Challenges in experimental data integration within genome-scale metabolic models

A report of the meeting "Challenges in experimental data integration within genome-scale metabolic models", Institut Henri Poincar\'e, Paris, October 10-11 2009, organized by the CNRS-MPG joint program in Systems Biology.Comment: 5 page

Paramétrisation du potentiel de ruissellement des bassins versants au moyen de la Télédétection et des systèmes d'Informations Géographiques. Application à des bassins versants du Pays de Caux

International audienceThe increasing number of run-off damages occurring in Pays de Caux is a serious concern for regional authorities. The suggested method aims the assessmenl of run-off parameters using Remote Sensing and GIS. This method allows an objective comparison of the intrinsic and anthropic pressures of cultivated catchment from 1000 to 5000 ha. The potenliaI ron-off characteristics are analysed using land use components increasing or limiting run-off. and their spoliaI distrihulion on three different functional units. The selected parameters are the grassland proportion and compacity around concentrated surficial water channels (80 m wide), the proportion and compacity of the soil surfaces contributive to run-off on the top of catchments and, finally, the simple proportion of grassland and forest upon high sloped areas. The temporal evolution of these indices and the comparison between calchments show the signiflcant recorded changes whÎch favour the increase of surfaces contributing la mn-off between 1990 and /997. The interest of Ihese indices is to identify areas sensitive to run-off and to act as a decision supporl tool for a lerritorial management policy aimed al run-off reduclion on catchments. The outlook of this study is to generalize these parameters for regional applications

The French EO high spatial resolution hyperspectral dual mission - an update

More than 25 years of airborne imaging spectroscopy and spaceborne sensors such as Hyperion [1] or HICO [2] have clearly demonstrated the ability of such a remote sensing technique to produce value added information regarding surface composition and physical properties for a large variety of applications [3]. Scheduled missions such as EnMAP [4], HISUI [5] or PRISMA [6] prove the increased interest of the scientific community for such a type of remote sensing data. In France, after gathering a group of Science and Defence users of imaging spectrometry data (Groupe de Synthèse Hyperspectral, GSH [7]) to establish an up-to-date review of possible applications, define instrument specifications required for accurate, quantitative retrieval of diagnostic parameters, and identify fields of application where imaging spectrometry is a major contribution, CNES (French Space Agency) decided a pre-phase A study for an hyperspectral mission concept called HYPXIM (HYPerspectral-X IMagery), the main fields of applications of which were to be vegetation, coastal and inland waters, geosciences, urban environment, atmospheric sciences, cryosphere and Defence. During this pre-phase A, the feasibility of such a platform was evaluated, based on specific studies supported by Defence and a more accurate definition of reference radiances and instrument characteristics. Results also pointed to applications where high spatial resolution was necessary and would not be covered by the other foreseen hyperspectral missions. For example, in the case of ecosystem studies, it is generally agreed that many model variables and processes are not accurately represented and that upcoming sensors with improved spatial and spectral capabilities, such as higher resolution imaging spectrometers, are needed to further improve the quality and accuracy of model variables [8, 9]. The growing interest for urban environment related applications also emphasized the need for an increased spatial resolution [10, 11]. Finally, short revisit time is an issue for security and Defense as well as crisis monitoring. Table 1 summarizes the Science and Defence mission requirements at the end of pre-phase A. Two instrument designs were proposed by the industry (EADS-Astrium and Thales Alenia Space) based on these new requirements [12]: HYPXIM-Challenging, on a micro-satellite platform, with a 15 m pixel and HYPXIM-Performance, on a mini-satellite platform, with a 8 m pixel, and possible TIR hyperspectral capabilities. Both scenarios included a PAN camera with a 1.85 m pixel. Platform agility would allow for “on-event mode” with a 3-day revisit time. CNES decided to select HYPXIM-Performance, the system providing a higher spatial resolution (pixel ≤ 8 m, [13, 14]), but without TIR capabilities, for a phase A study [15]. This phase A was to start at the beginning of 2013 but is currently stopped due to budget constraints. An important part of the activities has been focusing on getting the French community more involved through various surveys and workshops in preparation for the CNES prospective meeting, an important step for the future of the mission. During this prospective meeting, which took place last March, decision was taken to keep HYPXIM alive as a mid-term (2020-2025) mission. The attendance at the recent workshop organized by the SFPT-GH (Société Française de Photogrammétrie et Télédétection, Groupe Hyperspectral) which gathered more than 90 participants from various field of application, including the industry (see http://www.sfpt.fr/hyperspectral for more details), demonstrates the interest and support of the French scientific community for a high spatial resolution imaging spectrometry mission

Monastères et couvents de montagne : circulation, réseaux, influences au Moyen Âge

Au Moyen Âge, des religieux trouvent en montagne l’isolement nécessaire à l’épanouissement de leur spiritualité. Les maisons de prière qu’ils y fondent participent néanmoins au développement des relations entre les hauteurs et la plaine : en dépit de leur idéal de solitude, elles n’en sont pas moins ouvertes sur le monde extérieur, beaucoup d’entre elles sont aussi des lieux de passage, des points de contact, des espaces symboliques dans les activités humaines et économiques. En croisant des perspectives historiques, archéologiques et géographiques, cet ouvrage collectif apporte un nouveau regard sur les monastères et les couvents de montagne. Le Congrès national des sociétés historiques et scientifiques rassemble chaque année universitaires, membres de sociétés savantes et jeunes chercheurs. Ce recueil est issu de travaux présentés lors du 142e Congrès sur le thème « Circulations montagnardes, circulations européennes »

Genome-scale models of bacterial metabolism: reconstruction and applications

Genome-scale metabolic models bridge the gap between genome-derived biochemical information and metabolic phenotypes in a principled manner, providing a solid interpretative framework for experimental data related to metabolic states, and enabling simple in silico experiments with whole-cell metabolism. Models have been reconstructed for almost 20 bacterial species, so far mainly through expert curation efforts integrating information from the literature with genome annotation. A wide variety of computational methods exploiting metabolic models have been developed and applied to bacteria, yielding valuable insights into bacterial metabolism and evolution, and providing a sound basis for computer-assisted design in metabolic engineering. Recent advances in computational systems biology and high-throughput experimental technologies pave the way for the systematic reconstruction of metabolic models from genomes of new species, and a corresponding expansion of the scope of their applications. In this review, we provide an introduction to the key ideas of metabolic modeling, survey the methods, and resources that enable model reconstruction and refinement, and chart applications to the investigation of global properties of metabolic systems, the interpretation of experimental results, and the re-engineering of their biochemical capabilities

Problématiques statistiques à l'heure de la post-génomique

Article de vulgarisation pour la revue "Variances" des anciens élèves d'ENSAE ParisTec

Parsimonious Markov models and application to biological sequence analysis

Les chaînes de Markov constituent une famille de modèle statistique incontournable dans de nombreuses applications, dont le spectre s'étend de la compression de texte à l'analyse des séquences biologiques. Un problème récurrent dans leur mise en oeuvre face à des données réelles est la nécessité de compromettre l'ordre du modèle, qui conditionne la complexité des interactions modélisées, avec la quantité d'information fournies par les données, dont la limitation impacte négativement la qualité des estimations menées. Les arbres de contexte permettent une granularité fine dans l'établissement de ce compromis, en permettant de recourir à des longueurs de mémoire variables selon le contexte rencontré dans la séquence. Ils ont donné lieu à des outils populaires tant pour l'indexation des textes que pour leur compression (Context Tree Maximisation – CTM - et Context Tree Weighting - CTW). Nous proposons une extension de cette classe de modèles, en introduisant les arbres de contexte parcimonieux, obtenus par fusion de noeuds issus du même parent dans l'arbre. Ces fusions permettent une augmentation radicale de la granularité de la sélection de modèle, permettant ainsi de meilleurs compromis entre complexité du modèle et qualité de l'estimation, au prix d'une extension importante de la quantité de modèles mise en concurrence. Cependant, grâce à une approche bayésienne très similaire à celle employée dans CTM et CTW, nous avons pu concevoir une méthode de sélection de modèles optimisant de manière exacte le critère bayésien de sélection de modèles tout en bénéficiant d'une programmation dynamique. Il en résulte un algorithme atteignant la borne inférieure de la complexité du problème d'optimisation, et pratiquement tractable pour des alphabets de taille inférieure à 10 symboles. Diverses démonstrations de la performance atteinte par cette procédure sont fournies en dernière partie.Markov chains, as a universal model accounting for finite memory, discrete valued processes, are omnipresent in applied statistics. Their applications range from text compression to the analysis of biological sequences. Their practical use with finite samples, however, systematically require to draw a compromise between the memory length of the model used, which conditions the complexity of the interactions the model may capture, and the amount of information carried by the data, whose limitation negatively impacts the quality of estimation. Context trees, as an extension of the model class of Markov chains, provide the modeller with a finer granularity in this model selection process, by allowing the memory length to vary across contexts. Several popular modelling methods are based on this class of models, in fields such as text indexation of text compression (Context Tree Maximization and Context Tree Weighting). We propose an extension of the models class of context trees, the Parcimonious context trees, which further allow the fusion of sibling nodes in the context tree. They provide the modeller with a yet finer granularity to perform the model selection task, at the cost of an increased computational cost for performing it. Thanks to a bayesian approach of this problem borrowed from compression techniques, we succeeded at desiging an algorithm that exactly optimizes the bayesian criterion, while it benefits from a dynamic programming scheme ensuring the minimisation of the computational complexity of the model selection task. This algorithm is able to perform in reasonable space and time on alphabets up to size 10, and has been applied on diverse datasets to establish the good performances achieved by this approach

VENTILATION NON INVASIVE EN PREHOSPITALIER (ETUDE SUR LA FAISABILITE ET L'INTERET DE LA CPAP BOUSSIGNAC-VYGON* EN TRANSPORT PRIMAIRE AU SMUR DE LONGJUMEAU)

PARIS7-Villemin (751102101) / SudocPARIS-BIUM (751062103) / SudocSudocFranceF