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Bioinformatics Advance Access originally published online on January 24, 2008
Bioinformatics 2008 24(6):840-847; doi:10.1093/bioinformatics/btn018
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Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Flexible informatics for linking experimental data to mathematical models via DataRail

Julio Saez-Rodriguez 1,2,{dagger}, Arthur Goldsipe 1,3,{dagger}, Jeremy Muhlich 1,2, Leonidas G. Alexopoulos 1,2, Bjorn Millard 1,2, Douglas A. Lauffenburger 1,3 and Peter K. Sorger 1,2,3,*

1Center for Cell Decision Processes, 2Department of Systems Biology, Harvard Medical School, Boston, MA 02115 and 3Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139

*To whom correspondence should be addressed.


  Abstract

Motivation: Linking experimental data to mathematical models in biology is impeded by the lack of suitable software to manage and transform data. Model calibration would be facilitated and models would increase in value were it possible to preserve links to training data along with a record of all normalization, scaling, and fusion routines used to assemble the training data from primary results.

Results: We describe the implementation of DataRail, an open source MATLAB-based toolbox that stores experimental data in flexible multi-dimensional arrays, transforms arrays so as to maximize information content, and then constructs models using internal or external tools. Data integrity is maintained via a containment hierarchy for arrays, imposition of a metadata standard based on a newly proposed MIDAS format, assignment of semantically typed universal identifiers, and implementation of a procedure for storing the history of all transformations with the array. We illustrate the utility of DataRail by processing a newly collected set of ~22 000 measurements of protein activities obtained from cytokine-stimulated primary and transformed human liver cells.

Availability: DataRail is distributed under the GNU General Public License and available at http://code.google.com/p/sbpipeline/

Contact: sbpipeline{at}hms.harvard.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Trey Ideker

{dagger}The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

Received on October 10, 2007; revised on December 11, 2007; accepted on January 9, 2008

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