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

On the Usefulness of Clause Strengthening in Parallel SAT Solving

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Community and LBD-Based Clause Sharing Policy for Parallel SAT Solving

Due to the coronavirus COVID-19 pandemic, the conference was held virtually.International audienceModern parallel SAT solvers rely heavily on effective clause sharing policies for their performance. The core problem being addressed by these policies can be succinctly stated as “the problem of identifying high-quality learnt clauses”. These clauses, when shared between the worker nodes of parallel solvers, should lead to better performance. The term “high-quality clauses” is often defined in terms of metrics that solver designers have identified over years of empirical study. Some of the more well-known metrics to identify high-quality clauses for sharing include clause length, literal block distance (LBD), and clause usage in propagation.In this paper, we propose a new metric aimed at identifying high-quality learnt clauses and a concomitant clause-sharing policy based on a combination of LBD and community structure of Boolean formulas. The concept of community structure has been proposed as a possible explanation for the extraordinary performance of SAT solvers in industrial instances. Hence, it is a natural candidate as a basis for a metric to identify high-quality clauses. To be more precise, our metric identifies clauses that have low LBD and low community number as ones that are high-quality for applications such as verification and testing. The community number of a clause C measures the number of different communities of a formula that the variables in C span. We perform extensive empirical analysis of our metric and clause-sharing policy, and show that our method significantly outperforms state-of-the-art techniques on the benchmark from the parallel track of the last four SAT competitions

Modular and Efficient Divide-and-Conquer SAT Solver on Top of the Painless Framework

International audienceOver the last decade, parallel SATisfiability solving has been widely studied from both theoretical and practical aspects. There are two main approaches. First, divide-and-conquer (D&C) splits the search space, each solver being in charge of a particular subspace. The second one, portfolio launches multiple solvers in parallel, and the first to find a solution ends the computation. However although D&C based approaches seem to be the natural way to work in parallel, portfolio ones experimentally provide better performances. An explanation resides on the difficulties to use the native formulation of the SAT problem (i.e., the CNF form) to compute an apriori good search space partitioning (i.e.,all parallel solvers process their sub-spaces in comparable computational time). To avoid this, dynamic load balancing of the search subspaces is implemented. Unfortunately, this isdifficult to compare load balancing strategies since state-of-the-art SAT solvers appropriately dealing with these aspects are hardly adaptable tovarious strategies than the ones they have been designed for. This paper aims at providing a way to overcome this problem by proposing an implementation and evaluation of different types of divide-and-conquer inspired from the literature. These are relying on thePainless framework, which provides concurrent facilities to elaborate such parallel SAT solvers. Comparison of the various strategies are thendiscussed

Environmental history of water resources

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