Repetitive Allocation Modeling with MARTE

Invited paper, Author names alphabetically orderedInternational audienceWith the advent of multi-processor Systems-on-Chip (MpSoC), the need for modeling the distribution of a parallel application onto a parallel hardware architecture is increasing. The recent standard profile for the modeling and analysis of real-time and embedded systems (MARTE) provides a notation for the modeling of regular distributions. This notation allows to distribute computations to processing elements, data to shared or distributed memories, etc. In this paper we will highlight the expressivity of this notation and clarify its usage through examples and comparisons to other distribution notations such as in High Performance Fortran

Introducing control in the gaspard2 data-parallel metamodel: Synchronous approach

Abstract. In this paper, we study the introduction of control into the Gaspard2 application UML metamodel by using the principles of synchronous reactive systems. This allows to take the change of running mode into account in the case of data parallel applications, and to study more general ways of mixing control and data parallel processing. Our study is applied to a particular context using two different models, exclusively dedicated to the process of computation or control. The computation part represents the Gaspard2 application metamodels based on the Array-OL language which is often used to specify the data dependencies and the potential parallelism in intensive applications treating multidimensional data. The control part is represented by an automaton structure based on the mode-automata concept which makes it possible to clearly identify the different modes of a task and the switching conditions between modes. The proposed UML metamodel makes it possible to describe the control automata, the different running modes and the link between control and computation parts. It also allows to clearly separate the control and data parts, and to respect the concurrency, the parallelism, the determinism and the compositionality of the Gaspard2 models.

Comparative transcriptomics of anadromous and resident brook charr Salvelinus fontinalis before their first salt water transition

Most salmonid taxa have an anadromous life history strategy, whereby fish migrate to saltwater habitats for a growth period before returning to freshwater habitats for spawning. Moreover, several species are characterized by different life history tactics whereby resident and anadromous forms may occur in genetically differentiated populations within a same species, as well as polymorphism within a population. The molecular mechanisms underlying the physiological differences between anadromous and resident forms during the first transition from freshwater to saltwater environments are only partially understood. Insofar research has typically focused on species of the genus Salmo. Here, using a 16,000 cDNA array, we tested the hypothesis that anadromous brook charr Salvelinus fontinalis are characterized by differences in their transcriptome relative to resident brook charr before the anadromous fish migration. Families originating from parapatric populations of anadromous and resident charr were reared in controlled environments mimicking natural temperature and photoperiod, and sampled in spring, while still in fresh water. While anadromous and resident charr showed similar transcriptome profiles in white muscle, they were characterized by striking differences in their gill transcriptome profiles. Genes that were upregulated in the gills of anadromous charr were principally involved in metabolism (mitochondrial electron transport chain, glucose metabolism, and protein synthesis), development (tissue differentiation) and innate immunity. We discuss the nature of these transcriptomic differences in relation to molecular mechanisms underlying the expression of anadromous and resident life history tactics and suggest that the anadromous charr express some of the molecular processes present in other migratory salmonids [Current Zoology 58 (1): 158–170, 2012]

Synchronous Modeling of Data Intensive Applications

apport de recherch

Gaspard2: from MARTE to SystemC Simulation

International audienc

ChemHouse, a research and development centre for chemometrics

International audienceIntroductionChemHouse is a research group of around 50 members, bringing together experts in chemometrics, users and PhD students from partner institutes and companies. The objective of ChemHouse is to help its partners to overcome methodological barriers and difficulties in the use of chemometrics by: -scientific animation in chemometrics, -welcoming students and researchers, -chemometric tools (CheMoocs, ChemFlow, ChemData), -workshops and research schools (ChemOmics, ChemSchool)-project building.Material and methods Every fortnight, a member (or an outsider, invited by a member) leads a scientific seminar based on a presentation on a topic of his choice, related to operational and research issues in chemometrics. At the same time, students and researchers are regularly welcomed (for weeks to months) to exchange on scientific subjects, and to improve their data processing skills. A Massive Open Online Course (MOOC), CheMoocs, was also created to train students and researchers on chemometric methods that ChemHouse members use or have developed. CheMoocs exercices are based on the Galaxy instance ‘ChemFlow’, and an open database ‘ChemData’.ChemHouse members organize workshops and chemometrics events. In addition, because of similarities and complementarities between chemometrics and metabolomics, the two communities meet and exchange during collaborations and conferences. ChemOmics is a group of researchers and users formed to regularly organize joint schools.ChemHouse members initiate and collaborate together on research projects, to go deeper into data analysis by developing workflows, tools and algorithms.Results and discussionAround 20 scientific presentations are held each year on different topics such as: Near Infrared Spectroscopy data modeling, pre-processing of spectra, variable selection, variants of PLS modelling… In parallel, researchers are hosted on average 9 months per year.CheMoocs is currently composed of 28 modules gathered into 2 sessions: unsupervised and supervised methods. This course is annually followed by around 1500 people. With ChemFlow, a free and open-source software, they can upload various data types, create interactive graphs, and apply conventional and more advanced chemometric methods. ChemData collects datasets from the MOOC, from public projects of the ChemHouse group, or from external repositories.Concerning the events, ChemHouse organizes in collaboration with the COST action Sensorfint, a workshop 'ChemSchool' in September. The third session of ‘ChemOmics’ will also take place this year in October. In addition, ChemHouse participates in the setting up and implementation of national (Digitbio-MIMS) and international (Explore, AVITech) projects.ConclusionChemHouse offers a complete environment designed by and for chemometrics, grouped together in ‘ChemProject’ (https://chemproject.org/). ChemProject is aimed to enable as many people as possible to practice chemometrics. It is based on 3 pillars: CheMoocs which provides theoretical knowledge in chemometrics, ChemFlow which offers the main methods encountered in chemometrics, and ChemData that contains downloadable public data. ChemHouse is also open to methodological exchanges, collaboration on scientific projects, and offers training activities

ChemHouse, a research and development centre for chemometrics

International audienceIntroductionChemHouse is a research group of around 50 members, bringing together experts in chemometrics, users and PhD students from partner institutes and companies. The objective of ChemHouse is to help its partners to overcome methodological barriers and difficulties in the use of chemometrics by: -scientific animation in chemometrics, -welcoming students and researchers, -chemometric tools (CheMoocs, ChemFlow, ChemData), -workshops and research schools (ChemOmics, ChemSchool)-project building.Material and methods Every fortnight, a member (or an outsider, invited by a member) leads a scientific seminar based on a presentation on a topic of his choice, related to operational and research issues in chemometrics. At the same time, students and researchers are regularly welcomed (for weeks to months) to exchange on scientific subjects, and to improve their data processing skills. A Massive Open Online Course (MOOC), CheMoocs, was also created to train students and researchers on chemometric methods that ChemHouse members use or have developed. CheMoocs exercices are based on the Galaxy instance ‘ChemFlow’, and an open database ‘ChemData’.ChemHouse members organize workshops and chemometrics events. In addition, because of similarities and complementarities between chemometrics and metabolomics, the two communities meet and exchange during collaborations and conferences. ChemOmics is a group of researchers and users formed to regularly organize joint schools.ChemHouse members initiate and collaborate together on research projects, to go deeper into data analysis by developing workflows, tools and algorithms.Results and discussionAround 20 scientific presentations are held each year on different topics such as: Near Infrared Spectroscopy data modeling, pre-processing of spectra, variable selection, variants of PLS modelling… In parallel, researchers are hosted on average 9 months per year.CheMoocs is currently composed of 28 modules gathered into 2 sessions: unsupervised and supervised methods. This course is annually followed by around 1500 people. With ChemFlow, a free and open-source software, they can upload various data types, create interactive graphs, and apply conventional and more advanced chemometric methods. ChemData collects datasets from the MOOC, from public projects of the ChemHouse group, or from external repositories.Concerning the events, ChemHouse organizes in collaboration with the COST action Sensorfint, a workshop 'ChemSchool' in September. The third session of ‘ChemOmics’ will also take place this year in October. In addition, ChemHouse participates in the setting up and implementation of national (Digitbio-MIMS) and international (Explore, AVITech) projects.ConclusionChemHouse offers a complete environment designed by and for chemometrics, grouped together in ‘ChemProject’ (https://chemproject.org/). ChemProject is aimed to enable as many people as possible to practice chemometrics. It is based on 3 pillars: CheMoocs which provides theoretical knowledge in chemometrics, ChemFlow which offers the main methods encountered in chemometrics, and ChemData that contains downloadable public data. ChemHouse is also open to methodological exchanges, collaboration on scientific projects, and offers training activities