PAnalyzer: A software tool for protein inference in shotgun proteomics

Background Protein inference from peptide identifications in shotgun proteomics must deal with ambiguities that arise due to the presence of peptides shared between different proteins, which is common in higher eukaryotes. Recently data independent acquisition (DIA) approaches have emerged as an alternative to the traditional data dependent acquisition (DDA) in shotgun proteomics experiments. MSE is the term used to name one of the DIA approaches used in QTOF instruments. MSE data require specialized software to process acquired spectra and to perform peptide and protein identifications. However the software available at the moment does not group the identified proteins in a transparent way by taking into account peptide evidence categories. Furthermore the inspection, comparison and report of the obtained results require tedious manual intervention. Here we report a software tool to address these limitations for MSE data. Results In this paper we present PAnalyzer, a software tool focused on the protein inference process of shotgun proteomics. Our approach considers all the identified proteins and groups them when necessary indicating their confidence using different evidence categories. PAnalyzer can read protein identification files in the XML output format of the ProteinLynx Global Server (PLGS) software provided by Waters Corporation for their MSE data, and also in the mzIdentML format recently standardized by HUPO-PSI. Multiple files can also be read simultaneously and are considered as technical replicates. Results are saved to CSV, HTML and mzIdentML (in the case of a single mzIdentML input file) files. An MSE analysis of a real sample is presented to compare the results of PAnalyzer and ProteinLynx Global Server. Conclusions We present a software tool to deal with the ambiguities that arise in the protein inference process. Key contributions are support for MSE data analysis by ProteinLynx Global Server and technical replicates integration. PAnalyzer is an easy to use multiplatform and free software tool.

Aprendizaje basado en proyectos aplicado a la asignatura Ingeniería del software : guía del docente y guía del estudiante

Este informe recoge las guías del docente y del estudiante para la puesta en marcha, seguimiento continuo y evaluación de la asignatura Ingeniería del Software del segundo curso del Grado en Ingeniería Informática. Todo ello basado en metodologías activas, concretamente la metodología de Aprendizaje Basado en Proyectos (ABP, o PBL de Project Based Learning). El trabajo publicado en este informe es el resultado obtenido por los autores dentro del programa de formación del profesorado en metodologías activas (ERAGIN), auspiciado por el Vicerrectorado de Calidad e Innovación Docente de la Universidad del País Vasco (UPV/EHU).

Implantar un Sistema de Gestion Integral en Software libre

El proyecto de fin de carrera “Implantar un Sistema de Gestión Integral en Software libre” se ha desarrollado en la empresa Avanzosc con sede en Azkoitia. Una peculiaridad del proyecto es que a su vez se ha utilizado como cliente otra empresa, q2K, Soluciones Informáticas en Gestión Estratégica. El objetivo del proyecto es implantar en q2K un sistema de planificación de recursos empresariales (ERP, Enterprise Resource Planning), esto le permite reunir en una única aplicación todos los procesos de negocio de la empresa. La implantación de un ERP requiere de una importante inversión ya que el coste de la licencia de un sistema ERP propietario es elevado. Una interesante alternativa para evitar este desembolso es optar por un de ERP de software libre con todas las ventajas de configuración y personalización. En nuestro caso se ha adoptado OpenERP que es un software integral, modular y adaptable, adecuado para pequeñas y medianas empresas. El desarrollo del proyecto ha estado supervisado por el equipo de trabajo de Avanzosc, empresa líder en España en implantación de OpenErp, siguiendo la metodología de trabajo propia de esta empresa.

Invariant-free deduction systems for temporal logic

In this thesis we propose a new approach to deduction methods for temporal logic. Our proposal is based on an inductive definition of eventualities that is different from the usual one. On the basis of this non-customary inductive definition for eventualities, we first provide dual systems of tableaux and sequents for Propositional Linear-time Temporal Logic (PLTL). Then, we adapt the deductive approach introduced by means of these dual tableau and sequent systems to the resolution framework and we present a clausal temporal resolution method for PLTL. Finally, we make use of this new clausal temporal resolution method for establishing logical foundations for declarative temporal logic programming languages. The key element in the deduction systems for temporal logic is to deal with eventualities and hidden invariants that may prevent the fulfillment of eventualities. Different ways of addressing this issue can be found in the works on deduction systems for temporal logic. Traditional tableau systems for temporal logic generate an auxiliary graph in a first pass.Then, in a second pass, unsatisfiable nodes are pruned. In particular, the second pass must check whether the eventualities are fulfilled. The one-pass tableau calculus introduced by S. Schwendimann requires an additional handling of information in order to detect cyclic branches that contain unfulfilled eventualities. Regarding traditional sequent calculi for temporal logic, the issue of eventualities and hidden invariants is tackled by making use of a kind of inference rules (mainly, invariant-based rules or infinitary rules) that complicates their automation. A remarkable consequence of using either a two-pass approach based on auxiliary graphs or aone-pass approach that requires an additional handling of information in the tableau framework, and either invariant-based rules or infinitary rules in the sequent framework, is that temporal logic fails to carry out the classical correspondence between tableaux and sequents. In this thesis, we first provide a one-pass tableau method TTM that instead of a graph obtains a cyclic tree to decide whether a set of PLTL-formulas is satisfiable. In TTM tableaux are classical-like. For unsatisfiable sets of formulas, TTM produces tableaux whose leaves contain a formula and its negation. In the case of satisfiable sets of formulas, TTM builds tableaux where each fully expanded open branch characterizes a collection of models for the set of formulas in the root. The tableau method TTM is complete and yields a decision procedure for PLTL. This tableau method is directly associated to a one-sided sequent calculus called TTC. Since TTM is free from all the structural rules that hinder the mechanization of deduction, e.g. weakening and contraction, then the resulting sequent calculus TTC is also free from this kind of structural rules. In particular, TTC is free of any kind of cut, including invariant-based cut. From the deduction system TTC, we obtain a two-sided sequent calculus GTC that preserves all these good freeness properties and is finitary, sound and complete for PLTL. Therefore, we show that the classical correspondence between tableaux and sequent calculi can be extended to temporal logic. The most fruitful approach in the literature on resolution methods for temporal logic, which was started with the seminal paper of M. Fisher, deals with PLTL and requires to generate invariants for performing resolution on eventualities. In this thesis, we present a new approach to resolution for PLTL. The main novelty of our approach is that we do not generate invariants for performing resolution on eventualities. Our method is based on the dual methods of tableaux and sequents for PLTL mentioned above. Our resolution method involves translation into a clausal normal form that is a direct extension of classical CNF. We first show that any PLTL-formula can be transformed into this clausal normal form. Then, we present our temporal resolution method, called TRS-resolution, that extends classical propositional resolution. Finally, we prove that TRS-resolution is sound and complete. In fact, it finishes for any input formula deciding its satisfiability, hence it gives rise to a new decision procedure for PLTL. In the field of temporal logic programming, the declarative proposals that provide a completeness result do not allow eventualities, whereas the proposals that follow the imperative future approach either restrict the use of eventualities or deal with them by calculating an upper bound based on the small model property for PLTL. In the latter, when the length of a derivation reaches the upper bound, the derivation is given up and backtracking is used to try another possible derivation. In this thesis we present a declarative propositional temporal logic programming language, called TeDiLog, that is a combination of the temporal and disjunctive paradigms in Logic Programming. We establish the logical foundations of our proposal by formally defining operational and logical semantics for TeDiLog and by proving their equivalence. Since TeDiLog is, syntactically, a sublanguage of PLTL, the logical semantics of TeDiLog is supported by PLTL logical consequence. The operational semantics of TeDiLog is based on TRS-resolution. TeDiLog allows both eventualities and always-formulas to occur in clause heads and also in clause bodies. To the best of our knowledge, TeDiLog is the first declarative temporal logic programming language that achieves this high degree of expressiveness. Since the tableau method presented in this thesis is able to detect that the fulfillment of an eventuality is prevented by a hidden invariant without checking for it by means of an extra process, since our finitary sequent calculi do not include invariant-based rules and since our resolution method dispenses with invariant generation, we say that our deduction methods are invariant-free.

Cine Digital y sus Contenedores. Herramientas de Software libre basadas en las Especificaciones DCI

El Cine Digital es aquel que utiliza la tecnología digital para grabar, distribuir y proyectar películas. En los años 90, el cine comenzó un proceso de transición, del soporte fílmico a la tecnología digital. Pero el salto definitivo se dio con las grandes superproducciones de principios del 2000. Con este cambio de era y debido a la rápida difusión del digital y la proliferación de formatos se creo el DCI (Digital Cinema Initiative), para cambiar el modo en que las personas consumen cine. Trabajando junto con los miembros del comité SMPTE (Organización americana encargada de crear los estándares de la industria audiovisual formada por ingenieros, técnicos y fabricantes) publicó un sistema de especificaciones que han adoptado las mayores productoras estadounidenses. Mediante este acuerdo, aseguraban la calidad técnica de las producciones, la compatibilidad entre sistemas y como no, su hegemonía particular. Entre las especificaciones técnicas que suscribieron que son la base actual del DCI figuran la resolución de fotograma, el espacio de color, la compresión de imagen, la encriptación y el método de empaquetado de archivos. Y hoy en día son un estándar en la masterización, distribución y en la proyección final en las salas de cine. Una de las grandes esperanzas que hay puestas en la tecnología digital es la democratización en el mundo del cine y la supuesta abolición de las barreras económicas a la hora de realizar películas, dado lo barato que puede resultar la grabación digital y la posibilidad de pasar el material a video y editarlo en un ordenador domestico. Independientemente de los sistemas de edición que se utilicen, el formato de archivo o incluso el códec usado, los servidores de cine digital solo aceptan un tipo de archivo llamado DCP (Digital Cinema Package). Hay que aclarar que el DCP es abierto, documentado y que esta basado en los estándares SMPTE. Por lo tanto, existen en el mercado actual herramientas de software libre que permiten crear un DCP válido según las normas del DCI y compatible con los actuales servidores de cine digital. El propósito de este proyecto principalmente es documentar desde un punto de vista técnico la creación de un archivo DCP y analizar las diferentes herramientas existentes en el mercado para poder realizarlo: tanto las de uso comercial, como las de software libre. Como base se partirá de las aplicaciones creadas por la empresa alemana Fraunhofer (EasyDCP Creator, Player) - es el software utilizado en el estudio REC - y de otras herramientas más rudimentarias y escritas en C++ como (asdcplib) de Cinecert.

Reuse of software components orientated to iOS mobile devices

Within the next few pages, I will try to give a wide description of the project that I have been doing for IK4-Ikerlan. For the last six months, I have been working in developing a socket-based application for Apple devices. These devices work under the iOS operative system, which is programmed in Objective-C, a language similar to C. Although I did not have the chance to develop this application for Apple TV, I was able to create an application for iPhone and another one for iPad. The only difference between both applications was the screen resolution, but we decided to make them separately, as it would be really hard to combine both resolutions, and wallpapers, everything in the same workspace. Finally, it is necessary to add that the main goal was not to create a new application for iOS, but to translate an Android application into iOS. To achieve this, it is required to translate Java code into Objective- C, which is the language used to develop applications for all kinds of Apple devices. Fortunately, there is a tool created by Google, which helped us with this exercise. This tool is called j2ObjC, and it is still being developed.

Software de control desarrollado en ROS para teleoperar de manera eficiente el robot Kuka Lightweight mediante el háptico Phantom Omni

La teleoperación o telerobótica es un campo de la robótica que se basa en el control remoto de robots esclavo por parte de un usuario encargado de gobernar, mediante un dispositivo maestro, la fuerza y movimiento del robot. Sobre dicho usuario recaen también las tareas de percepción del entorno, planificación y manipulación compleja. Concretamente se pretende desarrollar el control software necesario para teleoperar un manipulador esclavo, Kuka Lightweigh mediante un dispositivo háptico Phamton Omni, que se comporta como maestro, sin que afecten las diferencias dinámicas y estructurales existentes entre ambos dispositivos, aportando información adicional al operador para facilitar la operación. La principal motivación de la evolución de esta tecnología se debe a la necesidad de realizar trabajos en entornos hostiles, de difícil acceso, o perjudiciales para la salud del usuario.

Aprendizaje Basado en Proyectos para la asignatura Ingeniería del Software

Duración (en horas): Más de 50 horas. Destinatario: Estudiante y Docente

Detection of Atomic Scale Changes in the Free Volume Void Size of Three-Dimensional Colorectal Cancer Cell Culture Using Positron Annihilation Lifetime Spectroscopy

5 p.

Metal-Free Polymethyl Methacrylate (PMMA) Nanoparticles by Enamine "Click" Chemistry at Room Temperature

"Click" chemistry has become an efficient avenue to unimolecular polymeric nanoparticles through the self-crosslinking of individual polymer chains containing appropriate functional groups. Herein we report the synthesis of ultra-small (7 nm in size) polymethyl methacrylate (PMMA) nanoparticles (NPs) by the "metal-free" cross-linking of PMMA-precursor chains prepared by reversible addition-fragmentation chain transfer (RAFT) polymerization containing beta-ketoester functional groups. Intramolecular collapse was performed by the one-pot reaction of beta-ketoester moieties with alkyl diamines in tetrahydrofurane at r.t. (i.e., by enamine formation). The collapsing process was followed by size exclusion chromatography and by nuclear magnetic resonance spectroscopy. The size of the resulting PMMA-NPs was determined by dynamic light scattering. Enamine "click" chemistry increases the synthetic toolbox for the efficient synthesis of metal-free, ultra-small polymeric NPs.

Novel Papillomaviruses in Free-Ranging Iberian Bats: No Virus-Host Co-evolution, No Strict Host Specificity, and Hints for Recombination

Papillomaviruses (PVs) are widespread pathogens. However, the extent of PV infections in bats remains largely unknown. This work represents the first comprehensive study of PVs in Iberian bats. We identified four novel PVs in the mucosa of free-ranging Eptesicus serotinus (EserPV1, EserPV2, and EserPV3) and Rhinolophus ferrumequinum (RferPV1) individuals and analyzed their phylogenetic relationships within the viral family. We further assessed their prevalence in different populations of E. serotinus and its close relative E. isabellinus. Although it is frequent to read that PVs co-evolve with their host, that PVs are highly species-specific, and that PVs do not usually recombine, our results suggest otherwise. First, strict virus-host co-evolution is rejected by the existence of five, distantly related bat PV lineages and by the lack of congruence between bats and bat PVs phylogenies. Second, the ability of EserPV2 and EserPV3 to infect two different bat species (E. serotinus and E. isabellinus) argues against strict host specificity. Finally, the description of a second noncoding region in the RferPV1 genome reinforces the view of an increased susceptibility to recombination in the E2-L2 genomic region. These findings prompt the question of whether the prevailing paradigms regarding PVs evolution should be reconsidered.

Chemosensory response of marine flagellate towards L- and D- dissolved free amino acids generated during heavy grazing on bacteria

This study investigated the generation of dissolved free amino acids (DFAA) by the bacterivorous flagellate Rhynchomonas nasuta when feeding on abundant prey. Specifically, it examined whether this flagellate protist exhibits a chemosensory response towards those amino acids. The concentrations of glycine and the and D-enantiomers of glutamate, serine, threonine, alanine, and leucine were determined in co-cultures of the flagellate and bacteria. Glycine, L- and D-alanine, and L-serine were found to accumulate under these conditions in amounts that correlated positively with flagellate abundance, suggesting that protists are involved in their generation. Investigations of the chemotactic response of young and old foraging protists to the same amino acids, offered in concentrations similar to those previously generated, showed that glycine elicited the strongest attraction in both age groups. Young protists were strongly attracted to all the assayed amino acids, whereas older protists maintained a high level of attraction only for glycine. These results suggest that glycine generated by protists actively grazing in bacterially enriched patches functions as an infochemical, signaling to foraging protists the presence of available prey in the aquatic environment.

Técnicas Conceptuales en la Gestión de Proyectos Software

205 p.

Sistema software para el control de producción de la unidad de rodajes

El presente proyecto consiste en el análisis y búsqueda de soluciones para el control de producción de la unidad de rodajes de la compañía CAF S.A. Para ello, se ha tenido que analizar procesos de producción, capturar requerimientos, desarrollar unas herramientas de control de producción temporales y elaborar una especificación de requisitos. Sin olvidar la gestión e interlocución con proveedores. Estas líneas de trabajo se encuentran descritas en esta memoria, junto con análisis de resultados, conclusiones y unas líneas futuras donde se seguirá trabajando.

Uso de la Realidad Aumentada para facilitar la lectura e interpretación de planos

[ES] Este proyecto genera productos adicionales de trabajos también disponibles en el repositori, en concreto: