Search results for "DATABASES"
showing 10 items of 937 documents
The gypsy database (GyDB) of mobile genetic elements: release 2.0
2011
This article introduces the second release of the Gypsy Database of Mobile Genetic Elements (GyDB 2.0): a research project devoted to the evolutionary dynamics of viruses and transposable elements based on their phylogenetic classification (per lineage and protein domain). The Gypsy Database (GyDB) is a long-term project that is continuously progressing, and that owing to the high molecular diversity of mobile elements requires to be completed in several stages. GyDB 2.0 has been powered with a wiki to allow other researchers participate in the project. The current database stage and scope are long terminal repeats (LTR) retroelements and relatives. GyDB 2.0 is an update based on the analys…
GenExP, un logiciel simulateur de paysages agricoles pour l'étude de la diffusion de transgènes
2007
; The software GENEXP allows to simulate 2-dimensional agricultural landscapes by using a traditional algorithmic geometry. Based on real or realistic field-patterns, GENEXP provides multiannual maps of agricultural landscapes, which are used by softwares simulating the dispersal of GM pollen grains and seeds at various scales.; GENEXP est un simulateur de paysages agricoles qui engendre des découpages parcellaires en utilisant une géométrie algorithmique classique. GENEXP fournit, sur la base de parcellaires réels ou réalistes, des cartes pluriannuelles de paysages agricoles utilisables par des logiciels qui simulent la dispersion des pollens et des graines d'OGM à différentes échelles.
Towards sustainable and multifunctional agriculture in farmland landscapes: Lessons from the integrative approach of a French LTSER platform
2018
International audience; Agriculture is currently facing unprecedented challenges: ensuring food, fiber and energy production in the face of global change, maintaining the economic performance of farmers and preserving natural resources such as biodiversity and associated key ecosystem services for sustainable agriculture. Addressing these challenges requires innovative landscape scale farming systems that account for changing economic and environmental targets. These novel agricultural systems need to be recognized, accepted and promoted by all stakeholders, including local residents, and supported by public policies. Agroecosystems should be considered as socio-ecological systems and alter…
Vegetation structure and greenness in Central Africa from Modis multi-temporal data.
2013
African forests within the Congo Basin are generally mapped at regional scale as broad-leaved evergreen forests, with a main distinction between terra-firme and swamp forests types. At the same time, commercial forest inventories, as well as national maps, have highlighted a strong spatial heterogeneity of forest types. A detailed vegetation map generated using consistent methods is needed to inform decision makers about spatial forest organisation and theirs relationships with environmental drivers in the context of global change. We propose a multi-temporal remotely sensed data approach to characterize vegetation types using vegetation index annual profiles. The classifications identified…
Rings for Privacy: an Architecture for Large Scale Privacy-Preserving Data Mining
2021
This article proposes a new architecture for privacy-preserving data mining based on Multi Party Computation (MPC) and secure sums. While traditional MPC approaches rely on a small number of aggregation peers replacing a centralized trusted entity, the current study puts forth a distributed solution that involves all data sources in the aggregation process, with the help of a single server for storing intermediate results. A large-scale scenario is examined and the possibility that data become inaccessible during the aggregation process is considered, a possibility that traditional schemes often neglect. Here, it is explicitly examined, as it might be provoked by intermittent network connec…
Towards a Reference Architecture for Archival Systems: Use Case With Product Data
2014
Long-term preservation of product data is imperative for many organizations. A product data archive should be designed to ensure information accessibility and understanding over time. Approaches, such as the Open Archival Information System Reference Model (OAIS RM) and the Audit and Certification of Trustworthy Digital Repositories (ACTDR), provide a framework for conceptually describing and evaluating archives. These approaches are generic and do not focus on particular contexts or content types such as product data. Moreover, these approaches offer no guidance on how to formally and comprehensively describe archival systems. Such descriptions should include the business activities that a…
Graph-theoretical derivation of brain structural connectivity
2020
Brain connectivity at the single neuron level can provide fundamental insights into how information is integrated and propagated within and between brain regions. However, it is almost impossible to adequately study this problem experimentally and, despite intense efforts in the field, no mathematical description has been obtained so far. Here, we present a mathematical framework based on a graph-theoretical approach that, starting from experimental data obtained from a few small subsets of neurons, can quantitatively explain and predict the corresponding full network properties. This model also changes the paradigm with which large-scale model networks can be built, from using probabilisti…
Beyond cells – The virome in the human holobiont
2019
Viromics, or viral metagenomics, is a relatively new and burgeoning field of research that studies the complete collection of viruses forming part of the microbiota in any given niche. It has strong foundations rooted in over a century of discoveries in the field of virology and recent advances in molecular biology and sequencing technologies. Historically, most studies have deconstructed the concept of viruses into a simplified perception of viral agents as mere pathogens, which demerits the scope of large-scale viromic analyses. Viruses are, in fact, much more than regular parasites. They are by far the most dynamic and abundant entity and the greatest killers on the planet, as well as th…
Eawag-Soil in enviPath: a new resource for exploring regulatory pesticide soil biodegradation pathways and half-life data.
2017
Developing models for the prediction of microbial biotransformation pathways and half-lives of trace organic contaminants in different environments requires as training data easily accessible and sufficiently large collections of respective biotransformation data that are annotated with metadata on study conditions. Here, we present the Eawag-Soil package, a public database that has been developed to contain all freely accessible regulatory data on pesticide degradation in laboratory soil simulation studies for pesticides registered in the EU (282 degradation pathways, 1535 reactions, 1619 compounds and 4716 biotransformation half-life values with corresponding metadata on study conditions)…
Computational processing and quality control of Hi-C, capture Hi-C and capture-C data
2019
Hi-C, capture Hi-C (CHC) and Capture-C have contributed greatly to our present understanding of the three-dimensional organization of genomes in the context of transcriptional regulation by characterizing the roles of topological associated domains, enhancer promoter loops and other three-dimensional genomic interactions. The analysis is based on counts of chimeric read pairs that map to interacting regions of the genome. However, the processing and quality control presents a number of unique challenges. We review here the experimental and computational foundations and explain how the characteristics of restriction digests, sonication fragments and read pairs can be exploited to distinguish…