Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks

International audienceIncreasing amounts of sequence data are becoming available for a wide range of non-model organisms. Investigating and modelling the metabolic behaviour of those organisms is highly relevant to understand their biology and ecology. As sequences are often incomplete and poorly annotated, draft networks of their metabolism largely suffer from incompleteness. Appropriate gap-filling methods to identify and add missing reactions are therefore required to address this issue. However, current tools rely on phenotypic or taxonomic information, or are very sensitive to the stoichiometric balance of metabolic reactions, especially concerning the co-factors. This type of information is often not available or at least prone to errors for newly-explored organisms. Here we introduce Meneco, a tool dedicated to the topological gap-filling of genome-scale draft metabolic networks. Meneco reformulates gap-filling as a qualitative combinatorial optimization problem, omitting constraints raised by the stoichiometry of a metabolic network considered in other methods, and solves this problem using Answer Set Programming. Run on several artificial test sets gathering 10,800 degraded Escherichia coli networks Meneco was able to efficiently identify essential reactions missing in networks at high degradation rates, outperforming the stoichiometry-based tools in scalability. To demonstrate the utility of Meneco we applied it to two case studies. Its application to recent metabolic networks reconstructed for the brown algal model Ectocarpus siliculosus and an associated bacterium Candidatus Phaeomarinobacter ectocarpi revealed several candidate metabolic pathways for algal-bacterial interactions. Then Meneco was used to reconstruct, from transcriptomic and metabolomic data, the first metabolic network for the microalga Euglena mutabilis. These two case studies show that Meneco is a versatile tool to complete draft genome-scale metabolic networks produced from heterogeneous data, and to suggest relevant reactions that explain the metabolic capacity of a biological system

Altimetry for the future: Building on 25 years of progress

In 2018 we celebrated 25 years of development of radar altimetry, and the progress achieved by this methodology in the fields of global and coastal oceanography, hydrology, geodesy and cryospheric sciences. Many symbolic major events have celebrated these developments, e.g., in Venice, Italy, the 15th (2006) and 20th (2012) years of progress and more recently, in 2018, in Ponta Delgada, Portugal, 25 Years of Progress in Radar Altimetry. On this latter occasion it was decided to collect contributions of scientists, engineers and managers involved in the worldwide altimetry community to depict the state of altimetry and propose recommendations for the altimetry of the future. This paper summarizes contributions and recommendations that were collected and provides guidance for future mission design, research activities, and sustainable operational radar altimetry data exploitation. Recommendations provided are fundamental for optimizing further scientific and operational advances of oceanographic observations by altimetry, including requirements for spatial and temporal resolution of altimetric measurements, their accuracy and continuity. There are also new challenges and new openings mentioned in the paper that are particularly crucial for observations at higher latitudes, for coastal oceanography, for cryospheric studies and for hydrology. The paper starts with a general introduction followed by a section on Earth System Science including Ocean Dynamics, Sea Level, the Coastal Ocean, Hydrology, the Cryosphere and Polar Oceans and the ‘‘Green” Ocean, extending the frontier from biogeochemistry to marine ecology. Applications are described in a subsequent section, which covers Operational Oceanography, Weather, Hurricane Wave and Wind Forecasting, Climate projection. Instruments’ development and satellite missions’ evolutions are described in a fourth section. A fifth section covers the key observations that altimeters provide and their potential complements, from other Earth observation measurements to in situ data. Section 6 identifies the data and methods and provides some accuracy and resolution requirements for the wet tropospheric correction, the orbit and other geodetic requirements, the Mean Sea Surface, Geoid and Mean Dynamic Topography, Calibration and Validation, data accuracy, data access and handling (including the DUACS system). Section 7 brings a transversal view on scales, integration, artificial intelligence, and capacity building (education and training). Section 8 reviews the programmatic issues followed by a conclusion

Altimetry for the future: building on 25 years of progress

In 2018 we celebrated 25 years of development of radar altimetry, and the progress achieved by this methodology in the fields of global and coastal oceanography, hydrology, geodesy and cryospheric sciences. Many symbolic major events have celebrated these developments, e.g., in Venice, Italy, the 15th (2006) and 20th (2012) years of progress and more recently, in 2018, in Ponta Delgada, Portugal, 25 Years of Progress in Radar Altimetry. On this latter occasion it was decided to collect contributions of scientists, engineers and managers involved in the worldwide altimetry community to depict the state of altimetry and propose recommendations for the altimetry of the future. This paper summarizes contributions and recommendations that were collected and provides guidance for future mission design, research activities, and sustainable operational radar altimetry data exploitation. Recommendations provided are fundamental for optimizing further scientific and operational advances of oceanographic observations by altimetry, including requirements for spatial and temporal resolution of altimetric measurements, their accuracy and continuity. There are also new challenges and new openings mentioned in the paper that are particularly crucial for observations at higher latitudes, for coastal oceanography, for cryospheric studies and for hydrology. The paper starts with a general introduction followed by a section on Earth System Science including Ocean Dynamics, Sea Level, the Coastal Ocean, Hydrology, the Cryosphere and Polar Oceans and the “Green” Ocean, extending the frontier from biogeochemistry to marine ecology. Applications are described in a subsequent section, which covers Operational Oceanography, Weather, Hurricane Wave and Wind Forecasting, Climate projection. Instruments’ development and satellite missions’ evolutions are described in a fourth section. A fifth section covers the key observations that altimeters provide and their potential complements, from other Earth observation measurements to in situ data. Section 6 identifies the data and methods and provides some accuracy and resolution requirements for the wet tropospheric correction, the orbit and other geodetic requirements, the Mean Sea Surface, Geoid and Mean Dynamic Topography, Calibration and Validation, data accuracy, data access and handling (including the DUACS system). Section 7 brings a transversal view on scales, integration, artificial intelligence, and capacity building (education and training). Section 8 reviews the programmatic issues followed by a conclusion

Integrating Tools and Infrastructures for Generic Multi-Agent Systems

In this paper, we present MadKit/SEdit, an agent infrastructure combined with a generic design tool for multi-agent systems. This toolkit is based on a organizational metaphor to integrate highly heterogeneous agent systems

MadKit: une architecture de plate-forme multi-agent générique

Dans ce rapport, nous présentons l’architecture de MadKit (pour “Multi-Agent Development Kit”), une plate-forme générique de conception et d’exécution de systèmes multi-agents. Cette plate-forme a l’originalité d’être basé sur un modèle organisationnel plutôt qu’une architecture d’agent ou un modèle d’interaction spécifique. L’utilisation de groupes et de roles associés à des agents est mis en oeuvre tant en tant qu’outil de modèlisation et de conception pour les développeurs de systèmes multi-agents, que de principe d’architecture de la plate-forme elle-même. Cette architecture est basée sur un noyau agent minimal découplé de tout modèle individuel d’agent. Dans cette plate-forme, les services classiques de passage de message distribués, de migration ou de surveillance sont fournis au meta-niveau par des agents spécialisés afin d’obtenir un maximum de flexibilité. Une interface graphique componentielle et découplée du noyau et des agents permets de supporter différentes modes d’utilisation et d’exploitation de la plate-forme. Nous illustrons notre propos en présentant certaines conséquences et déclinaisons de cette plateforme, ainsi que quelques applications construites avec MadKit

MADKIT: une expérience d'architecture de plateforme multi-agent générique

International audienceDans cet article, nous présentons l'architecture de MADKIT (pour "Multi-Agent Development Kit"), une plate-forme générique de conception et d'exécution de systèmes multi-agents. Cette plate-forme a l'originalité d'être basé sur un modèle organisationnel plutôt qu'une architecture d'agent ou un modèle d'interaction spécifique. L'utilisation de groupes et de rôles associés à des agents est mis en oeuvre en tant qu'outil de modélisation et de conception pour les développeurs de systèmes multi-agents, mais également comme principe d'architecture de la plate-forme elle-même. Cette architecture est basée sur un noyau agent minimal découplé de tout modèle individuel d'agent. Dans cette plate-forme, les services classiques de passage de message distribués, de migration ou de surveillance sont fournis au meta-niveau par des agents spécialisés afin d'ob-tenir un maximum de flexibilité. Une interface graphique componentielle et découplée du noyau et des agents permet de supporter différentes modes d'utilisation et d'exploitation de la plate-forme. Nous illustrons notre propos en présentant certaines conséquences, déclinaisons et applications de cette plateforme

Agent/Group/Roles: Simulating with Organizations

International audienceMulti-agent systems seem to provide a good basis to build complex agent based simulation systems, but this paper points out some of the drawbacks of classical “agent centered” multi- agent systems and propose a solution to these problems by using “organization centered multi-agent system”, or OCMAS for short. We propose a set of general principles from which true OCMAS may be designed. One of these principles is not to assume anything about the cognitive capabilities of agents. In order to show how OCMAS models may be designed, we show how a very concise and minimal OCMAS model called AGR, for Agent/Group/Role, may be used to build true OCMAS systems. We propose a set of notations and a methodological framework to help the designer to build MAS using AGR

Generic Simulation Tools Based on MAS Organization

This paper presents generic simulation tools which rely on an original methodological approach of designing multi-agent simulators

Agent/Group/Roles: Simulating with Organizations

International audienceMulti-agent systems seem to provide a good basis to build complex agent based simulation systems, but this paper points out some of the drawbacks of classical “agent centered” multi- agent systems and propose a solution to these problems by using “organization centered multi-agent system”, or OCMAS for short. We propose a set of general principles from which true OCMAS may be designed. One of these principles is not to assume anything about the cognitive capabilities of agents. In order to show how OCMAS models may be designed, we show how a very concise and minimal OCMAS model called AGR, for Agent/Group/Role, may be used to build true OCMAS systems. We propose a set of notations and a methodological framework to help the designer to build MAS using AGR

Biomass restoration and recovery of essential reactions due to completion of 10,800 degraded networks by Meneco.

<p>For the 10,800 degraded <i>iJR</i>904, <i>iAF</i>1260 and <i>iJO</i>1366 networks, the gap-filling results were classified according to their status: (i) restored biomass production (green and white stripes), (ii) recovery of all essential reactions (green), (iii) exactly one missed essential reaction (orange) and (iv) more than one missed essential reaction (red).</p