Asignatura de fotogrametría

Duración (en horas): De 31 a 40 horas. Destinatario: Estudiante

Comparisons of static, quasi-static and dynamic 3D porous media scale network models for two-phase immiscible flow in porous media

A dynamic 3D pore-scale network model is formulated for investigating the effect of interfacial tension and oil-water viscosity during chemical flooding. The model takes into account both viscous and capillary forces in analyzing the impact of chemical properties on flow behavior or displacement configuration, while the static model with conventional invasion percolation algorithm incorporates the capillary pressure only. From comparisons of simulation results from these models. it indicates that the static pore scale network model can be used successfully when the capillary number is low. With the capillary increases due to the enhancement of water viscosity or decrease of interfacial tension, only the quasi-static and dynamic model can give insight into the displacement mechanisms.

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.

Documentación geométrica del ninfeo y su entorno (Alfaro, La Rioja)

[ES] El objetivo consiste en la obtención de un conjunto de planos (planta, alzados y perspectivas) del Ninfeo mediante la restitución de pares estereoscópicos del Ninfeo. De forma auxiliar se ha generado un programa de ordenador que permite calcular una transformación tridimensional de coordenadas.

Research Software Sustainability: Report on Knowledge Exchange Workshop

The report introduces software sustainability, provides definitions, clearly demonstrates that software is not the same as data and illustrates aspects of sustainability in the software lifecycle. The recommendations state that improving software sustainability requires a number of changes: some technical and others societal, some small and others significant. We must start by raising awareness of researchers’ reliance on software. This goal will become easier if we recognise the valuable contribution that software makes to research – and reward those people who invest their time into developing reliable and reproducible software. The adoption of software has led to significant advances in research. But if we do not change our research practices, the continued rise in software use will be accompanied by a rise in retractions. Ultimately, anyone who is concerned about the reliability and reproducibility of research should be concerned about software sustainability. Beside highlighting the benefits of software sustainability and addressing the societal and technical barriers to software sustainability, the report provides access to expertise in software sustainability and outlines the role of funders. The report concludes with a short landscape of national activities in Europe and outside Europe. As a result of the workshop steps will be explored to establish European coordination and cooperation of national initiatives.