Papers by Marie-Josée Cros
In farming systems research, simulation is a common investigation tool that enables to study the ... more In farming systems research, simulation is a common investigation tool that enables to study the dynamic behavior of production systems in response to climatic factors and more or less sophisticated management strategies. SEPATOU is one such a simulator that reproduces the functioning of a rotational grazing dairy system. This paper considers simulation optimization as a means to derive the best values of some parameters involved in a management strategy. We evaluate a stochastic optimization algorithm, the Kiefer-Wolfowitz method, based on a stochastic approximation of the objective function gradient. It appears that this approach is reliable. However the algorithm requires a delicate parametrization that is specific to each application.
At the core of farm management lies the issue of work organization that concerns the configuratio... more At the core of farm management lies the issue of work organization that concerns the configuration of activities in space and time, the material requirements for their execution (resources, sensors), and the anticipated means to adapt or react to contingencies. At a more micro level work organization has also to deal with operational aspects: the conditions and manner in which one or more people use purposefully information and tools in order to fulfill the specific objective attached to a primitive operation. This paper argues in favor of an investigation approach of farm management based on a simulation model of the decision maker's behavior, the course of implementing operations and the interaction of the above processes with the biophysical ones and external events linked, in particular, to climatic factors. Simulation of the management process can be of great help in conceiving new production systems or in improving their efficiency, robustness and acceptability. The paper outlines the specific modeling needs when the decision-making behavior and work process play a central role in the intended study. It proposes a conceptualization of the structure and behavior of the management related aspects of a an agricultural production system.
Agricultural Systems, 2004
This paper argues in favour of a simulation approach relying on an explicit and rigorous modellin... more This paper argues in favour of a simulation approach relying on an explicit and rigorous modelling of the management strategy that underlies the farmerÕs decision-making behaviour. A strategy is defined as a roadmap of intended technical tasks over a management period. It is tied to an overall objective and specifies what to do depending on the situations encountered. An essential feature is its flexibility, enabling it to cope with stochastic fluctuations of the environment. In order to evaluate the worth of a strategy, the advocated approach relies on a simulation tool with which the effects of applying the strategy are evaluated under different hypothetical weather conditions. The example of a rotational grazing dairy production system is used to illustrate the modelling and simulation of a management strategy covering a production season. SEPATOU, the simulator built for this application domain, is designed to be used by extension services and farming system scientists. It provides a framework for virtual experimentation that can help to enhance decision-making capabilities of primary producers and find new or more profitable management strategies.
The paper presents the simulator SEPATOU that can reproduce the day-to-day dynamics of two intera... more The paper presents the simulator SEPATOU that can reproduce the day-to-day dynamics of two interactive systems: the decision system representing the dairy farmer's management behavior and the biophysical system that encompasses the herbage production, consumption and transformation into milk. The activities to be managed concern the type and amount of conserved feed, where to fertilize and how much, the choice of fields to cut and, most importantly, what field to graze next. Typically, SEPATOU is designed to be used by extension services and farming system scientists. It provides a flexible environment through which learning about a satisfying management strategy of a given dairy production system can take place by iterating simulation and evaluation of tentative ones.
Environment International, 2001
Dairy systems predominantly based on rotational grazing are notoriously hard to manage. In order ... more Dairy systems predominantly based on rotational grazing are notoriously hard to manage. In order to ensure profitability, this type of production requires quite good organisation, planning, and operating capability on the part of the farmer. A simulation-based decision support system, called SEPATOU, has been developed for this purpose. At the core of the decision support approach lies an explicit and rigorous modelling of the management strategy that underlies a dairy farmer's decision-making behaviour (real or hypothetical). The SEPATOU system is a discrete-event simulator that reproduces the day-to-day dynamics of the farmer's decision process and the response of the controlled biophysical system for which models of grass growth, animal consumption, and milk production are used. SEPATOU provides the means to evaluate and compare tentative strategies by simulating their application throughout the production season under different hypothetical weather conditions. The relative worth of a strategy can be assessed by analysing the effects on the biophysical system and their variability across the representative range of possible conditions that is considered. The activities to be managed concern the type and amount of conserved feed, where to fertilise and how much, the choice of fields to harvest, and most importantly, which field to graze next. Typically, SEPATOU is designed to be used by extension services and farming system scientists. It is implemented in C++ and is currently undergoing a validation process with the intended users. D
The management of dairy production systems based on rotational grazing and maize-concentrate feed... more The management of dairy production systems based on rotational grazing and maize-concentrate feeding requires a complex lookahead decision making procedure to elaborate a seasonal strategy that is sufficiently robust to uncertainty. In this paper, the problem is characterized rather precisely as finding for the late winter to early summer period an appropriate combination of commitments concerning the fields allocated to grazing, those kept just in case of need, the time profile of maizeconcentrate distribution, the nitrogen fertilization policy and the field rotation policy. A simulation tool designed to evaluate tentative man-made strategies under given climate scenarios is described.
The Computerized Greenhouse, 1993
... then translating the strategy from the language specifically developed for strategy represent... more ... then translating the strategy from the language specifically developed for strategy representation (LnU) into the C++ programming language in which ... chronicle of the executed actions concerning rotations, silage cutting, hay cutting and fertilization on each pasture (see Cros et al ...
Agronomie, 2003
This paper describes a biophysical dairy farm model developed as part of the SEPATOU system that ... more This paper describes a biophysical dairy farm model developed as part of the SEPATOU system that simulates pasture-dominated feeding strategies in a dairy cow enterprise. It can reproduce the effects of various technical management options applied to a set of grazing fields on a daily basis over a period of several months. The model is made up of three submodels that deal with the soil (availability of water), sward and animal (cow intake and milk yield) components. It includes as driving variables the main factors that farmers can control (nitrogen fertilizer rate, defoliation frequency and intensity, composition of cows' diet) in order to attain some objectives such as the intended grazing herbage contribution in the cows' diet or the amount of milk produced per cow or per ha. The intended purpose of the SEPATOU system has led to several original developments. In order to simulate various defoliation regimes, growth and senescence processes are dissociated as there is no longer synchronization between them, and the effect of grazing intensity is expressed in terms of the ratio between the herbage mass after and before grazing. The animal intake submodel that can deal with mixed feeding combines two approaches, one based on energy requirements and the other on the relationship between herbage mass, herbage digestibility and intake. The model of herbage digestibility is based on herbage mass and takes into account its variation down the sward profile; this latter aspect plays a key role in the plant-animal interaction. The model has been validated using typical farm cases in Brittany. It provides realistic estimates of the state variables involved in the processes, such as herbage mass and daily milk yield, and it credibly predicts the timing of key events (e.g. date of turnout to grass, end of first grazing cycle).
The Computerized Greenhouse, 1993
2002 Chicago, IL July 28-31, 2002, 2002
This paper argues in favor of an investigation approach of farm management based on a simulation ... more This paper argues in favor of an investigation approach of farm management based on a simulation model of the decision maker's behavior and of the process of implementing the operations decided. Its originality lies in the consideration of the decision and work processes together with the complex dynamics of the biophysical process underlying the production process. Simulation of the management process can be of great help in conceiving new production systems or in improving their efficiency, robustness and acceptability.
Nucleic Acids Research, 2003
EUGÈ NE'HOM is a gene prediction software for eukaryotic organisms based on comparative analysis.... more EUGÈ NE'HOM is a gene prediction software for eukaryotic organisms based on comparative analysis. EUGÈ NE'HOM is able to take into account multiple homologous sequences from more or less closely related organisms. It integrates the results of TBLASTX analysis, splice site and start codon prediction and a robust coding/non-coding probabilistic model which allows EUGÈ NE'HOM to handle sequences from a variety of organisms. The current target of EUGÈ NE'HOM is plant sequences. The EUGÈ NE'HOM web site is available at
Nucleic Acids Research, 2009
Bioinformatic analysis of the intergenic regions of Staphylococcus aureus predicted multiple regu... more Bioinformatic analysis of the intergenic regions of Staphylococcus aureus predicted multiple regulatory regions. From this analysis, we characterized 11 novel noncoding RNAs (RsaAÀK) that are expressed in several S. aureus strains under different experimental conditions. Many of them accumulate in the late-exponential phase of growth. All ncRNAs are stable and their expression is Hfq-independent. The transcription of several of them is regulated by the alternative sigma B factor (RsaA, D and F) while the expression of RsaE is agrA-dependent. Six of these ncRNAs are specific to S. aureus, four are conserved in other Staphylococci, and RsaE is also present in Bacillaceae. Transcriptomic and proteomic analysis indicated that RsaE regulates the synthesis of proteins involved in various metabolic pathways. Phylogenetic analysis combined with RNA structure probing, searches for RsaEÀmRNA base pairing, and toeprinting assays indicate that a conserved and unpaired UCCC sequence motif of RsaE binds to target mRNAs and prevents the formation of the ribosomal initiation complex. This study unexpectedly shows that most of the novel ncRNAs carry the conserved CÀrich motif, suggesting that they are members of a class of ncRNAs that target mRNAs by a shared mechanism.
Citeseer, 2006
... Carrere 1 , Emmanuel Courcelle 1 , Marie-Josée Cros 3 , Sylvain Foissac 3 , Annick Moisan 3 ,... more ... Carrere 1 , Emmanuel Courcelle 1 , Marie-Josée Cros 3 , Sylvain Foissac 3 , Annick Moisan 3 , ...MENS provides a variety of pre-computed analyses and tools to quickly and thoroughly explore gene ... Bateman, A., L. Coin, R. Durbin, RD Finn, V. Hollich, et al (2004) The Pfam ...
At the core of farm management lies the issue of work organization that concerns the configuratio... more At the core of farm management lies the issue of work organization that concerns the configuration of activities in space and time, the material requirements for their execution (resources, sensors), and the anticipated means to adapt or react to contingencies. At a more micro level work organization has also to deal with operational aspects: the conditions and manner in which one or more people use purposefully information and tools in order to fulfill the specific objective attached to a primitive operation. This paper argues in favor of an investigation approach of farm management based on a simulation model of the decision maker's behavior, the course of implementing operations and the interaction of the above processes with the biophysical ones and external events linked, in particular, to climatic factors. Simulation of the management process can be of great help in conceiving new production systems or in improving their efficiency, robustness and acceptability. The paper outlines the specific modeling needs when the decision-making behavior and work process play a central role in the intended study. It proposes a conceptualization of the structure and behavior of the management related aspects of a an agricultural production system.
This paper describes a biophysical dairy farm model developed as part of the SEPATOU system that ... more This paper describes a biophysical dairy farm model developed as part of the SEPATOU system that simulates pasture-dominated feeding strategies in a dairy cow enterprise. It can reproduce the effects of various technical management options applied to a set of grazing fields on a daily basis over a period of several months. The model is made up of three submodels that deal with the soil (availability of water), sward and animal (cow intake and milk yield) components. It includes as driving variables the main factors that farmers can control (nitrogen fertilizer rate, defoliation frequency and intensity, composition of cows' diet) in order to attain some objectives such as the intended grazing herbage contribution in the cows' diet or the amount of milk produced per cow or per ha. The intended purpose of the SEPATOU system has led to several original developments. In order to simulate various defoliation regimes, growth and senescence processes are dissociated as there is no longer synchronization between them, and the effect of grazing intensity is expressed in terms of the ratio between the herbage mass after and before grazing. The animal intake submodel that can deal with mixed feeding combines two approaches, one based on energy requirements and the other on the relationship between herbage mass, herbage digestibility and intake. The model of herbage digestibility is based on herbage mass and takes into account its variation down the sward profile; this latter aspect plays a key role in the plant-animal interaction. The model has been validated using typical farm cases in Brittany. It provides realistic estimates of the state variables involved in the processes, such as herbage mass and daily milk yield, and it credibly predicts the timing of key events (e.g. date of turnout to grass, end of first grazing cycle).
RNA, 2011
The annotation of noncoding RNA genes remains a major bottleneck in genome sequencing projects. M... more The annotation of noncoding RNA genes remains a major bottleneck in genome sequencing projects. Most genome sequences released today still come with sets of tRNAs and rRNAs as the only annotated RNA elements, ignoring hundreds of other RNA families. We have developed a web environment that is dedicated to noncoding RNA (ncRNA) prediction, annotation, and analysis and allows users to run a variety of tools in an integrated and flexible manner. This environment offers complementary ncRNA gene finders and a set of tools for the comparison, visualization, editing, and export of ncRNA candidates. Predictions can be filtered according to a large set of characteristics. Based on this environment, we created a public website located at http://RNAspace.org. It accepts genomic sequences up to 5 Mb, which permits for an online annotation of a complete bacterial genome or a small eukaryotic chromosome. The project is hosted as a Source Forge project (http://rnaspace.sourceforge.net/).
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Papers by Marie-Josée Cros