title: A toolkit for ARB to integrate custom databases and externally built phylogenies.
abstract: 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.
  
  
  BACKGROUND
  http://www.ece.drexel.edu/gailr/EESI/tutorial.php.
authors.affiliation: Department of Electrical & Computer Engineering, Drexel University, Philadelphia, Pennsylvania, United States of America.
authors.forename: Steven D
authors.initials: SD
authors.lastname: Essinger
authors.affiliation: Department of Biomedical Engineering, Science, and Health Systems, Drexel University, Philadelphia, Pennsylvania, United States of America.
authors.forename: Erin
authors.initials: E
authors.lastname: Reichenberger
authors.affiliation: Department of Electrical & Computer Engineering, Drexel University, Philadelphia, Pennsylvania, United States of America.
authors.forename: Calvin
authors.initials: C
authors.lastname: Morrison
authors.affiliation: Department of Biological Sciences, Kent State University, Kent, Ohio, United States of America.
authors.forename: Christopher B
authors.initials: CB
authors.lastname: Blackwood
authors.affiliation: Department of Electrical & Computer Engineering, Drexel University, Philadelphia, Pennsylvania, United States of America.
authors.forename: Gail L
authors.initials: GL
authors.lastname: Rosen
mesh_terms: D008957:Models, Genetic; D010802:Phylogeny; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software