Flexible Informatics for Linking Experimental Data to Mathematical Models via DataRail. Export

@article{citeulike:2307570, 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@hms.harvard.edu Supplementary information: Supplementary data are available at Bioinformatics online. 10.1093/bioinformatics/btn018}, address = {Center for Cell Decision Processes Harvard Medical School, Department of Systems Biology, Boston, MA 02115.}, author = {Saez-Rodriguez, Julio and Goldsipe, Arthur and Muhlich, Jeremy and Alexopoulos, Leonidas G. G. and Millard, Bjorn and Lauffenburger, Douglas A. A. and Sorger, Peter K. K.}, citeulike-article-id = {2307570}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btn018}, citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/24/6/840}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/18218655}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=18218655}, day = {15}, doi = {10.1093/bioinformatics/btn018}, issn = {1460-2059}, journal = {Bioinformatics}, month = {March}, number = {6}, pages = {840--847}, posted-at = {2008-09-18 18:25:26}, priority = {2}, title = {Flexible Informatics for Linking Experimental Data to Mathematical Models via DataRail.}, url = {http://dx.doi.org/10.1093/bioinformatics/btn018}, volume = {24}, year = {2008} }

TY - JOUR ID - citeulike:2307570 L3 - citeulike-article-id:2307570 N2 - 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@hms.harvard.edu Supplementary information: Supplementary data are available at Bioinformatics online. 10.1093/bioinformatics/btn018 IS - 6 JF - Bioinformatics SN - 1460-2059 AD - Center for Cell Decision Processes Harvard Medical School, Department of Systems Biology, Boston, MA 02115. EP - 847 TI - Flexible Informatics for Linking Experimental Data to Mathematical Models via DataRail. VL - 24 SP - 840 AU - Saez-Rodriguez, Julio AU - Goldsipe, Arthur AU - Muhlich, Jeremy AU - Alexopoulos, Leonidas AU - Millard, Bjorn AU - Lauffenburger, Douglas AU - Sorger, Peter PY - 2008/03/15/ UR - http://dx.doi.org/10.1093/bioinformatics/btn018 ER -