GINSENG (Global Initiative for Sentinel E-health Network on Grid)

The GINSENG (Global Initiative for Sentinel E-health Network on Grid) project aims to implement a grid infrastructure for ehealthand epidemiology in Auvergne. A distributed medical database is created upon a secure network for epidemiologicalstudies. Our goal is to create a decentralized information system using grid technologies. The medical sites involved in theproject are clustered around two themes: cancer monitoring and perinatal care. On each medical site a server whichduplicates the medical database, is deployed with grid services. At the same time, full control of the information is kept by theorganizations storing patients' files. This solution allows for a high level of security, privacy, availability, and fault tolerance.Queries made on the distributed medical databases are made via a secure web portal. Public health authorities use thisinfrastructure for health monitoring, epidemiological studies and evaluation of specific medical practices

Détermination de sondes oligonucléotidiques pour biopuces phylogénétiques en environnement grille de calcul

Détermination de sondes oligonucléotidiques pour biopuces phylogénétiques en environnement grille de calcu

Réécriture du module réseau de Quattor pour l’expérience LHCb au CERN

Quattor est une solution logicielle qui permet l’installation, la configuration et la maintenance de milliers d’ordinateurs à distance. En centralisant ainsi ces tâches les gains en termes de temps et de simplicité sont énormes. Pour atteindre ses objectifs, Quattor utilise, selon ce qui lui est demandé, différents modules, dont un dédié à la configuration des réseaux. Durant les 5 mois qu’ont durés mon stage au CERN et plus précisément dans l’expérience LHCb, il m’a été attribué la tâche de réécrire totalement depuis le départ, ce composant réseau, en y ajoutant des fonctionnalités. Il m’a été demandé de conserver les fonctionnalités existantes et de faire en sorte que le nouveau composant soit compatible avec les anciennes configurations. De plus, je devais ajouter une gestion de la configuration qui puisse se réaliser sans qu’il soit nécessaire de devoir redémarrer le service réseau du nœud à configurer. J’ai nommé cette configuration, « configuration dynamique » ou « configuration à la volée », car elle s’oppose pour moi à la configuration statique qui s’appuie sur les données écrites dans des fichiers et qui seront utilisées lors d’un redémarrage de la machine ou du service réseau. Le nouveau composant réseau de Quattor sera capable de conformer des nœuds ne possédant pas de disques, sans les déconnecter du réseau. Il aura été entièrement repensé, et codé en suivant les principes de robustesse, d’efficacité, de maintenabilité et d’évolution

Gestion d’échantillons pour la recherche scientifique avec Collec-Science

National audienceScientific teams for environmental research collect many samples (biological or physical) from fields for their analysis, and have to store them for a long while. The management of such samples requires a strategy relying on an efficient Laboratory Information Management System, with regards to the specific needs of this domain. This paper exposes such a strategy, and how it is implemented inside a software named Collec-Science. In particular, it adresses the need for tracability, security, and a greater genericity and freedom for researchers. The whole information system has to be integrated inside an ecosystem of tools for the research, and we explain how we face the challenge in terms of organisation and interoperability around the solution.Les acteurs des laboratoires de recherche scientifique environnementale collectent régulièrement de nombreux échantillons qui sont ensuite analysés et stockés. Leur gestion sur le long terme s’inscrit dans une stratégie qu’il s’agit de définir puis de mettre en œuvre via des outils informatiques adaptés. Cet article présente cette stratégie, puis sa déclinaison dans un système d’information développé sous le nom de Collec-Science, offrant un support adéquat pour la traçabilité, la diversité des données à traiter et l’autonomie des utilisateurs. Il présente également les perspectives de ces travaux en matière d’animation de communauté scientifique, à la fois sur les plans organisationnels et opérationnels, dans le contexte d’une science ouverte

Large Scale Explorative Oligonucleotide Probe Selection for Thousands of Genetic Groups on a Computing Grid: Application to Phylogenetic Probe Design Using a Curated Small Subunit Ribosomal RNA Gene Database

Phylogenetic Oligonucleotide Arrays (POAs) were recently adapted for studying the huge microbial communities in a flexible and easy-to-use way. POA coupled with the use of explorative probes to detect the unknown part is now one of the most powerful approaches for a better understanding of microbial community functioning. However, the selection of probes remains a very difficult task. The rapid growth of environmental databases has led to an exponential increase of data to be managed for an efficient design. Consequently, the use of high performance computing facilities is mandatory. In this paper, we present an efficient parallelization method to select known and explorative oligonucleotide probes at large scale using computing grids. We implemented a software that generates and monitors thousands of jobs over the European Computing Grid Infrastructure (EGI). We also developed a new algorithm for the construction of a high-quality curated phylogenetic database to avoid erroneous design due to bad sequence affiliation. We present here the performance and statistics of our method on real biological datasets based on a phylogenetic prokaryotic database at the genus level and a complete design of about 20,000 probes for 2,069 genera of prokaryotes

Towards better traceability of field sampling data

International audienceEnsuring traceability of both field experimental data and laboratory sampling data for a reproducible research remains a challenge nowadays. Between the time when geolocalized specimens are taken, and the time the resulting data ends up in analysis published within a study, many manual operations take place that are prone to generate errors. The French nodes of the European Long-Term Socio-Ecological Research Infrastructure called ”Zones Ateliers” propose a solution as generic as possible to this problem of monitoring of the samples and the data associated with them. Compared to existing solutions such as Laboratory Information Management Systems, we target a robust solution for labelling adapted to outdoor working conditions, with the management of storages and movements of samples. We designed and realized a software package tested from end to end, using open source licenses and cheap hardware, including small printers (mobile or not) and Raspberry Pis. This system provides sufficient flexibility so that it can facilitate working with a wide variety of existing protocols. One of the most interesting feature consists to record all contextual data associated with the samples, which constitute important parameters of the subsequent analyses. Furthermore, not only traceability is thus guaranteed, but also we can expect a reduced handling times and an increased streamlining of the storage of samples that will improve the return on investment

Equations of state and free volume content

Peer reviewed: YesNRC publication: Ye

Towards better traceability of field sampling data

PosterInternational audienceEnsuring traceability of field experimental data or laboratory sampling data to conduct reproducible research is a challenge at the present time. Between the time when geolocalized specimens (biotic or abiotic) are taken, and the time the resulting data ends up in analysis published within a study, many manual operations take place and may generate errors. The French LTSER have joined forces at the national level to propose a solution as generic as possible to this problem of monitoring of the samples and the data associated with them. Compared to existing solutions (such as Laboratory Information Management Systems), we target a robust labeling solution adapted to outdoor working conditions, with the management of stocks and movements of samples. We designed and realized a prototype tested from end to end, using an open source software (https://github.com/Irstea/collec), cheap Zebra printers (mobile or not) and raspberries as devices. This solution provides sufficient flexibility for the wide variety of existing protocols. Its strength is the record of all contextual data associated with the samples, which constitute important parameters of the subsequent analyzes. At last, not only traceability is guaranteed, but also a gain of time and a rationalization of the storage of samples that will induce a return on investment