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Karr JR*, Sanghvi JC*, Macklin DN, Gutschow MV, Jacobs JM, Bolival B, Assad-Garcia N, Glass JI, Covert MW. A Whole-Cell Computational Model Predicts Phenotype from Genotype. Cell 150, 389-401 (2012) View
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This package provides all code and training data for the first "whole-cell" model of the entire life cycle of a living organism, Mycoplasma genitalium. Please see the user guide for installation and usage instructions. View License
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This package provides all code for the publication. View License
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Kazakiewicz D*, Karr JR*, Langner KM & Plewczynski D. Combined systems and structural modeling repositions antibiotics for Mycoplasma genitalium. (In submission) (2015)
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Karr JR, Williams AH, Zucker JD, Raue A, Steiert B, Timmer J, Kreutz C, DREAM8 Parameter Estimation Challenge Consortium, Wilkinson S, Allgood BA, Bot BM, Hoff BR, Kellen MR, Covert MW, Stolovitzky GA, Meyer P. A Crowdsourced Approach to Parameter Estimation for Whole-Cell Modeling. (In preparation) (2014)
This package provides all code for the publication. View License
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Purcell O*, Jain B*, Karr JR, Covert MW, Lu TK. Towards a whole-cell modeling approach for synthetic biology. Chaos, 23, 025112 (2013) View
This package provides all code and data for WholeCellKB. Please visit http://www.wholecellkb.org to browse the database. Please see the user guide for installation and usage instructions. View License
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Karr JR, Sanghvi JC, Macklin DN, Arora A, Covert MW. WholeCellKB: Pathway/Genome Databases for Comprehensive Whole-Cell Models. 41, D787-D792 (2013) View
This package provides all code for WholeCellDB. Please visit http://wholecelldb.stanford.edu to browse the database. Please see the user guide for usage instructions, and the developer's guide for installation instructions. View License
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Karr JR*, Phillips NC*, Covert MW. WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions. Database. (2014) View
WholeCellViz is a web-based software program for visually analyzing whole-cell simulations. View License
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Lee R*, Karr JR*, Covert MW. WholeCellViz: Data visualization for whole-cell models. BMC Bioinformatics 14, 253 (2013) View