Welcome to the whole-cell wiki. This is a community resource for whole-cell modeling. Please register to contribute to the wiki.
What is whole-cell modeling?
The goal of whole-cell modeling is predict how genotype determines phenotype. Whole-cell models account for the specific function of every gene product and predict the dynamics of every molecule over the entire life cycle. Whole-cell models have the potential to enable engineers to rationally design cells to perform useful functions such as synthesizing drugs, sensing disease, and decontaminating waste. In addition, they have the potential to enable physicians to provide personalized medical care.
Please see the reviews below for more information.
Getting started with whole-cell modeling
- Use software
- Download code
- Frequently asked questions
- Virtual machine containing model, KB, visualization, and simulation database software. See instructions.
- MATLAB Component Runtime (MCR) binaries for Linux 2012b
M. genitalium tables
- Knoweldge base / training data
- State row/column IDs
- Metabolic reactions
- In silico cell phenotypes
M. genitalium metabolic sub-model
- SBML format
- lpsolve .lp format
- cplex .lpt format
- Lindo .ltx format
- Xpress .lpx format
- MathProg .mod format
- LPFML .xml format
- ZIMPL .zpl format
- Spring 2016: Whole-cell modeling summer school TBA
- March 2015: Whole-cell modeling summer school
- June-October 2013: Whole-cell parameter estimation DREAM challenge
- Macklin DN, Ruggero NA & Covert MW (2014). The future of whole-cell modeling. Curr Opin Biotechnol 28, 111-5. PubMed
- Covert MW (2014). Simulating a living cell. Sci Am 310, 44-51. PubMed
- Freddolino PL & Tavazoie S (2012). The dawn of virtual cell biology. Cell 150, 248-50. PubMed
- Gunawardena J (2012). Silicon dreams of cells into symbols. Nat Biotechnol 30, 838-40. PubMed
- Karr JR, Sanghvi JC, Macklin DN, Gutschow MV, Jacobs JM, Bolival B, Assad-Garcia N, Glass JI & Covert MW (2012). A whole-cell computational model predicts phenotype from genotype. Cell 150, 389–401. PubMed
- Covert MW, Xiao N, Chen TJ, and Karr JR (2008). Integrated flux balance analysis model of Escherichia coli. Bioinformatics 24, 2044–50. PubMed
- Sanghvi JC, Regot S, Carrasco S, Karr JR, Gutschow MV, Bolival B & Covert MW (2013). Accelerated discovery via a whole-cell model. Nat Methods 10, 1192–5. PubMed
- Birch EW, Udell M & Covert MW (2014). Incorporation of flexible objectives and time-linked simulation with flux balance analysis. J Theor Biol 345, 12-21. PubMed
- Purcell O, Jain B, Karr JR, Covert MW & Lu T (2013). Towards a whole-cell modeling approach for synthetic biology. Chaos 23, 025112. PubMed
- Karr JR, Sanghvi JC, Macklin DN, Arora A & Covert MW (2013). WholeCellKB: model organism databases for comprehensive whole-cell models. Nucleic Acids Res 41, D787–92. PubMed
- Lee R, Karr JR & Covert MW (2013). WholeCellViz: data visualization for whole-cell models. BMC Bioinformatics 14, 253. PubMed
- Karr JR, Phillips NC & Covert MW (2014). WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions. Database 2014, bau095. PubMed
Please visit the whole-cell forum.