Flexible informatics for linking experimental data to mathematical models via DataRail
| Autor: | Leonidas G. Alexopoulos, Julio Saez-Rodriguez, Bjorn Millard, Peter K. Sorger, Arthur Goldsipe, Jeremy L. Muhlich, Douglas A. Lauffenburger |
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| Rok vydání: | 2008 |
| Předmět: |
Statistics and Probability
Proteome Computer science Information Storage and Retrieval computer.software_genre Models Biological Biochemistry Article Software Data integrity Computer Simulation Databases Protein MATLAB Molecular Biology computer.programming_language business.industry Metadata standard Computational Biology Experimental data Computer Science Applications Computational Mathematics Computational Theory and Mathematics Research Design Database Management Systems Programming Languages Data mining business computer Algorithms |
| Zdroj: | Bioinformatics. 24:840-847 |
| ISSN: | 1367-4811 1367-4803 |
| DOI: | 10.1093/bioinformatics/btn018 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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