Half a billion simulations: evolutionary algorithms and distributed computing for calibrating the SimpopLocal geographical model

Multi-agent geographical models integrate very large numbers of spatial interactions. In order to validate those models large amount of computing is necessary for their simulation and calibration. Here a new data processing chain including an automated calibration procedure is experimented on a computational grid using evolutionary algorithms. This is applied for the first time to a geographical model designed to simulate the evolution of an early urban settlement system. The method enables us to reduce the computing time and provides robust results. Using this method, we identify several parameter settings that minimise three objective functions that quantify how closely the model results match a reference pattern. As the values of each parameter in different settings are very close, this estimation considerably reduces the initial possible domain of variation of the parameters. The model is thus a useful tool for further multiple applications on empirical historical situations

Le Palais Nord d’Ougarit

Le Palais Nord de Ras Shamra-Ougarit, découvert en 1968, a fait l’objet de plusieurs rapports préliminaires ; nous proposons ici un essai de synthèse monographique. Situé au nord de la « Forteresse Royale », cet édifice apparaît comme un ensemble architectural cohérent, constitué par un certain nombre de secteurs fonctionnels, organisés selon des modèles spécifiques, où se déroulaient, pensons-nous, les activités quotidiennes, publiques et privées, d’un système politique et économique de type palatial. Construit au xvie siècle av. J.-C., à la charnière entre le Bronze moyen et le Bronze récent, le Palais Nord est un monument atypique, quelque peu hybride. Les formules planimétriques et certains éléments structurels représentent autant d’innovations caractéristiques de l’architecture monumentale classique d’Ougarit  ; d’autres procédés de construction reflètent, au contraire, le poids des traditions syriennes archaïques de la première moitié du IIe millénaire av. J.-C.Ras Shamra‑Ugarit North Palace, discovered in 1968, was subject of several preliminary reports; we herewith suggest a monographic synthesis. Located to the north of the “Royal Fortress”, this building appears like a coherent architectural complex structured in functional areas organized according to specific layouts where we believe daily public and private activities of a palatial political and economical system were taking place. Constructed during the 16th century bc, at the turning point between Middle Bronze and Late Bronze Age, the North Palace is an atypical monument, somehow syncretic. The planimetric concepts and some structural components are characteristic innovations of Ugarit classical monumental architecture; other construction techniques reflect however the weight of archaic syrian traditions from the first half of the 2nd millennium bc.خلاصة – كان القصر الشمالي لرأس شمرا-أوغاريت، المكتشف سنة 1968 موضوع عدّة تقارير تمهيدية. نقترح في هذا البحث عرضاً شاملاً أُحادياً لها. بحكم موقعه شمال « القلعة الملكية» يظهر هذا البناء كمجموعة معمارية متناسقة، مؤلفة من عدّة أقسام، حسب الإحتياجات الحياتية الخاصة والعامة لنظام سياسي وإقتصادي ملكي وهي منظمة وفق نماذج خاصة. هذا القصر شُيّد في القرن السادس عشر ق.م. في حقبة مفصلية بين العصر البرونزي الوسيط والبرونزي الحديث وهو مبنى ذات طابع غير نموذجي إلى حدّ ما هجين. تقدم طرق المساحة والقياسات الهندسية المعتمدة بالإضافة إلى بعض العناصر الهندسية للصروح في أوغاريت إبتكارات مميزة للهندسة الكلاسيكية، بينما تُظهر بعض طرق البناء وخلافا لما سبق تأثيراً سورياً قديماً يعود إلى النصف الأوّل من الألف الثاني ق.م

Assessing the precision of high-throughput computational and laboratory approaches for the genome-wide identification of protein subcellular localization in bacteria

BACKGROUND: Identification of a bacterial protein's subcellular localization (SCL) is important for genome annotation, function prediction and drug or vaccine target identification. Subcellular fractionation techniques combined with recent proteomics technology permits the identification of large numbers of proteins from distinct bacterial compartments. However, the fractionation of a complex structure like the cell into several subcellular compartments is not a trivial task. Contamination from other compartments may occur, and some proteins may reside in multiple localizations. New computational methods have been reported over the past few years that now permit much more accurate, genome-wide analysis of the SCL of protein sequences deduced from genomes. There is a need to compare such computational methods with laboratory proteomics approaches to identify the most effective current approach for genome-wide localization characterization and annotation. RESULTS: In this study, ten subcellular proteome analyses of bacterial compartments were reviewed. PSORTb version 2.0 was used to computationally predict the localization of proteins reported in these publications, and these computational predictions were then compared to the localizations determined by the proteomics study. By using a combined approach, we were able to identify a number of contaminants and proteins with dual localizations, and were able to more accurately identify membrane subproteomes. Our results allowed us to estimate the precision level of laboratory subproteome studies and we show here that, on average, recent high-precision computational methods such as PSORTb now have a lower error rate than laboratory methods. CONCLUSION: We have performed the first focused comparison of genome-wide proteomic and computational methods for subcellular localization identification, and show that computational methods have now attained a level of precision that is exceeding that of high-throughput laboratory approaches. We note that analysis of all cellular fractions collectively is required to effectively provide localization information from laboratory studies, and we propose an overall approach to genome-wide subcellular localization characterization that capitalizes on the complementary nature of current laboratory and computational methods

Webscraping : enjeux techniques et éthiques

National audienceInternet regorge de données dont certaines sont potentiellement très utiles pour la recherche en géographie et analyse spatiale. Dans cette présentation, nous essaierons d’assumer le principe que toutes les informations visibles sur le web, du moment où elles sont consultables, peuvent être récupérées. Dans un contexte mondialisé où l’accès à l’information est parfois comparé à une nouvelle ruée vers l’or, un ensemble de moyens techniques et juridiques sont mis en œuvre par les entreprises pour protéger leurs données (parfois synonymes de clients) tout en captant celle des autres.Nous essaierons de répondre sur les enjeux techniques en présentant plusieurs cas concrets de collecte et d’utilisation de données géographiques propres à différents contextes d’études – flux d’avions, congestion du trafic, sites de vente ou de location en ligne, ou encore réseaux sociaux.Avec l’évolution rapide du cadre juridique (RGPD, TOS +/- légale), la collecte de ces données au-delà du cadre juridique prévu par les entreprises soulève évidemment des considérations éthiques. Avec le RGPD nous pensons qu’il est important de reconsidérer cette collecte par le prisme d’un triptyque asymétrique que forment les utilisateurs d’un service web, les propriétaires des plateformes et les utilisateurs tiers qui récoltent des données, surtout si ces dernières sont de natures individuelles et géolocalisées

Le Calcul pour la simulation des systèmes complexes en géographie

National audienc

Crystallisation of a highly metastable hydrated calcium pyrophosphate phase

A simple and fast synthesis method was set up to obtain pure hydrated calcium pyrophosphate (CPP)phases of biological interest. This work focused on a specific phase synthesised at 25 uC and pH 4.5 in a stirred tank reactor. Powder X-ray diffraction, FTIR spectroscopy, scanning electron microscopy and thermogravimetric analyses revealed that the phase is unknown but presents similarities with a monoclinic tetrahydrated CPP phase (Ca2P2O7?4H2O, m-CPPT b phase) synthesised under the same conditions of pH and temperature. Characterisation of the unreferenced phase (u-CPP) has been performed, especially to better identify its composition, structure and stability, as well as its possible relation to the m-CPPT b phase or to other hydrated CPP phases

Introduction à Docker

École thématiqueDocker est un projet open source (Apache 2.0) écrit en GO et hébergé sur GitHub: https://github.com/docker (https://github.com/docker). Initialement porté par la startup DotCloud (renommée depuis Docker) fondée par deux français anciens de l'Epitech. Docker est composé de trois éléments : le daemon Docker qui s'exécute en arrière-plan et qui s'occupe de gérer les conteneurs (Containerd avec runC) une API de type REST qui permet de communiquer avec le daemon Le client en CLI (command line interface) : commande docker Par défaut, le client communique avec le daemon Docker via un socket Unix (/var/run/docker.sock) mais il est possible d'utiliser un socket TCP. Docker c'est aussi un dépôt d'images (aussi appelé registry) : https://store.docker.com (https://store.docker.com) Il contient les images officielles maintenues par Docker mais aussi celles mises à disposition par d'autres contributeurs. Quelques concepts: une image est un ensemble de fichiers inertes en read-only. Un conteneur est une instance une active (started) ou inactive (stopped) d'une image. L'execution d'un conteneur n'altère jamais une image. Lexique Conteneur : Image exécutable d'un environnement complet incluant code

Structure of the calcium pyrophosphate monohydrate phase (Ca2P2O7·H2O): towards understanding the dehydration process in calcium pyrophosphate hydrates

Calcium pyrophosphate hydrate (CPP, Ca2P2O7·nH2O) and calcium orthophosphate compounds (including apatite, octa­calcium phosphate etc.) are among the most prevalent pathological calcifications in joints. Even though only two dihydrated forms of CPP (CPPD) have been detected in vivo (monoclinic and triclinic CPPD), investigations of other hydrated forms such as tetra­hydrated or amorphous CPP are relevant to a further understanding of the physicochemistry of those phases of biological inter­est. The synthesis of single crystals of calcium pyrophosphate monohydrate (CPPM; Ca2P2O7·H2O) by diffusion in silica gel at ambient temperature and the structural analysis of this phase are reported in this paper. Complementarily, data from synchrotron X-ray diffraction on a CPPM powder sample have been fitted to the crystal parameters. Finally, the relationship between the resolved structure for the CPPM phase and the structure of the tetra­hydrated calcium pyrophosphate [beta] phase (CPPT-[beta]) is discussed

Influence of ionic additives on triclinic calcium pyrophosphate dihydrate precipitation

Triclinic calcium pyrophosphate dihydrate (t- CPPD) crystals are one of the two polymorphs of microcrystals that have been found in the joints of patients suffering from pseudogout. However, there is currently no treatment for inhibiting the formation of these crystals, which present a high inflammatory potential. In this context we studied in vitro the precipitation of t-CPPD in a stirred reactor under pH- and temperature-controlled conditions and determined the effect of selected biologically relevant ionic additives (Mg2+, Cu2+, Fe3+, Zn2+, S2O3 2−) on its formation. The results showed that 1 mM Fe3+, Zn2+, or Cu2+ induced the most significant changes by partly inhibiting the crystallization of t-CPPD and favoring the formation of an amorphous-CPP phase (98 wt %) in the presence of Fe3+ or a monoclinic-CPPD phase (78 or 71 wt %, respectively) in the presence of Zn2+ or Cu2+. Correlations between 31P solid-state NMR, XRD, and elemental analyses showed that the additive cations are inserted into the monoclinic-CPPD and/or amorphous-CPP phases. This study, which combines structural, morphological, and elemental analyses, paves the way toward a deeper comprehension of the role of ionic additives in preventing the formation of CPPD crystalline phases, and is a key step in long-term development of an effective therapeutic treatmen

PSORTdb: a protein subcellular localization database for bacteria

Information about bacterial subcellular localization (SCL) is important for protein function prediction and identification of suitable drug/vaccine/diagnostic targets. PSORTdb (http://db.psort.org/) is a web-accessible database of SCL for bacteria that contains both information determined through laboratory experimentation and computational predictions. The dataset of experimentally verified information (∼2000 proteins) was manually curated by us and represents the largest dataset of its kind. Earlier versions have been used for training SCL predictors, and its incorporation now into this new PSORTdb resource, with its associated additional annotation information and dataset version control, should aid researchers in future development of improved SCL predictors. The second component of this database contains computational analyses of proteins deduced from the most recent NCBI dataset of completely sequenced genomes. Analyses are currently calculated using PSORTb, the most precise automated SCL predictor for bacterial proteins. Both datasets can be accessed through the web using a very flexible text search engine, a data browser, or using BLAST, and the entire database or search results may be downloaded in various formats. Features such as GO ontologies and multiple accession numbers are incorporated to facilitate integration with other bioinformatics resources. PSORTdb is freely available under GNU General Public License