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  • 1
    Publication Date: 2016-07-20
    Description: The creation of a magnitude-homogenized catalogue is often one of the most fundamental steps in seismic hazard analysis. The process of homogenizing multiple catalogues of earthquakes into a single unified catalogue typically requires careful appraisal of available bulletins, identification of common events within multiple bulletins and the development and application of empirical models to convert from each catalogue's native scale into the required target. The database of the International Seismological Center (ISC) provides the most exhaustive compilation of records from local bulletins, in addition to its reviewed global bulletin. New open-source tools are developed that can utilize this, or any other compiled database, to explore the relations between earthquake solutions provided by different recording networks, and to build and apply empirical models in order to harmonize magnitude scales for the purpose of creating magnitude-homogeneous earthquake catalogues. These tools are described and their application illustrated in two different contexts. The first is a simple application in the Sub-Saharan Africa region where the spatial coverage and magnitude scales for different local recording networks are compared, and their relation to global magnitude scales explored. In the second application the tools are used on a global scale for the purpose of creating an extended magnitude-homogeneous global earthquake catalogue. Several existing high-quality earthquake databases, such as the ISC-GEM and the ISC Reviewed Bulletins, are harmonized into moment magnitude to form a catalogue of more than 562 840 events. This extended catalogue, while not an appropriate substitute for a locally calibrated analysis, can help in studying global patterns in seismicity and hazard, and is therefore released with the accompanying software.
    Keywords: Seismology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 2
    Publication Date: 2012-03-31
    Description: : Biogem provides a software development environment for the Ruby programming language, which encourages community-based software development for bioinformatics while lowering the barrier to entry and encouraging best practices. Biogem, with its targeted modular and decentralized approach, software generator, tools and tight web integration, is an improved general model for scaling up collaborative open source software development in bioinformatics. Availability: Biogem and modules are free and are OSS. Biogem runs on all systems that support recent versions of Ruby, including Linux, Mac OS X and Windows. Further information at http://www.biogems.info . A tutorial is available at http://www.biogems.info/howto.html Contact: bonnal@ingm.org
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 3
    Publication Date: 2015-07-02
    Description: The miRBase is the official miRNA repository which keeps the annotation updated on newly discovered miRNAs: it is also used as a reference for the design of miRNA profiling platforms. Nomenclature ambiguities generated by loosely updated platforms and design errors lead to incompatibilities among platforms, even from the same vendor. Published miRNA lists are thus generated with different profiling platforms that refer to diverse and not updated annotations. This greatly compromises searches, comparisons and analyses that rely on miRNA names only without taking into account the mature sequences, which is particularly critic when such analyses are carried over automatically. In this paper we introduce miRiadne, a web tool to harmonize miRNA nomenclature, which takes into account the original miRBase versions from 10 up to 21, and annotations of 40 common profiling platforms from nine brands that we manually curated. miRiadne uses the miRNA mature sequence to link miRBase versions and/or platforms to prevent nomenclature ambiguities. miRiadne was designed to simplify and support biologists and bioinformaticians in re-annotating their own miRNA lists and/or data sets. As Ariadne helped Theseus in escaping the mythological maze, miRiadne will help the miRNA researcher in escaping the nomenclature maze. miRiadne is freely accessible from the URL http://www.miriadne.org .
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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