NetCDF based data archiving system applied to ITER Fast Plant System Control prototype

EURATOM/CIEMAT and Technical University of Madrid (UPM) have been involved in the development of a FPSC [1] (Fast Plant System Control) prototype for ITER, based on PXIe (PCI eXtensions for Instrumentation). One of the main focuses of this project has been data acquisition and all the related issues, including scientific data archiving. Additionally, a new data archiving solution has been developed to demonstrate the obtainable performances and possible bottlenecks of scientific data archiving in Fast Plant System Control. The presented system implements a fault tolerant architecture over a GEthernet network where FPSC data are reliably archived on remote, while remaining accessible to be redistributed, within the duration of a pulse. The storing service is supported by a clustering solution to guaranty scalability, so that FPSC management and configuration may be simplified, and a unique view of all archived data provided. All the involved components have been integrated under EPICS [2] (Experimental Physics and Industrial Control System), implementing in each case the necessary extensions, state machines and configuration process variables. The prototyped solution is based on the NetCDF-4 [3] and [4] (Network Common Data Format) file format in order to incorporate important features, such as scientific data models support, huge size files management, platform independent codification, or single-writer/multiple-readers concurrency. In this contribution, a complete description of the above mentioned solution is presented, together with the most relevant results of the tests performed, while focusing in the benefits and limitations of the applied technologies.

Archiving Primary Data: Solutions for Long-Term Studies.

The recent trend for journals to require open access to primary data included in publications has been embraced by many biologists, but has caused apprehension amongst researchers engaged in long-term ecological and evolutionary studies. A worldwide survey of 73 principal investigators (Pls) with long-term studies revealed positive attitudes towards sharing data with the agreement or involvement of the PI, and 93% of PIs have historically shared data. Only 8% were in favor of uncontrolled, open access to primary data while 63% expressed serious concern. We present here their viewpoint on an issue that can have non-trivial scientific consequences. We discuss potential costs of public data archiving and provide possible solutions to meet the needs of journals and researchers.

Rising to the impossible challenge: the storage of all research data, forever?

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Data compilation on the biological response to ocean acidification: environmental and experimental context of data sets and related literature

The exponential growth of studies on the biological response to ocean acidification over the last few decades has generated a large amount of data. To facilitate data comparison, a data compilation hosted at the data publisher PANGAEA was initiated in 2008 and is updated on a regular basis (doi:10.1594/PANGAEA.149999). By January 2015, a total of 581 data sets (over 4 000 000 data points) from 539 papers had been archived. Here we present the developments of this data compilation five years since its first description by Nisumaa et al. (2010). Most of study sites from which data archived are still in the Northern Hemisphere and the number of archived data from studies from the Southern Hemisphere and polar oceans are still relatively low. Data from 60 studies that investigated the response of a mix of organisms or natural communities were all added after 2010, indicating a welcomed shift from the study of individual organisms to communities and ecosystems. The initial imbalance of considerably more data archived on calcification and primary production than on other processes has improved. There is also a clear tendency towards more data archived from multifactorial studies after 2010. For easier and more effective access to ocean acidification data, the ocean acidification community is strongly encouraged to contribute to the data archiving effort, and help develop standard vocabularies describing the variables and define best practices for archiving ocean acidification data.

Using SeaDataNet Management System to preserve the XBT Data-Set of the Mediterranean Sea

significant amount of Expendable Bathythermograph (XBT) data has been collected in the Mediterranean Sea since 1999 in the framework of operational oceanography activities. The management and storage of such a volume of data poses significant challenges and opportunities. The SeaDataNet project, a pan-European infrastructure for marine data diffusion, provides a convenient way to avoid dispersion of these temperature vertical profiles and to facilitate access to a wider public. The XBT data flow, along with the recent improvements in the quality check procedures and the consistence of the available historical data set are described. The main features of SeaDataNet services and the advantage of using this system for long-term data archiving are presented. Finally, focus on the Ligurian Sea is included in order to provide an example of the kind of information and final products devoted to different users can be easily derived from the SeaDataNet web portal.

Estudi i implementació d'un arxivat de dades per a les plataformes SAP Enterprise 4.7 x 200 d'una gran empresa

En aquest projecte s'ha implementat un sistema de data archiving amb SAP-IXOS per a una empresa després que aquesta demanés consell a la nostra consultora per reduir espai en la base de dades, ja que només els quedava lliure un 14% de l'ocupació total, i d'aquesta forma millorar el rendiment del sistema. S'ha realitzat un estudi de la base de dades, ocupació en Mb i creixement mensual de les dades en les taules. S'han parametritzat objectes d'arxivat, creat i definits repositoris de contingut, fitxers lògics i s'han programat reports addicionals per arxivar les dades correctament. El resultat ha estat reduir la base de dades en un 22% sent posible l'entrada de noves dades obtenint una resposta més àgil del sistema.

Navigating the labyrinth: a guide to sequence-based, community ecology of arbuscular mycorrhizal fungi

Data generated from next generation sequencing (NGS) will soon comprise the majority of information about arbuscular mycorrhizal fungal (AMF) communities. Although these approaches give deeper insight, analysing NGS data involves decisions that can significantly affect results and conclusions. This is particularly true for AMF community studies, because much remains to be known about their basic biology and genetics. During a workshop in 2013, representatives from seven research groups using NGS for AMF community ecology gathered to discuss common challenges and directions for future research. Our goal was to improve the quality and accessibility of NGS data for the AMF research community. Discussions spanned sampling design, sample preservation, sequencing, bioinformatics and data archiving. With concrete examples we demonstrated how different approaches can significantly alter analysis outcomes. Failure to consider the consequences of these decisions may compound bias introduced at each step along the workflow. The products of these discussions have been summarized in this paper in order to serve as a guide for any researcher undertaking NGS sequencing of AMF communities.

Archiving and Accessing Qualitative Data Programme

There is a growing body of qualitative research data being made available in data archives in both Ireland and the UK. Examples of Irish qualitative data currently available for further analysis include Growing Up in Ireland (GUI) and Life Histories and Social Change in 20th Century Ireland. The Timescapes Research Programme, at the University of Leeds, hosts a wide variety of economic and social research data relevant to child and family researchers; data which is available to researchers in both Northern Ireland and the Republic of Ireland. Access to this data provides researchers with greater opportunities to explore the issues that affect children, their families and their  communities and which may ultimately contribute to informing children's policy. In this the second master class of the Children's Research Network for Ireland and Northern Ireland, participants will learn about the various qualitativ edatasets that are publicly-available for research purposes in the Republic of Ireland and Northern Ireland.

Webcast Archiving and Accessing Qualitative Data

View the webcast of the presentations at the Archiving and Accessing Qualitative data master class, February 2012.

The Purdue University Research Repository (PURR): An institutional data management service with a virtual research environment, data publication, and archiving

Poster at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Archiving Montana’s Geologic Data

Since the 19th century, enormous amounts of time and money were invested in the exploration and development of Montana’s natural resources. These investments generated tremendous volumes of geologic, geophysical, and environmental data. Over the years, many of these data have been stored, forgotten, lost, or destroyed. In this lecture, Peggy discusses the steps the Bureau is taking to rescue and make the data available to the public.

Environmental data : major effort is needed to improve NOAA's data management and archiving : report to the Chairman, Committee on Commerce, Science and Transportation, U.S. Senate /

"B-241021"--P. l.

Digital radiology and Picture Archiving and Communication System (PACS)

Plain radiography still accounts for the vast majority of imaging studies that are performed at multiple clinical instances. Digital detectors are now prominent in many imaging facilities and they are the main driving force towards filmless environments. There has been a working paradigm shift due to the functional separation of acquisition, visualization, and storage with deep impact in the imaging workflows. Moreover with direct digital detectors images are made available almost immediately. Digital radiology is now completely integrated in Picture Archiving and Communication System (PACS) environments governed by the Digital Imaging and Communications in Medicine (DICOM) standard. In this chapter a brief overview of PACS architectures and components is presented together with a necessarily brief account of the DICOM standard. Special focus is given to the DICOM digital radiology objects and how specific attributes may now be used to improve and increase the metadata repository associated with image data. Regular scrutiny of the metadata repository may serve as a valuable tool for improved, cost-effective, and multidimensional quality control procedures.

Author Rights vs Self-Archiving in Spanish Scientific Journals

The paper analyzes publishers" copyright policies and self-archiving conditions of Spanish scientific journals. Data are extracted from the directory DULCINEA that contains information of 1318 Spanish journals, of which 775 (61%) allow some form of self-archiving to be about 60% of the post-print version and allowing them 87% of the deposit of the version of record. In 72% of journals the deposit can be performed immediately after publication and in 16% after article acceptance. 72% of the journals are freely available without charge to the user this figure raises up to 86% if free access after an embargo is considered. Only 18% of the journals use Creative Commons licenses. The adoption of different open access journals model in Spain is favorable, however there is still a high percentage of journals (39%) that do not provide any information about authors and publishers rights and that difficult or inhibits reuse of published articles.