Search results for "repository"
showing 10 items of 37 documents
Drosophila Evolution over Space and Time (DEST) - A New Population Genomics Resource
2021
Abstract Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome datasets from natural populations of this species have been published over the last 20 years. A major challenge is the integration of these disparate datasets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution and population structure of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequenc…
The shear strength of Opalinus Clay shale in the remoulded state
2020
Abstract The Opalinus Clay shale formation is considered as a potential host geomaterial for the Swiss deep geological repository for radioactive waste. It presents different facies and it is characterised by a multi-scale heterogeneous composition, by a typical fissile structure with well-defined bedding planes and by anisotropic hydro-mechanical behaviour. This peculiar complexity makes it difficult to assign a unique set of geomechanical parameters to the material. This paper presents an experimental study aimed at characterising the lowest values of the shear strength parameters. In this sense, the shear behaviour was investigated on remoulded samples where the fabric and the diagenetic…
The Software Crisis of Synthetic Biology
2016
In fifteen years, Synthetic Biology (SB) has moved from proof-of-concept designs to several flagship achievements. Standardisation efforts are still under way, basic engineering concepts such as modularity and orthogonality are still controversial in biology, and making predictions from computer models is still unreliable. A deep characterization in the pattern of re-use of biological blocks in SB has not been attempted to date. We have compared the topological organisation of two different technological networks, one associated to a standard, large-scale software repository and the second provided by the Registry of Standard Biological Parts (RSBP). Our results strongly suggest that softwa…
A discrete-choice experiment to assess patients’ preferences for osteoarthritis treatment: An ESCEO working group
2020
Objective: To evaluate the preferences of patients with osteoarthritis for treatment.Methods: A discrete-choice experiment was conducted among adult OA patients who were presented with 12 choice sets of two treatment options and asked in each to select the treatment they would prefer. Based on literature reviews, expert consultation, patient survey and expert meeting, treatment options were characterized by seven attributes: improvement in pain, improvement in walking, ability to manage domestic activities, ability to manage social activities, improvement in overall energy and well-being, risk of moderate/severe side effects and impact on disease progression. Random parameters logit model w…
Metadata to Support Data Warehouse Evolution
2009
The focus of this chapter is metadata necessary to support data warehouse evolution. We present the data warehouse framework that is able to track evolution process and adapt data warehouse schemata and data extraction, transformation, and loading (ETL) processes. We discuss the significant part of the framework, the metadata repository that stores information about the data warehouse, logical and physical schemata and their versions. We propose the physical implementation of multiversion data warehouse in a relational DBMS. For each modification of a data warehouse schema, we outline the changes that need to be made to the repository metadata and in the database.
PyCellBase, an efficient python package for easy retrieval of biological data from heterogeneous sources.
2019
Background Biological databases and repositories are incrementing in diversity and complexity over the years. This rapid expansion of current and new sources of biological knowledge raises serious problems of data accessibility and integration. To handle the growing necessity of unification, CellBase was created as an integrative solution. CellBase provides a centralized NoSQL database containing biological information from different and heterogeneous sources. Access to this information is done through a RESTful web service API, which provides an efficient interface to the data. Results In this work we present PyCellBase, a Python package that provides programmatic access to the rich RESTfu…
Direct lookup and hash-based metadata placement for local file systems
2013
New challenges to file systems' metadata performance are imposed by the continuously growing number of files existing in file systems. The total amount of metadata can become too big to be cached, potentially leading to multiple storage device accesses for a single metadata lookup operation. This paper takes a look at the limitations of traditional file system designs and discusses an alternative metadata handling approach, using hash-based concepts already established for metadata and data placement in distributed storage systems. Furthermore, a POSIX compliant prototype implementation based on these concepts is introduced and benchmarked. A variety of file system metadata and data operati…
New geo-portal for MODIS/SEVIRI image products with geolocation-based retrieval functionality
2015
A large number of remote sensing data sets have been collected in recent years by Earth observation instruments such as the moderate resolution imaging spectroradiometer (MODIS) aboard the Terra/Aqua satellite and the spinning enhanced visible and infrared imager (SEVIRI) aboard the geostationary platform Meteosat Second Generation. The advanced remote sensing products resulting from the analysis of these data are useful in a wide variety of appli- cations but require significant resources in terms of storage, retrieval, and analysis. Despite the wide availability of these MODIS/SEVIRI products, the data coming from these instruments are spread among different locations and retrieved from d…
Even a low-dose of moderate-to-vigorous physical activity reduces mortality by 22% in adults aged ≥60 years: a systematic review and meta-analysis
2015
Type de document : revue de littérature; International audience; Background The health benefits of 150 min a week of moderate-to-vigorous-intensity physical activity (MVPA) in older adults, as currently recommended, are well established, but the suggested dose in older adults is often not reached.Objectives We aimed to determine whether a lower dose of MVPA was effective in reducing mortality, in participants older than 60 years.Methods The PubMed and Embase databases were searched from inception to February 2015. Only prospective cohorts were included. Risk ratios of death were established into four doses based on weekly Metabolic Equivalent of Task (MET)-minutes, defined as inactive (refe…
The availability of raw data in substance abuse scientific journals
2018
[Objective]: The availability of research data sets is an important milestone since it can enhance the dynamics of research. This study aims to analyse the PubMed Central repository to determine the availability and type of raw data sets in Substance Abuse journals indexed in the Journal Citation Reports.