Sunday, October 14, 2018
Marc Alexander Voigt1,2, Colton J. Lloyd3, Laurence Yang3, Zachary A. King3, Oliver Kohlbacher2,4,5,6, Kay Nieselt2,7 and Andreas Dräger1,2, (1)Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens, Center for Bioinformatics Tübingen (ZBIT), Tübingen, Germany, (2)Department of Computer Science, University of Tübingen, Tübingen, Germany, (3)Bioengineering, University of California, San Diego, La Jolla, CA, (4)Max Planck Institute for Developmental Biology, Tübingen, Germany, (5)Center for Personalized Medicine (ZPM), University of Tübingen, Tübingen, Germany, (6)Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany, (7)Integrative Transcriptomics, Center for Bioinformatics Tübingen (ZBIT), Tübingen, Germany
Metabolism and Expression models (ME-models) [1] are a constraint-based modeling approach, which explicitly accounts for the cost of macromolecular biosynthesis. This allows ME-models to investigate genotype-phenotype relationships with a quantitative incorporation of '-omics' data. Common standards are a prerequisite for interoperability of systems biology tools. Novel approaches often require additional or changed data structures that cannot be represented in existing standards. This has been the case for ME-models. ME-models are powerful tools, but a lack of standards for encoding and creation, and the increased complexity of these models prevented widespread use.
SBMLme is an extension of current model encoding standards that enables SBML representations of ME-models that were reconstructed using COBRAme [2]. A prototype of the extension has been created in Java together with a standalone, bi-directional converter, between this extension and COBRAme's model storage format. The converter showed that SBMLme could fully and correctly encode a COBRAme model.
The use of SBMLme enables ME-models to be shared more efficiently, and a wider variety of tools to access ME-models. This should promote the propagation of ME-models. SBMLme may be used as a proof-of-concept for an official SBML package for ME-models. The standardization process requires ongoing discussion, the identification of a consensus SBML draft standard, and the implementation of the existing validation rules.
SBMLme is freely available at https://github.com/draeger-lab/SBMLme under the terms of the MIT license.
- Ines Thiele, Ronan M. T. Fleming, Richard Que, Aarash Bordbar, Dinh Diep, and Bernhard O. Palsson. Multiscale Modeling of Metabolism and Macromolecular Synthesis in E. coli and Its Application to the Evolution of Codon Usage. PLOS ONE, 7(9):1-18, 09 2012
- Colton J Lloyd, Ali Ebrahim, Laurence Yang, Zachary Andrew King, Edward Catoiu, Edward J O'Brien, Joanne K Liu, and Bernhard O Palsson. COBRAme: A Computational Framework for Models of Metabolism and Gene Expression. bioRxiv, 2017.
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