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A toolkit for ARB to integrate custom databases and externally built phylogenies
Journal article   Open access   Peer reviewed

A toolkit for ARB to integrate custom databases and externally built phylogenies

Steven D Essinger, Erin Reichenberger, Calvin Morrison, Christopher B Blackwood, Gail L Rosen and Drexel Univ., Philadelphia, PA (United States)
PloS one, v 10(1), pp e0109277-e0109277
2015
DOI: https://doi.org/10.1371/journal.pone.0109277
PMID: 25607539
Featured in Collection :   UN Sustainable Development Goals @ Drexel
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https://doi.org/10.1371/journal.pone.0109277View
Published, Version of Record (VoR)CC BY V4.0,  Open

Abstract

Models, Genetic Phylogeny Sequence Analysis, DNA - methods Software
Researchers are perpetually amassing biological sequence data. The computational approaches employed by ecologists for organizing this data (e.g. alignment, phylogeny, etc.) typically scale nonlinearly in execution time with the size of the dataset. This often serves as a bottleneck for processing experimental data since many molecular studies are characterized by massive datasets. To keep up with experimental data demands, ecologists are forced to choose between continually upgrading expensive in-house computer hardware or outsourcing the most demanding computations to the cloud. Outsourcing is attractive since it is the least expensive option, but does not necessarily allow direct user interaction with the data for exploratory analysis. Desktop analytical tools such as ARB are indispensable for this purpose, but they do not necessarily offer a convenient solution for the coordination and integration of datasets between local and outsourced destinations. Therefore, researchers are currently left with an undesirable tradeoff between computational throughput and analytical capability. To mitigate this tradeoff we introduce a software package to leverage the utility of the interactive exploratory tools offered by ARB with the computational throughput of cloud-based resources. Our pipeline serves as middleware between the desktop and the cloud allowing researchers to form local custom databases containing sequences and metadata from multiple resources and a method for linking data outsourced for computation back to the local database. A tutorial implementation of the toolkit is provided in the supporting information, S1 Tutorial. http://www.ece.drexel.edu/gailr/EESI/tutorial.php.

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Collaboration types
Domestic collaboration
Web of Science research areas
Biochemistry & Molecular Biology
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