traditional molecular modeling community.

Mòdul per a Moodle que possibilita la utilització de mapes conceptuals als creadors de cursos.

Actualment, i amb la ràpida expansió en el món educatiu de les plataformes d'aprenentatge virtual, s'experimenta una demanda de funcionalitats que puguen ser usades des d'aquestes plataformes i que donen resposta als reptes educatius dins d'aquest nou paradigma d'aprenentatge.En aquest treball s'ha fet una tasca d'integració d'eines que possibiliten la creació, modificació, visualització i magatzematge de mapes conceptuals dins d'una plataforma d'aprenentatge molt usada actualment, tant en ensenyament secundari com universitari. La plataforma moodle.L'eina per construir mapes conceptuals triada ha segut l'anomenada VUE, desenvolupada en la universitat de Tufts.Ambdues eines moodle i VUE s'han desenvolupat amb codi obert i baix llicències de programari lliure, així es poden tindre tots els avantatges que aquestes llicències proporcionen.El resultat és una integració que possibilita la utilització de mapes conceptuals dins de la plataforma moodle.

Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study.

The identification of genetically homogeneous groups of individuals is a long standing issue in population genetics. A recent Bayesian algorithm implemented in the software STRUCTURE allows the identification of such groups. However, the ability of this algorithm to detect the true number of clusters (K) in a sample of individuals when patterns of dispersal among populations are not homogeneous has not been tested. The goal of this study is to carry out such tests, using various dispersal scenarios from data generated with an individual-based model. We found that in most cases the estimated 'log probability of data' does not provide a correct estimation of the number of clusters, K. However, using an ad hoc statistic DeltaK based on the rate of change in the log probability of data between successive K values, we found that STRUCTURE accurately detects the uppermost hierarchical level of structure for the scenarios we tested. As might be expected, the results are sensitive to the type of genetic marker used (AFLP vs. microsatellite), the number of loci scored, the number of populations sampled, and the number of individuals typed in each sample.

Software de gestión de reclamaciones y denuncias on-line

Alta y gestión de reclamaciones de consumo a través de la web.