Abstract. This paper presents Synapse, a scalable protocol for information retrieval over the inter-connection of heterogeneous overlay networks. Applications on top of Synapse see those intra-overlay networks as a unique inter-overlay network. Scalability in Synapse is achieved via co-located nodes, i.e. nodes that are part of multiple overlay networks at the same time. Co-located nodes, playing the role of neural synapses and connected to several overlay networks, allow a larger search area and provide alternative routing. Synapse can either work with "open" overlays adapting their protocol to synapse interconnection requirements, or with "closed" overlays that will not accept any change to their protocol. Results from simulation and experiments show that Synapse is scalable, with a communication and state overhead scaling similarly as the networks interconnected. Thanks to alternate routing paths, Synapse also gives a practical solution to network partitions. We precisely capture the behavior of traditional metrics of overlay networks within Synapse and present results from simulations as well as some actual experiments of a client prototype on the Grid'5000 platform. The prototype developed implements the Synapse protocol in the particular case of the interconnection of many Chord overlay networks.

BackgroundRecent advances in high-throughput sequencing allow for much deeper exploitation of natural and engineered microbial communities, and to unravel so-called “microbial dark matter” (microbes that until now have evaded cultivation). Metagenomic analyses result in a large number of genomic fragments (contigs) that need to be grouped (binned) in order to reconstruct draft microbial genomes. While several contig binning algorithms have been developed in the past 2 years, they often lack consensus. Furthermore, these software tools typically lack a provision for the visualization of data and bin characteristics.ResultsWe present ICoVeR, the Interactive Contig-bin Verification and Refinement tool, which allows the visualization of genome bins. More specifically, ICoVeR allows curation of bin assignments based on multiple binning algorithms. Its visualization window is composed of two connected and interactive main views, including a parallel coordinates view and a dimensionality reduction plot. To demonstrate ICoVeR’s utility, we used it to refine disparate genome bins automatically generated using MetaBAT, CONCOCT and MyCC for an anaerobic digestion metagenomic (AD microbiome) dataset. Out of 31 refined genome bins, 23 were characterized with higher completeness and lower contamination in comparison to their respective, automatically generated, genome bins. Additionally, to benchmark ICoVeR against a previously validated dataset, we used Sharon’s dataset representing an infant gut metagenome.ConclusionsICoVeR is an open source software package that allows curation of disparate genome bins generated with automatic binning algorithms. It is freely available under the GPLv3 license at https://git.list.lu/eScience/ICoVeR. The data management and analytical functions of ICoVeR are implemented in R, therefore the software can be easily installed on any system for which R is available. Installation and usage guide together with the example files ready to be visualized are also provided via the project wiki. ICoVeR running instance preloaded with AD microbiome and Sharon’s datasets can be accessed via the website.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-017-1653-5) contains supplementary material, which is available to authorized users.

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Abstract. Cloud applications are composed of a set of interconnected software components distributed over several virtual machines. There is a need for protocols that can dynamically reconfigure such distributed applications. In this paper, we present a novel protocol, which is able to resolve dependencies in these applications, by (dis)connecting and starting/stopping components in a specific order. These virtual machines interact through a publish-subscribe communication media and reconfigure themselves upon demand in a decentralised fashion. Designing such protocols is an error-prone task. Therefore, we decided to specify the protocol with the LNT value-passing process algebra and to verify it using the model checking tools available in the CADP toolbox. As a result, the introduction of formal techniques and tools help to deeply revise the protocol, and these improvements have been taken into account in the corresponding Java implementation.