{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,5]],"date-time":"2026-06-05T02:52:55Z","timestamp":1780627975753,"version":"3.54.1"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":3174,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>\n               <jats:p>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 \u223c22 000 measurements of protein activities obtained from cytokine-stimulated primary and transformed human liver cells.<\/jats:p>\n               <jats:p>Availability: \u00a0DataRail is distributed under the GNU General Public License and available at http:\/\/code.google.com\/p\/sbpipeline\/<\/jats:p>\n               <jats:p>Contact: \u00a0sbpipeline@hms.harvard.edu<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn018","type":"journal-article","created":{"date-parts":[[2008,1,25]],"date-time":"2008-01-25T01:24:39Z","timestamp":1201224279000},"page":"840-847","source":"Crossref","is-referenced-by-count":68,"title":["Flexible informatics for linking experimental data to mathematical models via <i>DataRail<\/i>"],"prefix":"10.1093","volume":"24","author":[{"given":"Julio","family":"Saez-Rodriguez","sequence":"first","affiliation":[{"name":"1 Center 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"},{"name":"1 Center 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"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arthur","family":"Goldsipe","sequence":"additional","affiliation":[{"name":"1 Center 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"},{"name":"1 Center for Cell Decision Processes, 2Department 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