Galaxy based BLAST submission to distributed national high throughput computing resources. Hayashi, S., Gesing, S., Quick, R., Teige, S., Ganote, C., Wu, L., & Prout, E. In Proceedings of Science, volume 23-28-Marc, 2014. Proceedings of Science (PoS).
Galaxy based BLAST submission to distributed national high throughput computing resources [link]Website  abstract   bibtex   
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. © Copyright owned by the author(s) under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike Licence.
@inproceedings{
 title = {Galaxy based BLAST submission to distributed national high throughput computing resources},
 type = {inproceedings},
 year = {2014},
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 keywords = {Bioinformatics; Cost effectiveness; Throughput,Cost-effective solutions; Cyber infrastructures;,Galaxies},
 volume = {23-28-Marc},
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 publisher = {Proceedings of Science (PoS)},
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 notes = {cited By 1; Conference of International Symposium on Grids and Clouds, ISGC 2014 ; Conference Date: 23 March 2014 Through 28 March 2014; Conference Code:121995},
 private_publication = {false},
 abstract = {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. © Copyright owned by the author(s) under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike Licence.},
 bibtype = {inproceedings},
 author = {Hayashi, S and Gesing, S and Quick, R and Teige, S and Ganote, C and Wu, L.-S. and Prout, E},
 booktitle = {Proceedings of Science}
}

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