Browsing by Author "Gesing, Sandra"

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    Galaxy based BLAST submission to distributed national high throughput computing resources
    (2013-03) Hayashi, Soichi; Gesing, Sandra; Quick, Rob; Teige, Scott; Ganote, Carrie; Wu, Le-shin; Prout, Elizabeth
    To assist the bioinformatic community in leveraging the national cyberinfrastructure, the National Center for Genomic Analysis Support (NCGAS) along with Indiana University's High Throughput Computing (HTC) group have engineered a method to use the Galaxy to submit BLAST jobs to the Open Science Grid (OSG). OSG is a collaboration of resource providers that utilize opportunistic cycles at more than 100 universities and research centers in the US. BLAST jobs make a significant portion of the research conducted on NCGAS resources, moving jobs that are conducive to an HTC environment to the national cyberinfrastructure would alleviate load on resources at NCGAS and provide a cost effective solution for getting more cycles to reduce the unmet needs of bioinformatic researchers. To this point researchers have tackled this issue by purchasing additional resources or enlisting collaborators doing the same type of research, while HTC experts have focused on expanding the number of resources available to historically HTC friendly science workflows. In this paper, we bring together expertise from both areas to address how a bioinformatics researcher using their normal interface, Galaxy, can seamlessly access the OSG which routinely supplies researchers with millions of compute hours daily. Efficient use of these results will supply additional compute time to researcher and help provide a yet unmet need for BLAST computing cycles.
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    Towards a Science Gateway Reference Architecture
    (2018-06-15) Pierce, Marlon E.; Miller, Mark A.; Brookes, Emre H.; Wong, Mona; Afgan, Enis; Liu, Yan; Gesing, Sandra; Dahan, Maytal; Marru, Suresh; Walker, Tony
    Paper given at the 10t​h International Workshop on Science Gateways (IWSG 2018), 13-15 June 2018 in Endinburgh, Scotland. Science gateways have been developed over the last twenty years and have grown into a large community of practice, as evidenced by international workshops and conferences. Because of the diversity of approaches to creating science gateways and the always changing landscape of technologies, the community lacks a common definition for the term “science gateway” itself and common terminology for describing the common components of a gateway architecture. Instead, a wide range of definitions and understandings exist and are used in different communities; this is evident, for example, in discussions whether science gateways are the same as virtual research environments. This paper attempts to address these issues by focusing on how science gateways support scientific research and considering the consequences on cyberinfrastructure.