Whole-Cell Computational Model of Mycoplasma genitalium
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M. genitalium whole-cell model
Code update
Dec 03, 2012

Updates to publication releaseNotes  View License

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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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Model-driven drug reposition..
Publication release
Mar 04, 2015

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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Parameter est. DREAM Challenge
Code for 2013 whole-cell model parameter estimation DREAM challenge
Competition release
May 23, 2013

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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)


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Synthetic networks
Publication release
May 23, 2013

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


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WholeCellKB
Publication release
Aug 10, 2012

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


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WholeCellSimDB
Publication release
Mar 09, 2014

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


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WholeCellViz
Publication release
Sep 06, 2012

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


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