title: Optimized R functions for analysis of ecological community data using the R virtual laboratory (RvLab).
abstract: BACKGROUND
  Parallel data manipulation using R has previously been addressed by members of the R community, however most of these studies producead hocsolutions that are not readily available to the average R user. Our targeted users, ranging from the expert ecologist/microbiologists to computational biologists, often experience difficulties in finding optimal ways to exploit the full capacity of their computational resources. In addition, improving performance of commonly used R scripts becomes increasingly difficult especially with large datasets. Furthermore, the implementations described here can be of significant interest to expert bioinformaticians or R developers. Therefore, our goals can be summarized as: (i) description of a complete methodology for the analysis of large datasets by combining capabilities of diverse R packages, (ii) presentation of their application through a virtual R laboratory (RvLab) that makes execution of complex functions and visualization of results easy and readily available to the end-user.
  
  
  CONCLUSIONS
  In this paper, the novelty stems from implementations of parallel methodologies which rely on the processing of data on different levels of abstraction and the availability of these processes through an integrated portal. Parallel implementation R packages, such as thepbdMPI(Programming with Big Data - Interface to MPI) package, are used to implement Single Program Multiple Data (SPMD) parallelization on primitive mathematical operations, allowing for interplay with functions of theveganpackage. ThedplyrandRPostgreSQLR packages are further integrated offering connections to dataframe like objects (databases) as secondary storage solutions whenever memory demands exceed available RAM resources. The RvLab is running on a PC cluster, using version 3.1.2 (2014-10-31) on a x86_64-pc-linux-gnu (64-bit) platform, and offers an intuitive virtual environmet interface enabling users to perform analysis of ecological and microbial communities based on optimizedveganfunctions. A beta version of the RvLab is available after registration at: https://portal.lifewatchgreece.eu/.
authors.affiliation: Institute of Computer Science, Foundation of Research and Technology Hellas, Heraklion, Greece.
authors.forename: Constantinos
authors.initials: C
authors.lastname: Varsos
authors.affiliation: Institute of Computer Science, Foundation of Research and Technology Hellas, Heraklion, Greece.
authors.forename: Theodore
authors.initials: T
authors.lastname: Patkos
authors.affiliation: Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece.
authors.forename: Anastasis
authors.initials: A
authors.lastname: Oulas
authors.affiliation: Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece; Department of Biology, University of Ghent, Ghent, Belgium, Department of Microbial Ecophysiology, University of Bremen, Bremen, Germany.
authors.forename: Christina
authors.initials: C
authors.lastname: Pavloudi
authors.affiliation: Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece.
authors.forename: Alexandros
authors.initials: A
authors.lastname: Gougousis
authors.affiliation: University of Glasgow, Glasgow, United Kingdom.
authors.forename: Umer Zeeshan
authors.initials: UZ
authors.lastname: Ijaz
authors.affiliation: Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece.
authors.forename: Irene
authors.initials: I
authors.lastname: Filiopoulou
authors.affiliation: Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece.
authors.forename: Nikolaos
authors.initials: N
authors.lastname: Pattakos
authors.affiliation: Vrije Universiteit Brussels, 1050, Brussels, Belgium.
authors.forename: Edward
authors.initials: E
authors.lastname: Vanden Berghe
authors.affiliation: University of Oxford, Oxford e-Research Centre, Oxford, United Kingdom.
authors.forename: Antonio
authors.initials: A
authors.lastname: Fernández-Guerra
authors.affiliation: Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece.
authors.forename: Sarah
authors.initials: S
authors.lastname: Faulwetter
authors.affiliation: Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece.
authors.forename: Eva
authors.initials: E
authors.lastname: Chatzinikolaou
authors.affiliation: Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece.
authors.forename: Evangelos
authors.initials: E
authors.lastname: Pafilis
authors.affiliation: Institute of Computer Science, Foundation of Research and Technology Hellas, Heraklion, Greece.
authors.forename: Chryssoula
authors.initials: C
authors.lastname: Bekiari
authors.affiliation: Institute of Computer Science, Foundation of Research and Technology Hellas, Heraklion, Greece.
authors.forename: Martin
authors.initials: M
authors.lastname: Doerr
authors.affiliation: Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece.
authors.forename: Christos
authors.initials: C
authors.lastname: Arvanitidis
keywords: Parallel data manipulation; R; Single Program Multiple Data (SPMD) parallelization; biodiversity analyses; ecological analyses; pbdMPI package; vegan package; virtual enviroment