Building modular FSPM under OpenAlea: concepts and applications

International audienceThe OpenAlea platform (Pradal et al., 2008) was designed to facilitate the integration and inter-operability of heterogeneous models to get comprehensive FSPMs. It relies on Python gluing capabilities, that allow non intrusive integration of programs written in various languages (Fortran, C, C++, R, L-system); and on the dataflow computing paradigm, that promotes decomposition of applications into independent components that can be recombined dynamically into customized workflows. Still, a plugable collection of components is not by itself a solution to the modularity problem in FSPM modeling. First, heterogeneities between components inputs and outputs can lead to exponential needs for specific adaptors and converters to get functional assemblies. Second, several ways exist to decompose models into independent components. This can lead to incompatibilities or difficulties for re-assembly into comprehensive models. Last, users of the platform may find difficult to build applications, without some knowledge on how a simulation has to be reasoned within the data-flow computing paradigm. Here, we propose a modeling strategy to help for building coherent, yet modular FSPM under OpenAlea. We first define the key concepts of this strategy, illustrate how they can be used under Visualea and how it lead to a first set of reusable components resulting from various ecophysiological studies

Cadomian S-type granites as basement rocks of the Variscan belt (Massif Central, France): Implications for the crustal evolution of the north Gondwana margin

International audienceFrom the Neoproterozoic to the early Paleozoic, the northern Gondwana margin was sequentially shaped by the Cadomian accretionary and the Variscan collisional orogens which offers the opportunity to investigate the relative extent of crust production/reworking in both geodynamic settings. In the eastern part of the Variscan French Massif Central (FMC), the Velay Orthogneiss Formation (VOF) represents a consistent lithological unit of the pre-Variscan basement and comprises augen gneisses and leucogneisses. Such rocks constitute a unique record of the pre-Variscan magmatic history and bear critical information on the crustal evolution of the northern Gondwana margin.Here, we present whole–rock major and trace element compositions indicating that: (i) the VOF shows a remarkable geochemical homogeneity; (ii) the protolith of the augen gneisses corresponds to strongly peraluminous, “S-type” porphyritic granites originating from partial melting of an Ediacaran sedimentary sequence; (iii) the leucogneisses are former leucogranites generated by fractionation of the magma at the origin of the porphyritic granites; and (iv) the whole suite emplaced at shallow crustal levels (< 7 km). U–Pb LA–(MC–)ICP–MS analyses on zircon yielded similar emplacement ages of c. 542 Ma and a narrow range of εHf(t) clustering around 0 for the protoliths of both augen and leucogneisses. This homogeneous Hf isotope signature, notably uncommon for S-type granites, would originate from a sequential process of: (i) inherited zircon dissolution during melting and ascent in the crust due to Zr-undersaturated conditions, (ii) isotopic homogenization of the melt by advection and elemental/isotopic diffusion, followed by (iii) early saturation upon emplacement owing to rapid cooling at shallow crustal levels.We propose that partial melting of Ediacaran sediments occurred during inversion of a Cadomian back-arc basin and was promoted by the high thermal gradient typical of thinned crust domains. Therefore, the VOF and other Cadomian S-type granitoids from the northern Gondwana margin are indicative of substantial crust reworking away from any proper continental collision zone

Data collection and analysis tools for food security and nutrition. Towards enhancing effective, inclusive, evidence-informed, decision making

Throughout the world, high-quality, timely and relevant data are key to inform actions that promote better access to food and improved nutrition. • Despite the abundant and growing availability of data and information relevant to food security and nutrition, often policymakers are not aware of the existence and relevance of such data or do not use them appropriately, due to challenges at each step of the data cycle, which includes: defining priorities and data needs; reviewing, consolidating, collecting and curating data; analyzing the data using appropriate tools; translating data into relevant insights to be disseminated and discussed; and, finally, using data for decision-making. • Fundamental data gaps still exist to correctly guide action and inform policymaking, especially in terms of timely and sufficiently granular data on people’s ability to locally produce and access food, on their actual food and nutrient consumption, and on their nutritional status. Increased and sustained financial investment is needed to overcome these gaps. • Several other constraints limit the effectiveness of data-informed policy action, especially in low-resource countries. Key among them is the low level of data literacy and analysis skills (for both qualitative and quantitative data) on the part of data and information users at all levels – from data collectors and analysts, to decision-makers, and to the people, as the ultimate beneficiaries of food security and nutrition policies. • The complexity of the system of public and private actors and institutions involved in food security and nutrition data, coupled with the rapidly changing characteristics of today’s data ecosystems due to the digital revolution and the pervasiveness of the internet, brings to centre stage the need for global coordination to improve data governance. Particularly urgent is the need to reach agreement on the nature of FSN data and information as a public good, and, on that basis, to establish a global legal framework that allows for the broadest possible circulation of relevant information, while preserving the rights of the people to whom the data ultimately belongs

Sharing efforts for modelling plant systems: from publications to reusable software components

http://www-sop.inria.fr/virtualplants/Publications/2009/FPCBLRCCBMSVEAG09/[email protected] audiencePlant models become increasingly complex and their implementation often implies the use of advanced techniques in computer science. This evolution has been accompanied by the production of dedicated plant modelling tools, such as simulation platforms, that facilitate research in this field. However, much less sharing is observed for plant models themselves, that is for computer programs produced by scientists to address their specific questions. Yet, these programs could be highly valuable for other researchers, to avoid redundant development of similar code or to help non-specialists to simulate parts of a complex system. Model descriptions found in academic publications, even combined with code sources, are generally not sufficient for model reuse. Most difficulties come from the heterogeneity of language used, the structure of the programs, the download and installation procedures, the accessibility to the source code of the model, and the availability of documentation. The OpenAlea initiative (http://openalea.gforge.inria.fr) has been launched to address these problems by providing plant modellers with collaborative tools and guidelines to increase software quality, hence re-usability of their models. The Alinea pilot project further tested these concepts in a sample community of ecophysiologists and biophysicists. Based on this experience, we illustrate pros and cons of the approach and discuss future direction of progress. We foresee three steps towards a better re-usability of models: a better interoperability of existing tools and simulation platforms, the emergence of design patterns for plant modelling, and the definition of standardised data structures

The fourth phase of the radiative transfer model intercomparison (RAMI) exercise : Actual canopy scenarios and conformity testing

The RAdiative transfer Model Intercomparison (RAMI) activity focuses on the benchmarking of canopy radiative transfer (RT) models. For the current fourth phase of RAMI, six highly realistic virtual plant environments were constructed on the basis of intensive field data collected from (both deciduous and coniferous) forest stands as well as test sites in Europe and South Africa. Twelve RT modelling groups provided simulations of canopy scale (directional and hemispherically integrated) radiative quantities, as well as a series of binary hemispherical photographs acquired from different locations within the virtual canopies. The simulation results showed much greater variance than those recently analysed for the abstract canopy scenarios of RAMI-IV. Canopy complexity is among the most likely drivers behind operator induced errors that gave rise to the discrepancies. Conformity testing was introduced to separate the simulation results into acceptable and non-acceptable contributions. More specifically, a shared risk approach is used to evaluate the compliance of RI model simulations on the basis of reference data generated with the weighted ensemble averaging technique from ISO-13528. However, using concepts from legal metrology, the uncertainty of this reference solution will be shown to prevent a confident assessment of model performance with respect to the selected tolerance intervals. As an alternative, guarded risk decision rules will be presented to account explicitly for the uncertainty associated with the reference and candidate methods. Both guarded acceptance and guarded rejection approaches are used to make confident statements about the acceptance and/or rejection of RT model simulations with respect to the predefined tolerance intervals. (C) 2015 The Authors. Published by Elsevier Inc.Peer reviewe

Could virtual plants be considered as lambertian objects in dense canopies?

International audienc

Développement d'un modèle de radiosité mixte pour simuler la distribution du rayonnement dans les couverts végétaux

*INRA, Bioclimatologie Grignon (FRA) Diffusion du document : INRA, Bioclimatologie Grignon (FRA) Diplôme : Dr. d'Universit