Cut generation for an integrated employee timetabling and production scheduling problem

International audienceThis paper investigates the integration of the employee timetabling and production scheduling problems. At the first level, we manage a classical employee timetabling problem. At the second level, we aim at supplying a feasible production schedule for a set of interruptible tasks with qualification requirements and time-windows. Instead of hierarchically solving these two problems as in the current practice, we try here to integrate them and propose two exact methods to solve the resulting problem. The former is based on a Benders decomposition while the latter relies on a specific decomposition and a cut generation process. The relevance of these different approaches is discussed here through experimental results

Couplage planification/ordonnancement : une approche par décomposition et génération de coupes.

International audienceCette étude porte sur un problème couplant les deux phases décisionnelles, dans un processus de production, que sont la planification d'agents et l'ordonnancement de production. D'un côté, nous devons gérer au moindre coût les emplois du temps d'un ensemble d'opérateurs (planification d'agents) et de l'autre, nous nous attelons à fournir un plan de production réalisable, compte tenu des ressources disponibles déduites de la phase de planification, et qui vise à satisfaire une certaine demande fournie en entrée (ordonnancement de production). Contrairement à la plupart des articles de la littérature, nous proposons ici des techniques de résolution résolvant simultanément ces deux problèmes. Deux approches exactes ont été étudiées : l'une d'elles est fondée sur une décomposition de Benders et l'autre est basée sur un processus spécifique de génération de coupes. L'intérêt de ces méthodes est discuté ici au travers de résultats expérimentaux

Branch and Bound hybride pour un problème de job-shop soumis à des contraintes de ressources humaines

National audienceNous considérons un problème couplant ordonnancement de production et planification d'agents. On se place ainsi dans un atelier où la production à réaliser requiert divers types de machines dans des séquences variées de type job-shop. Chaque machine nécessite pour son utilisation la présence d'un employé qualifié à son pilotage. Les ressources humaines sont assujetties à des contraintes légales restreignant leur disponibilité. La production doit être entièrement ordonnancée et le critère d'optimisation retenu est la minimisation des coûts salariaux. Pour résoudre ce problème, nous avons développé une méthode exacte hybridant approche arborescente de type Procédure de Séparation et Evaluation Séquentielle et technique de génération de coupes de réalisabilité. Cette méthode exploite la décomposition naturelle du problème global en deux sous-problèmes : un problème de planification d'agents et un problème de job-shop à contraintes de disponibilité. Des méthodes de génération d'inégalités valides en pré-process (notamment du probing) ont en outre été étudiées. Notre approche s'avère particulièrement adaptée à la problématique ; ses résultats dominent en effet ceux obtenus avec l'un des meilleurs solveurs commerciaux actuels (Ilog Cplex 12.1) et ceux obtenus avec les méthodes décrites dans la littérature

Solving an integrated Job-Shop problem with human resource constraints

This paper investigates the integration of the employee timetabling and production scheduling problems. At the first level, we have to manage a classical employee timetabling problem. At the second level, we aim at supplying a feasible production schedule for a job-shop scheduling problem (NP-hard problem). Instead of using a hierarchical approach as in the current practice, we here integrate the two decision stages and propose two exact methods for solving the resulting problem. The former is similar to the cut generation algorithm proposed in Guyon et. al. 2010) for a problem integrating a classical employee timetabling problem and a polynomially solvable production scheduling problem. The latter is based on a Branch-And-Cut process that exploits the same feasibility cuts than the first approach. Preliminar experimental results on instances proposed in (Artigues et al. 2009) reveal a real interest for the approaches described here

Planification d'agents et ordonnancement de production : règles d'élimination et heuristique

Nous nous intéressons à l'optimisation des systèmes de production avec d'un côté l'ordonnancement de production, dont le but est d'affecter dans le temps des ressources à des tâches à réaliser, et d'un autre côté la gestion du personnel visant généralement à minimiser les coûts de main d'œuvre. Bien qu'il soit admis que, pour obtenir l'optimum global, il faille prendre en compte simultanément ces deux problématiques, en pratique le problème global est souvent résolu dans un processus de décision à deux niveaux. Dans cette étude, nous intégrons ces deux phases de décision et proposons différentes méthodes pour résoudre le problème résultant

Solving an integrated job-shop problem with human resource constraints

International audienceWe propose two exact methods to solve an integrated employee-timetable and job-shop-scheduling problem. The problem is to find a minimum cost employee-timetable, where employees have different competences and work during shifts, so that the production, that corresponds to a job-shop with resource availability constraints, can be achieved. We introduce two new exact procedures: (1) a decomposition and cut generation approach and (2) a hybridization of a cut generation process with a branch and bound strategy. We also propose initial cuts that strongly improve these methods as well as a standard MIP approach. The computational performances of those methods on benchmark instances are compared to that of other methods from the literature

Ampelovirus and Vitivirus relationships in grapevine

Ampelovirus and Vitivirus relationships in grapevine. 16e Rencontres de Virologie Végétal

Curation of NISEED, an integrative framework for the digital representation of embryonic development

NISEED (Network for In situ Expression and Embryological Data) is a generic infrastructure for the creation, maintenance and integration of molecular and anatomical information on model organisms. We applied it to ascidians which are marine invertebrate chordates. These animals constitute model organisms of choice for developmental biology because their embryos develop with a small number of cells and an invariant lineage, allowing their study with a cellular level of resolution. In ANISEED (Ascidian NISEED), embryogenesis of ascidian is represented at the level of the genome via functional gene annotations, cis-regulatory elements or gene expression data, at the level of the cell by representing its morphology, fates, lineage, and relations with its neighbors, or at the level of the whole embryo by representing its anatomy and morphogenesis at successive developmental stages. The system provides also tool and standard to enter, annotate, curate and manage data. All results can be accessed through the ANISEED website at "http://aniseed-ibdm.univ-mrs.fr":http://aniseed-ibdm.univ-mrs.fr
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Retention of the virus-derived sequences in the nuclear genome of grapevine as a potential pathway to virus resistance

<p>Abstract</p> <p>Background</p> <p>Previous studies have revealed a wide-spread occurence of the partial and complete genomes of the reverse-transcribing pararetroviruses in the nuclear genomes of herbaceous plants. Although the absence of the virus-encoded integrases attests to the random and incidental incorporation of the viral sequences, their presence could have functional implications for the virus-host interactions.</p> <p>Hypothesis</p> <p>Analyses of two nuclear genomes of grapevine revealed multiple events of horizontal gene transfer from pararetroviruses. The ~200–800 bp inserts that corresponded to partial ORFs encoding reverse transcriptase apparently derived from unknown or extinct caulimoviruses and tungroviruses, were found in 11 grapevine chromosomes. In contrast to the previous reports, no reliable cases of the inserts derived from the positive-strand RNA viruses were found. Because grapevine is known to be infected by the diverse positive-strand RNA viruses, but not pararetroviruses, we hypothesize that pararetroviral inserts have conferred host resistance to these viruses. Furthermore, we propose that such resistance involves RNA interference-related mechanisms acting via small RNA-mediated methylation of pararetroviral DNAs and/or via degradation of the viral mRNAs.</p> <p>Conclusion</p> <p>The pararetroviral sequences in plant genomes may be maintained due to the benefits of virus resistance to this class of viruses conferred by their presence. Such resistance could be particularly significant for the woody plants that must withstand years- to centuries-long virus assault. Experimental research into the RNA interference pathways involving the integrated pararetroviral inserts is required to test this hypothesis.</p> <p>Reviewers</p> <p>This article was reviewed by Arcady R. Mushegian, I. King Jordan, and Eugene V. Koonin.</p

Comparison of Serological and Molecular Methods With High-Throughput Sequencing for the Detection and Quantification of Grapevine Fanleaf Virus in Vineyard Samples

Grapevine fanleaf virus (GFLV) is the main causal agent of fanleaf degeneration, the most damaging viral disease of grapevine. GFLV is included in most grapevine certification programs that rely on robust diagnostic tools such as biological indexing, serological methods, and molecular techniques, for the identification of clean stocks. The emergence of high throughput sequencing (HTS) offers new opportunities for detecting GFLV and other viruses in grapevine accessions of interest. Here, two HTS-based methods, i.e., RNAseq and smallRNAseq (focusing on the 21 to 27 nt) were explored for their potential to characterize the virome of grapevine samples from two 30-year-old GFLV-infected vineyards in the Champagne region of France. smallrnaseq was optimal for the detection of a wide range of viral species within a sample and RNAseq was the method of choice for full-length viral genome assembly. The implementation of a protocol to discriminate between low GFLV titer and in silico contamination (intra-lane contamination due to index misassignment) during data processing was critical for data analyses. Furthermore, we compared the performance of semi-quantitative DAS-ELISA (double antibody enzyme-linked immunosorbent assay), RT-qPCR (Reverse transcription-quantitative polymerase chain reaction), Immuno capture (IC)-RT-PCR, northern blot for viral small interfering RNA (vsiRNA) detection and RNAseq for the detection and quantification of GFLV. While detection limits were variable among methods, as expected, GFLV diagnosis was consistently achieved with all of these diagnostic methods. Together, this work highlights the robustness of DAS-ELISA, the current method routinely used in the French grapevine certification program, for the detection of GFLV and offers perspectives on the potential of HTS as an approach of high interest for certification