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.

Informational report: Bycatch reduction devices used in the Pink Shrimp trawl fishery

The California Fish and Game Commission (Commission) has the authority to require one or any combination of Bycatch Reduction Device (BRD) types in the trawl fishery within California waters for Pacific ocean shrimp (Pandalus jordani), most commonly referred to as pink shrimp. The purpose of this report is to provide the Commission with the best available information about the BRDs used in the pink shrimp trawl fishery. The mandatory requirement for BRDs occurred in California in 2002, and in Oregon and Washington in 2003, resulting from an effort to minimize bycatch of overfished and quota managed groundfish species. Three types of BRDs currently satisfy the requirement for this device in the California fishery: 1) the Nordmøre grate (rigid-grate excluder); 2) soft-panel excluder; and 3) fisheye excluder; however, the design, specifications, and efficacy differ by BRD type. Although no data has been collected on BRDs directly from the California pink shrimp fishery, extensive research on the efficacy and differences among BRD types has been conducted by the Oregon Department of Fish and Wildlife (ODFW) since the mid-1990s. Rigid-grate excluders are widely considered to be the most effective of the three BRD types at reducing groundfish bycatch. Over 90 percent of the Oregon pink shrimp fleet use rigid-grate excluders. The majority of the current California pink shrimp fleet also uses rigid-grate excluders, according to a telephone survey conducted by the California Department of Fish and Game (Department) in 2007-2008 of pink shrimp fishermen who have been active in the California fishery in recent years. Hinged rigid-grate excluders have been developed in recent years to reduce the bending of the BRD on vessels that employ net reels to stow and deploy their trawl nets, and they have been used successfully on both single- and double-rig vessels in Oregon. Soft-panel excluders have been demonstrated to be effective at reducing groundfish bycatch, although excessive shrimp loss and other problems have also been associated with this design. Fisheye excluders have been used in the California fishery in the past, but they were disapproved in Oregon and Washington in 2003 because they were found to be less effective at reducing groundfish bycatch than other designs. The reputation of the United States west coast pink shrimp fishery as one of the cleanest shrimp fisheries in the world is largely attributed to the effectiveness of BRDs at reducing groundfish bycatch. Nevertheless, BRD research and development is still a relatively new field and additional modifications and methods may further reduce bycatch rates in the pink shrimp fishery.(PDF contains 12 pages.)

Poverty reduction and aquatic resources

The Millennium Development Goals call for a reduction in the proportion of people living on less than $1 a day to half the 1990 level by 2015. This means reducing from 28.3 percent of all people in low and middle income economies to 14.2 percent. The Goals also call for halving the proportion of people who suffer from hunger between 1990 and 2015. If projected growth remains on track, global poverty rates will fall to 13 percent – less than half the 1990 level – and 360 million more people will avert extreme poverty. So while poverty would not be eradicated, that would bring us much closer to the day when we can say that all the world's people have at least the bare minimum to eat and clothe themselves. (Pdf contains 9 pages).

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.

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