Flexible informatics for linking experimental data to mathematical models via DataRail

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 n...

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Published in:	Bioinformatics Vol. 24; no. 6; pp. 840 - 847
Main Authors:	Saez-Rodriguez, Julio, Goldsipe, Arthur, Muhlich, Jeremy, Alexopoulos, Leonidas G., Millard, Bjorn, Lauffenburger, Douglas A., Sorger, Peter K.
Format:	Journal Article
Language:	English
Published:	Oxford Oxford University Press 15.03.2008 Oxford Publishing Limited (England)
Subjects:	Algorithms Bioinformatics Biological and medical sciences Computational Biology - methods Computer Simulation Database Management Systems Databases, Protein Experimental data Fundamental and applied biological sciences. Psychology General aspects Information Storage and Retrieval - methods Mathematical models Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) Models, Biological Programming Languages Proteome - metabolism Research Design Software Mathematical model Bioinformatics Experimental data
ISSN:	1367-4803, 1367-4811, 1460-2059, 1367-4811
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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.
AbstractList	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. 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 similar to 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. 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. 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 approximately 22 000 measurements of protein activities obtained from cytokine-stimulated primary and transformed human liver cells. DataRail is distributed under the GNU General Public License and available at http://code.google.com/p/sbpipeline/ 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.MOTIVATIONLinking 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.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 approximately 22 000 measurements of protein activities obtained from cytokine-stimulated primary and transformed human liver cells.RESULTSWe 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 approximately 22 000 measurements of protein activities obtained from cytokine-stimulated primary and transformed human liver cells.DataRail is distributed under the GNU General Public License and available at http://code.google.com/p/sbpipeline/AVAILABILITYDataRail is distributed under the GNU General Public License and available at http://code.google.com/p/sbpipeline/ 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. 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.
Author	Muhlich, Jeremy Goldsipe, Arthur Sorger, Peter K. Alexopoulos, Leonidas G. Millard, Bjorn Lauffenburger, Douglas A. Saez-Rodriguez, Julio
AuthorAffiliation	2 Harvard Medical School, Department of Systems Biology, Boston, MA 02115 1 Center for Cell Decision Processes, Boston, MA 02115 3 Massachusetts Institute of Technology, Department of Biological Engineering, Cambridge, MA 02139
AuthorAffiliation_xml	– name: 3 Massachusetts Institute of Technology, Department of Biological Engineering, Cambridge, MA 02139 – name: 2 Harvard Medical School, Department of Systems Biology, Boston, MA 02115 – name: 1 Center for Cell Decision Processes, Boston, MA 02115
Author_xml	– sequence: 1 givenname: Julio surname: Saez-Rodriguez fullname: Saez-Rodriguez, Julio organization: Center for Cell Decision Processes, Department of Systems Biology, Harvard Medical School, Boston, MA 02115 and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 – sequence: 2 givenname: Arthur surname: Goldsipe fullname: Goldsipe, Arthur organization: Center for Cell Decision Processes, Department of Systems Biology, Harvard Medical School, Boston, MA 02115 and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 – sequence: 3 givenname: Jeremy surname: Muhlich fullname: Muhlich, Jeremy organization: Center for Cell Decision Processes, Department of Systems Biology, Harvard Medical School, Boston, MA 02115 and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 – sequence: 4 givenname: Leonidas G. surname: Alexopoulos fullname: Alexopoulos, Leonidas G. organization: Center for Cell Decision Processes, Department of Systems Biology, Harvard Medical School, Boston, MA 02115 and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 – sequence: 5 givenname: Bjorn surname: Millard fullname: Millard, Bjorn organization: Center for Cell Decision Processes, Department of Systems Biology, Harvard Medical School, Boston, MA 02115 and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 – sequence: 6 givenname: Douglas A. surname: Lauffenburger fullname: Lauffenburger, Douglas A. organization: Center for Cell Decision Processes, Department of Systems Biology, Harvard Medical School, Boston, MA 02115 and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 – sequence: 7 givenname: Peter K. surname: Sorger fullname: Sorger, Peter K. organization: Center for Cell Decision Processes, Department of Systems Biology, Harvard Medical School, Boston, MA 02115 and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
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Cites_doi	10.1038/scientificamerican0501-34 10.1074/mcp.M500158-MCP200 10.1186/1752-0509-1-2 10.1186/gb-2004-5-10-r80 10.1152/ajplung.00331.2001 10.1093/bioinformatics/btm031 10.1186/1471-2105-7-176 10.1038/nrm2030 10.1023/A:1009726021843 10.4049/jimmunol.177.8.5604 10.1126/science.1082602
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Notes	To whom correspondence should be addressed. Associate Editor: Trey Ideker ArticleID:btn018 istex:6289B8E310076C5BFF58819C8A7CFC18FAFDA3A2 ark:/67375/HXZ-PGQ3FWZ6-5 ObjectType-Article-2 SourceType-Scholarly Journals-1 ObjectType-Feature-1 content type line 14 ObjectType-Article-1 ObjectType-Feature-2 content type line 23 ObjectType-Undefined-1 ObjectType-Feature-3 Contact: sbpipeline@hms.harvard.edu Associate Editor: Dr. Trey Ideker The first two authors contributed equally to this work.
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References	Jaqaman (2023020209513170800_B5) 2006; 7 Shah (2023020209513170800_B8) 2006; 23 Yan (2023020209513170800_B12) 2006; 177 Shannon (2023020209513170800_B9) 2006; 7 Berners-Lee (2023020209513170800_B1) 2001; 284 Gentleman (2023020209513170800_B3) 2004; 5 Swedlow (2023020209513170800_B10) 2003; 300 Wold (2023020209513170800_B11) 2004 Klamt (2023020209513170800_B6) 2007; 1 Pazdrak (2023020209513170800_B7) 2002; 283 Gray (2023020209513170800_B4) 1997; 1 Gaudet (2023020209513170800_B2) 2005; 4
References_xml	– volume: 284 start-page: 34 year: 2001 ident: 2023020209513170800_B1 article-title: The semantic web—a new form of web content that is meaningful to computers will unleash a revolution of new possibilities publication-title: Sci. Am doi: 10.1038/scientificamerican0501-34 – volume: 4 start-page: 1569 year: 2005 ident: 2023020209513170800_B2 article-title: A compendium of signals and responses triggered by prodeath and prosurvival cytokines publication-title: Mol. Cell. Proteomics doi: 10.1074/mcp.M500158-MCP200 – volume: 1 start-page: 2 year: 2007 ident: 2023020209513170800_B6 article-title: Structural and functional analysis of cellular networks with CellNetAnalyzer publication-title: BMC Syst. Biol doi: 10.1186/1752-0509-1-2 – volume: 5 start-page: R80 year: 2004 ident: 2023020209513170800_B3 article-title: Bioconductor: open software development for computational biology and bioinformatics publication-title: Genome Biol doi: 10.1186/gb-2004-5-10-r80 – volume: 283 start-page: L364 year: 2002 ident: 2023020209513170800_B7 article-title: MAPK activation is involved in posttranscriptional regulation of RSV-induced RANTES gene expression publication-title: Am. J. Physiol. Lung Cell. Mol. Physiol doi: 10.1152/ajplung.00331.2001 – year: 2004 ident: 2023020209513170800_B11 article-title: The PLS method and its applications in industrial RDP (research, development, and production) – volume: 23 start-page: 906 year: 2006 ident: 2023020209513170800_B8 article-title: Enabling high-throughput data management for systems biology: the bioinformatics resource manager publication-title: Bioinformatics doi: 10.1093/bioinformatics/btm031 – volume: 7 start-page: 176 year: 2006 ident: 2023020209513170800_B9 article-title: The Gaggle: an open-source software system for integrating bioinformatics software and data sources publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-7-176 – volume: 7 start-page: 813 year: 2006 ident: 2023020209513170800_B5 article-title: Linking data to models: data regression publication-title: Nat. Rev. Mol. Cell. Biol doi: 10.1038/nrm2030 – volume: 1 start-page: 29 year: 1997 ident: 2023020209513170800_B4 article-title: Data cube: a relational aggregation operator generalizing group-by, cross-tab, and sub-totals publication-title: Data Mining and Knowl. Discov doi: 10.1023/A:1009726021843 – volume: 177 start-page: 5604 year: 2006 ident: 2023020209513170800_B12 article-title: Differential pattern of inflammatory molecule regulation in intestinal epithelial cells stimulated with IL-1 publication-title: J. Immunology doi: 10.4049/jimmunol.177.8.5604 – volume: 300 start-page: 100 year: 2003 ident: 2023020209513170800_B10 article-title: Informatics and quantitative analysis in biological imaging publication-title: Science doi: 10.1126/science.1082602
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Snippet	Motivation: Linking experimental data to mathematical models in biology is impeded by the lack of suitable software to manage and transform data. Model... Linking experimental data to mathematical models in biology is impeded by the lack of suitable software to manage and transform data. Model calibration would... MOTIVATION: Linking experimental data to mathematical models in biology is impeded by the lack of suitable software to manage and transform data. Model...
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SubjectTerms	Algorithms Bioinformatics Biological and medical sciences Computational Biology - methods Computer Simulation Database Management Systems Databases, Protein Experimental data Fundamental and applied biological sciences. Psychology General aspects Information Storage and Retrieval - methods Mathematical models Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) Models, Biological Programming Languages Proteome - metabolism Research Design Software
Title	Flexible informatics for linking experimental data to mathematical models via DataRail
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Volume	24
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