Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

We show the distribution of SARS-CoV-2 genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three available genomic nomenclature systems for SARS-CoV-2 to all sequence data from the WHO European Region available during the COVID-19 pandemic until 10 July 2020. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation. We provide a comparison of the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2.Peer reviewe

Complexity analysis of benchmark software for supercomputers

10.1007/BF00127830The Journal of Supercomputing33235-242JOSU

Stroll: A Universal Filesystem-Based Interface for Seamless Task Deployment in Grid Computing

International audienceDeveloping applications for solving compute intensive problems is not trivial. Despite availability of a range of Grid computing platforms, domain specialists and scientists only rarely take advantage of these computing facilities. One reason for this is the complexity of Grid computing, and the need to learn a new programming environment to interact with the Grid. Typically, only a few programming languages are supported, and often scientists use special-purpose languages that are not supported by most Grid platforms. Moreover, users cannot easily deploy their compute tasks to multiple Grid platforms without rewriting their program to use different task submission interfaces.In this paper we present Stroll, a universal filesystem-based interface for seamless task submission to one or more Grid facilities. Users interact with the Grid through simple read and write filesystem commands. Stroll allows all categories of users to submit and manage compute tasks both manually, and from within their programs, which may be written in any language. Stroll has been implemented on Windows and Linux, and we demonstrate that we can submit the same compute tasks to both Condor and Unicore clusters. Our evaluation shows the overhead of Stroll to negligible. Comparing the code complexity of a Stroll compute task with command-line clients and Grid APIs show that Stroll can eliminated up to 95% of the complexity

Is it all lost? A study of inactive open source projects

Open Source Software (OSS) proponents suggest that when developers lose interest in their project, their last duty is to “hand it off to a competent successor.” However, the mechanisms of such a hand-off are not clear, or widely known among OSS developers. As a result, many OSS projects, after a certain long period of evolution, stop evolving, in fact becoming “inactive” or “abandoned” projects. This paper presents an analysis of the population of projects contained within one of the largest OSS repositories available (SourceForge.net), in order to describe how projects abandoned by their developers can be identified, and to discuss the attributes and characteristics of these inactive projects. In particular, the paper attempts to differentiate projects that experienced maintainability issues from those that are inactive for other reasons, in order to be able to correlate common characteristics to the “failure” of these projects