Genomic data is a rich source of information about population history. In particular, for actively recombining species the time to the last common ancestor (LCA) between two chromosomes might be ...different in different chromosome loci. Estimating local LCA time is important for many problems: it can be used to infer genes under selection, or to infer effective population size changes. The current state-of-the art method PSMC to infer local LCA time and effective population size is based on a Hidden Markov Model. In this work we propose a new deep learning framework for local LCA time inference at the full genome scale. We demonstrate that our method is accurate in both local LCA time and, as a consequence, at the LCA time distribution which in turn translates into effective population size trajectory. In future our approach can be generalised for complex population scenarios.
The LHCb Grid Simulation: Proof of Concept Hushchyn, M; Ustyuzhanin, A; Arzymatov, K ...
Journal of physics. Conference series,
10/2017, Letnik:
898, Številka:
5
Journal Article
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The Worldwide LHC Computing Grid provides access to data and computational resources to analyze it for researchers with different geographical locations. The grid has a hierarchical topology with ...multiple sites distributed over the world with varying number of CPUs, amount of disk storage and connection bandwidth. Job scheduling and data distribution strategy are key elements of grid performance. Optimization of algorithms for those tasks requires their testing on real grid which is hard to achieve. Having a grid simulator might simplify this task and therefore lead to more optimal scheduling and data placement algorithms. In this paper we demonstrate a grid simulator for the LHCb distributed computing software.
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