MyHits: improvements to an interactive resource for analyzing protein sequences.

The MyHits web site (http://myhits.isb-sib.ch) is an integrated service dedicated to the analysis of protein sequences. Since its first description in 2004, both the user interface and the back end of the server were improved. A number of tools (e.g. MAFFT, Jacop, Dotlet, Jalview, ESTScan) were added or updated to improve the usability of the service. The MySQL schema and its associated API were revamped and the database engine (HitKeeper) was separated from the web interface. This paper summarizes the current status of the server, with an emphasis on the new services.

Implementing interactive computing in an object-oriented environment

Statistical computing when input/output is driven by a Graphical User Interface is considered. A proposal is made for automatic control ofcomputational flow to ensure that only strictly required computationsare actually carried on. The computational flow is modeled by a directed graph for implementation in any object-oriented programming language with symbolic manipulation capabilities. A complete implementation example is presented to compute and display frequency based piecewise linear density estimators such as histograms or frequency polygons.

Calculation of radio electrical coverage in Medium-Wave Frequencies

The aim of this project is to accomplish an application software based on Matlab to calculate the radioelectrical coverage by surface wave of broadcast radiostations in the band of Medium Wave (WM) all around the world. Also, given the location of a transmitting and a receiving station, the software should be able to calculate the electric field that the receiver should receive at that specific site. In case of several transmitters, the program should search for the existence of Inter-Symbol Interference, and calculate the field strenght accordingly. The application should ask for the configuration parameters of the transmitter radiostation within a Graphical User Interface (GUI), and bring back the resulting coverage above a map of the area under study. For the development of this project, it has been used several conductivity databases of different countries, and a high-resolution elevation database (GLOBE). Also, to calculate the field strenght due to groundwave propagation, it has been used ITU GRWAVE program, which must be integrated into a Matlab interface to be used by the application developed.

Programació d'una aplicació gràfica per l'anàlisi de senyals usant LDB (Local Discriminant Bases) i MLDB (Modified LDB)

Tot seguit presentem un entorn per analitzar senyals de tot tipus amb LDB (Local Discriminant Bases) i MLDB (Modified Local Discriminant Bases). Aquest entorn utilitza funcions desenvolupades en el marc d’una tesi en fase de desenvolupament. Per entendre part d’aquestes funcions es requereix un nivell de coneixement avançat de processament de senyals. S’han extret dels treballs realitzats per Naoki Saito [3], que s’han agafat com a punt de partida per la realització de l’algorisme de la tesi doctoral no finalitzada de Jose Antonio Soria. Aquesta interfície desenvolupada accepta la incorporació de nous paquets i funcions. Hem deixat un menú preparat per integrar Sinus IV packet transform i Cosine IV packet transform, tot i que també podem incorporar-n’hi altres. L’aplicació consta de dues interfícies, un Assistent i una interfície principal. També hem creat una finestra per importar i exportar les variables desitjades a diferents entorns. Per fer aquesta aplicació s’han programat tots els elements de les finestres, en lloc d’utilitzar el GUIDE (Graphical User Interface Development Enviroment) de MATLAB, per tal que sigui compatible entre les diferents versions d’aquest programa. En total hem fet 73 funcions en la interfície principal (d’aquestes, 10 pertanyen a la finestra d’importar i exportar) i 23 en la de l’Assistent. En aquest treball només explicarem 6 funcions i les 3 de creació d’aquestes interfícies per no fer-lo excessivament extens. Les funcions que explicarem són les més importants, ja sigui perquè s’utilitzen sovint, perquè, segons la complexitat McCabe, són les més complicades o perquè són necessàries pel processament del senyal. Passem cada entrada de dades per part de l’usuari per funcions que ens detectaran errors en aquesta entrada, com eliminació de zeros o de caràcters que no siguin números, com comprovar que són enters o que estan dins dels límits màxims i mínims que li pertoquen.

Programa d'anàlisi d'imatges de provetes metal·logràfiques

L’objectiu del present TFM és explorar les possibilitats del programa matemàtic MATLAB i la seva eina Entorn de Disseny d’Interfícies Gràfiques d’Usuari (GUIDE), desenvolupant un programa d’anàlisi d’imatges de provetes metal·logràfiques que es pugui utilitzar per a realitzar pràctiques de laboratori de l’assignatura Tecnologia de Materials de la titulació de Grau en Enginyeria Mecatrònica que s’imparteix a la Universitat de Vic. Les àrees d’interès del treball són la Instrumentació Virtual, la programació MATLAB i les tècniques d’anàlisi d’imatges metal·logràfiques. En la memòria es posa un èmfasi especial en el disseny de la interfície i dels procediments per a efectuar les mesures. El resultat final és un programa que satisfà tots els requeriments que s’havien imposat en la proposta inicial. La interfície del programa és clara i neta, destinant molt espai a la imatge que s’analitza. L’estructura i disposició dels menús i dels comandaments ajuda a que la utilització del programa sigui fàcil i intuïtiva. El programa s’ha estructurat de manera que sigui fàcilment ampliable amb altres rutines de mesura, o amb l’automatització de les rutines existents. Al tractar-se d’un programa que funciona com un instrument de mesura, es dedica un capítol sencer de la memòria a mostrar el procediment de càlcul dels errors que s’ocasionen durant la seva utilització, amb la finalitat de conèixer el seu ordre de magnitud, i de saber-los calcular de nou en cas que variïn les condicions d’utilització. Pel que fa referència a la programació, malgrat que MATLAB no sigui un entorn de programació clàssic, sí que incorpora eines que permeten fer aplicacions no massa complexes, i orientades bàsicament a gràfics o a imatges. L’eina GUIDE simplifica la realització de la interfície d’usuari, malgrat que presenta problemes per tractar dissenys una mica complexos. Per altra banda, el codi generat per GUIDE no és accessible, cosa que no permet modificar manualment la interfície en aquells casos en els que GUIDE té problemes. Malgrat aquests petits problemes, la potència de càlcul de MATLAB compensa sobradament aquestes deficiències.

A rapid and effective vignetting correction for quantitative microscopy

Images acquired using optical microscopes are inherently subject to vignetting effects due to imperfect illumination and image acquisition. However, such vignetting effects hamper accurate extraction of quantitative information from biological images, leading to less effective image segmentation and increased noise in the measurements. Here, we describe a rapid and effective method for vignetting correction, which generates an estimate for a correction function from the background fluorescence without the need to acquire additional calibration images. We validate the usefulness of this algorithm using artificially distorted images as a gold standard for assessing the accuracy of the applied correction and then demonstrate that this correction method enables the reliable detection of biologically relevant variation in cell populations. A simple user interface called FlattifY was developed and integrated into the image analysis platform YeastQuant to facilitate easy application of vignetting correction to a wide range of images.

Genome-wide DNA polymorphism analyses using VariScan

BACKGROUND: DNA sequence polymorphisms analysis can provide valuable information on the evolutionary forces shaping nucleotide variation, and provides an insight into the functional significance of genomic regions. The recent ongoing genome projects will radically improve our capabilities to detect specific genomic regions shaped by natural selection. Current available methods and software, however, are unsatisfactory for such genome-wide analysis. RESULTS: We have developed methods for the analysis of DNA sequence polymorphisms at the genome-wide scale. These methods, which have been tested on a coalescent-simulated and actual data files from mouse and human, have been implemented in the VariScan software package version 2.0. Additionally, we have also incorporated a graphical-user interface. The main features of this software are: i) exhaustive population-genetic analyses including those based on the coalescent theory; ii) analysis adapted to the shallow data generated by the high-throughput genome projects; iii) use of genome annotations to conduct a comprehensive analyses separately for different functional regions; iv) identification of relevant genomic regions by the sliding-window and wavelet-multiresolution approaches; v) visualization of the results integrated with current genome annotations in commonly available genome browsers. CONCLUSION: VariScan is a powerful and flexible suite of software for the analysis of DNA polymorphisms. The current version implements new algorithms, methods, and capabilities, providing an important tool for an exhaustive exploratory analysis of genome-wide DNA polymorphism data.

ConnectomeViewer - Multi-Modal Multi-Level Network Visualization and Analysis.

Introduction: The field of Connectomic research is growing rapidly, resulting from methodological advances in structural neuroimaging on many spatial scales. Especially progress in Diffusion MRI data acquisition and processing made available macroscopic structural connectivity maps in vivo through Connectome Mapping Pipelines (Hagmann et al, 2008) into so-called Connectomes (Hagmann 2005, Sporns et al, 2005). They exhibit both spatial and topological information that constrain functional imaging studies and are relevant in their interpretation. The need for a special-purpose software tool for both clinical researchers and neuroscientists to support investigations of such connectome data has grown. Methods: We developed the ConnectomeViewer, a powerful, extensible software tool for visualization and analysis in connectomic research. It uses the novel defined container-like Connectome File Format, specifying networks (GraphML), surfaces (Gifti), volumes (Nifti), track data (TrackVis) and metadata. Usage of Python as programming language allows it to by cross-platform and have access to a multitude of scientific libraries. Results: Using a flexible plugin architecture, it is possible to enhance functionality for specific purposes easily. Following features are already implemented: * Ready usage of libraries, e.g. for complex network analysis (NetworkX) and data plotting (Matplotlib). More brain connectivity measures will be implemented in a future release (Rubinov et al, 2009). * 3D View of networks with node positioning based on corresponding ROI surface patch. Other layouts possible. * Picking functionality to select nodes, select edges, get more node information (ConnectomeWiki), toggle surface representations * Interactive thresholding and modality selection of edge properties using filters * Arbitrary metadata can be stored for networks, thereby allowing e.g. group-based analysis or meta-analysis. * Python Shell for scripting. Application data is exposed and can be modified or used for further post-processing. * Visualization pipelines using filters and modules can be composed with Mayavi (Ramachandran et al, 2008). * Interface to TrackVis to visualize track data. Selected nodes are converted to ROIs for fiber filtering The Connectome Mapping Pipeline (Hagmann et al, 2008) processed 20 healthy subjects into an average Connectome dataset. The Figures show the ConnectomeViewer user interface using this dataset. Connections are shown that occur in all 20 subjects. The dataset is freely available from the homepage (connectomeviewer.org). Conclusions: The ConnectomeViewer is a cross-platform, open-source software tool that provides extensive visualization and analysis capabilities for connectomic research. It has a modular architecture, integrates relevant datatypes and is completely scriptable. Visit www.connectomics.org to get involved as user or developer.

Plantilla genèrica per webs d'AMPES

Generació d'una plantilla genèrica per AMPES seguint el disseny centrat en l'usuari.

Diseño centrado en el usuario y usabilidad en un entorno web para la iniciación en las TIC's

Elaboración de un prototipo de alto nivel a través del diseño centrado en el usuario (DCU) y la usabilidad de una página web destinada a la iniciación en las nuevas tecnologías.

Three essays on major trends in a slow clockspeed industry : the case of industrial automation

The motivation for this research initiated from the abrupt rise and fall of minicomputers which were initially used both for industrial automation and business applications due to their significantly lower cost than their predecessors, the mainframes. Later industrial automation developed its own vertically integrated hardware and software to address the application needs of uninterrupted operations, real-time control and resilience to harsh environmental conditions. This has led to the creation of an independent industry, namely industrial automation used in PLC, DCS, SCADA and robot control systems. This industry employs today over 200'000 people in a profitable slow clockspeed context in contrast to the two mainstream computing industries of information technology (IT) focused on business applications and telecommunications focused on communications networks and hand-held devices. Already in 1990s it was foreseen that IT and communication would merge into one Information and communication industry (ICT). The fundamental question of the thesis is: Could industrial automation leverage a common technology platform with the newly formed ICT industry? Computer systems dominated by complex instruction set computers (CISC) were challenged during 1990s with higher performance reduced instruction set computers (RISC). RISC started to evolve parallel to the constant advancement of Moore's law. These developments created the high performance and low energy consumption System-on-Chip architecture (SoC). Unlike to the CISC processors RISC processor architecture is a separate industry from the RISC chip manufacturing industry. It also has several hardware independent software platforms consisting of integrated operating system, development environment, user interface and application market which enables customers to have more choices due to hardware independent real time capable software applications. An architecture disruption merged and the smartphone and tablet market were formed with new rules and new key players in the ICT industry. Today there are more RISC computer systems running Linux (or other Unix variants) than any other computer system. The astonishing rise of SoC based technologies and related software platforms in smartphones created in unit terms the largest installed base ever seen in the history of computers and is now being further extended by tablets. An underlying additional element of this transition is the increasing role of open source technologies both in software and hardware. This has driven the microprocessor based personal computer industry with few dominating closed operating system platforms into a steep decline. A significant factor in this process has been the separation of processor architecture and processor chip production and operating systems and application development platforms merger into integrated software platforms with proprietary application markets. Furthermore the pay-by-click marketing has changed the way applications development is compensated: Three essays on major trends in a slow clockspeed industry: The case of industrial automation 2014 freeware, ad based or licensed - all at a lower price and used by a wider customer base than ever before. Moreover, the concept of software maintenance contract is very remote in the app world. However, as a slow clockspeed industry, industrial automation has remained intact during the disruptions based on SoC and related software platforms in the ICT industries. Industrial automation incumbents continue to supply systems based on vertically integrated systems consisting of proprietary software and proprietary mainly microprocessor based hardware. They enjoy admirable profitability levels on a very narrow customer base due to strong technology-enabled customer lock-in and customers' high risk leverage as their production is dependent on fault-free operation of the industrial automation systems. When will this balance of power be disrupted? The thesis suggests how industrial automation could join the mainstream ICT industry and create an information, communication and automation (ICAT) industry. Lately the Internet of Things (loT) and weightless networks, a new standard leveraging frequency channels earlier occupied by TV broadcasting, have gradually started to change the rigid world of Machine to Machine (M2M) interaction. It is foreseeable that enough momentum will be created that the industrial automation market will in due course face an architecture disruption empowered by these new trends. This thesis examines the current state of industrial automation subject to the competition between the incumbents firstly through a research on cost competitiveness efforts in captive outsourcing of engineering, research and development and secondly researching process re- engineering in the case of complex system global software support. Thirdly we investigate the industry actors', namely customers, incumbents and newcomers, views on the future direction of industrial automation and conclude with our assessments of the possible routes industrial automation could advance taking into account the looming rise of the Internet of Things (loT) and weightless networks. Industrial automation is an industry dominated by a handful of global players each of them focusing on maintaining their own proprietary solutions. The rise of de facto standards like IBM PC, Unix and Linux and SoC leveraged by IBM, Compaq, Dell, HP, ARM, Apple, Google, Samsung and others have created new markets of personal computers, smartphone and tablets and will eventually also impact industrial automation through game changing commoditization and related control point and business model changes. This trend will inevitably continue, but the transition to a commoditized industrial automation will not happen in the near future.

Efficacy of modern antipsychotics in placebo-controlled trials in bipolar depression: a meta-analysis.

Randomized, controlled trials have demonstrated efficacy for second-generation antipsychotics in the treatment of acute mania in bipolar disorder. Despite depression being considered the hallmark of bipolar disorder, there are no published systematic reviews or meta-analyses to evaluate the efficacy of modern atypical antipsychotics in bipolar depression. We systematically reviewed published or registered randomized, double-blind, placebo-controlled trials (RCTs) of modern antipsychotics in adult bipolar I and/or II depressive patients (DSM-IV criteria). Efficacy outcomes were assessed based on changes in the Montgomery-Asberg Depression Rating Scale (MADRS) during an 8-wk period. Data were combined through meta-analysis using risk ratio as an effect size with a 95% confidence interval (95% CI) and with a level of statistical significance of 5% (p<0.05). We identified five RCTs; four involved antipsychotic monotherapy and one addressed both monotherapy and combination with an antidepressant. The two quetiapine trials analysed the safety and efficacy of two doses: 300 and 600 mg/d. The only olanzapine trial assessed olanzapine monotherapy within a range of 5-20 mg/d and olanzapine-fluoxetine combination within a range of 5-20 mg/d and 6-12 mg/d, respectively. The two aripiprazole placebo-controlled trials assessed doses of 5-30 mg/d. Quetiapine and olanzapine trials (3/5, 60%) demonstrated superiority over placebo (p<0.001). Only 2/5 (40%) (both aripiprazole trials) failed in the primary efficacy measure after the first 6 wk. Some modern antipsychotics (quetiapine and olanzapine) have demonstrated efficacy in bipolar depressive patients from week 1 onwards. Rapid onset of action seems to be a common feature of atypical antipsychotics in bipolar depression. Comment in The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface controlEfficacy of modern antipsychotics in placebo-controlled trials in bipolar depression: a meta-analysis--results to be interpreted with caution.

Genome-wide DNA polymorphism analyses using VariScan

BACKGROUND: DNA sequence polymorphisms analysis can provide valuable information on the evolutionary forces shaping nucleotide variation, and provides an insight into the functional significance of genomic regions. The recent ongoing genome projects will radically improve our capabilities to detect specific genomic regions shaped by natural selection. Current available methods and software, however, are unsatisfactory for such genome-wide analysis. RESULTS: We have developed methods for the analysis of DNA sequence polymorphisms at the genome-wide scale. These methods, which have been tested on a coalescent-simulated and actual data files from mouse and human, have been implemented in the VariScan software package version 2.0. Additionally, we have also incorporated a graphical-user interface. The main features of this software are: i) exhaustive population-genetic analyses including those based on the coalescent theory; ii) analysis adapted to the shallow data generated by the high-throughput genome projects; iii) use of genome annotations to conduct a comprehensive analyses separately for different functional regions; iv) identification of relevant genomic regions by the sliding-window and wavelet-multiresolution approaches; v) visualization of the results integrated with current genome annotations in commonly available genome browsers. CONCLUSION: VariScan is a powerful and flexible suite of software for the analysis of DNA polymorphisms. The current version implements new algorithms, methods, and capabilities, providing an important tool for an exhaustive exploratory analysis of genome-wide DNA polymorphism data.

Projecte Digital Look

Projecte de final de carrera basat en la creació de 3 prototips (aplicació mòbil, web i software d'escriptori) per gestionar un centre d'estudis de perruqueria. El desenvolupament és sempre des del punt de vista del disseny centrat en l'usuari.

Usabilidad de una biblioteca online con diseño centrado en el usuario

This thesis deals the aspects of usability and design of a web from a user's point of view. The thesis will examine the elements comprised in the development of a web (the human and technological aspects and how the interact). It will explain in depth how to approach these issues correctly or incorrectly, how to avoid dealing with them incorrectly and how to find a happy medium, which is as they say where the virtue lays. The thesis is completed with the practical example of a creation of a web site (the MARK'S SCIENCE on-line library).