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Bioinformatics Advance Access published online on January 24, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn018
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© 2008 The Author(s)
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 Mathemati-cal Models via DataRail

Julio Saez-Rodriguez 1,2,*, Arthur Goldsipe 1,3,*, 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,{dagger}

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

{dagger}To whom correspondence should be addressed. Peter K. Sorger, E-mail: sbpipeline{at}hms.harvard.edu


  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 in-formation content, and then constructs models using internal or external tools. Data integrity is maintained via a containment hier-archy 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: accompanies this paper.

Associate Editor: Dr. Trey Ideker

* The first two authors contributed equally to this work

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

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