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.

Estudio, análisis y clasificación de mecanismos con aplicación industrial

[ES]El uso de maquinaria en la industria es algo muy habitual en la actualidad. Dicha maquinaria necesita una serie de mecanismos para realizar una acción deseada, y en función de esa acción, se hará uso de un mecanismo u otro. Este informe representa el estudio y análisis cinemático que se ha llevado a cabo para la posterior clasificación de mecanismos planos que tengan un grado de libertad con aplicación industrial. Para todo ello se ha partido de un previo conocimiento de la materia que se ha ido complementando con diferentes fuentes de información especializadas. La clasificación de los mecanismos que se va a realizar en este trabajo no es más que una de las muchas posibilidades que hay a la hora de clasificarlos ya que se han hecho bastantes intentos para realizar clasificaciones de mecanismos, pero dada la complejidad de la tarea no se ha llegado a una clasificación general unificada. La línea de trabajo que se presenta aquí consiste en el análisis cinemático de diferentes mecanismos para la posterior creación de un prototipo de uno de ellos. La estructura de los contenidos que se desarrollan a continuación es la siguiente: En primer lugar se ha realizado una búsqueda de mecanismos que cumplan la condición de ser mecanismos planos que tengan un grado de libertad y que tengan utilidad demostrada. En segundo lugar se han recopilado los resultados cinemáticos del mecanismo, construcciones gráficas de los elementos que lo componen y se añadirán animaciones de cada mecanismo, haciendo después una valoración en función de los resultados obtenidos de los mismos. En tercer lugar se han clasificado en diferentes grupos dependiendo de su función o aplicación. En cuarto lugar, se ha realizado un prototipo de uno de los mecanismos para comprobar su funcionamiento.

Automatically exposing OpenLifeData via SADI semantic Web Services

Background: Two distinct trends are emerging with respect to how data is shared, collected, and analyzed within the bioinformatics community. First, Linked Data, exposed as SPARQL endpoints, promises to make data easier to collect and integrate by moving towards the harmonization of data syntax, descriptive vocabularies, and identifiers, as well as providing a standardized mechanism for data access. Second, Web Services, often linked together into workflows, normalize data access and create transparent, reproducible scientific methodologies that can, in principle, be re-used and customized to suit new scientific questions. Constructing queries that traverse semantically-rich Linked Data requires substantial expertise, yet traditional RESTful or SOAP Web Services cannot adequately describe the content of a SPARQL endpoint. We propose that content-driven Semantic Web Services can enable facile discovery of Linked Data, independent of their location. Results: We use a well-curated Linked Dataset - OpenLifeData - and utilize its descriptive metadata to automatically configure a series of more than 22,000 Semantic Web Services that expose all of its content via the SADI set of design principles. The OpenLifeData SADI services are discoverable via queries to the SHARE registry and easy to integrate into new or existing bioinformatics workflows and analytical pipelines. We demonstrate the utility of this system through comparison of Web Service-mediated data access with traditional SPARQL, and note that this approach not only simplifies data retrieval, but simultaneously provides protection against resource-intensive queries. Conclusions: We show, through a variety of different clients and examples of varying complexity, that data from the myriad OpenLifeData can be recovered without any need for prior-knowledge of the content or structure of the SPARQL endpoints. We also demonstrate that, via clients such as SHARE, the complexity of federated SPARQL queries is dramatically reduced.

Torlojutze sekuentzien optimizazioa elementu finituen bidez Offshore aplikazioetan.

[EU]Gradu Amaierako Lan honetan offshore presiopeko hodien (gasa nahiz petrolioa garraiatzen duten hodien) brida bidezko loturetako torlojutze sekuentziak aztertuko dira. Aplikazio hauek suposatzen duten inbertsio ekonomikoa dela eta, ihesak ekiditeko asmoz, ezinbestekoa da brida hauek elkarri lotzeko dituzten torlojuen kargak uniformeki bananduta egotea torloju guztietan, interakzio elastikoak eta pibotamendu mugimenduak helburu hori zailtzen badute ere. Gaur egun torlojutze sekuentziak ASME-k araututa baldin baditu ere, ez dira batere erosoak, torloju guztiak ordena zehatz batean estutu behar direlako, eta estutze hauek ez direlako egoerarik erosoenetan egiten, denbora asko galduz. Horregatik, sinpletasuna lortzeko eta denbora eta dirua aurrezteko, torlojutze sekuentzia horiek optimizatzea izango da helburu nagusia. Aipaturiko lana aurrera eramateko, bi brida modeloren torlojutze analisiak egin beharko dira, berauek parametro batzuen menpe jarrita, estutze sekuentzietan duten eragina ikusi ahal izateko.