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M. genitalium whole-cell model
Code update
Dec 03, 2012

Updates to publication releaseNotes

Download Links

Model code (current)

May 23, 2013
0
Any
Source code
WholeCell code (current) (Git repo)

Model and knowledge base code & data (old)

Dec 03, 2012
140 MB
Any
Source code
Provides all whole-cell model code, training data, and knowledge base browser code.

Model code (old)

Dec 03, 2012
78 MB
Any
Source code
Provides all whole-cell model code.

Example code to edit network and training data

Dec 03, 2012
6 KB
Any
Source code
Example code to edit network and training data

2012b MCR Linux binaries

Jun 07, 2013
283 MB
Linux
Application/binary
Whole-cell model binaries for use with 2012b Linux MCR

Virtual machine

Mar 20, 2014
0
Any
Application/binary
Ubuntu (Mint 14) virtual machine (10.5 GB). See instructions for username and password.

Documentation Links

Frequently asked questions

Jun 16, 2014
Frequently asked questions

Parameter table

May 30, 2013
Table of the model's parameters

Metabolic reactions table

May 30, 2013
Table of the model's metabolic reactions

State properties table

May 31, 2013
Table of the model's state properties

State property row and column IDs

May 31, 2013
Table of the row and column labels of model's state properties

Virtual machine instructions

May 24, 2013
Virtual machine instructions

Detailed installation instructions

May 24, 2013
Contains detailed instructions for installing whole-cell code on Mint Linux 14

FBA metabolic sub-model

Jul 23, 2013
Metabolic sub-model (FBA linear programming problem in Gurobi .lp format)

FBA metabolic sub-model

Jul 23, 2013
Metabolic sub-model (FBA linear programming problem in lpsolve .lp format)

FBA metabolic sub-model

Jul 23, 2013
Metabolic sub-model (FBA linear programming problem in cplex .lpt format)

FBA metabolic sub-model

Jul 23, 2013
Metabolic sub-model (FBA linear programming problem in Xpress .lpx format)

FBA metabolic sub-model

Jul 23, 2013
Metabolic sub-model (FBA linear programming problem in MathProg .mod format)

FBA metabolic sub-model

Jul 23, 2013
Metabolic sub-model (SBML format)

FBA metabolic sub-model

Jul 23, 2013
Metabolic sub-model (FBA linear programming problem in LPFML .xml format)

FBA metabolic sub-model

Jul 23, 2013
Metabolic sub-model (FBA linear programming problem in ZIMPL .zpl format)

FBA metabolic sub-model

Jul 23, 2013
Metabolic sub-model (FBA linear programming problem in Lindo .ltx format)

PLEASE CITE THESE PAPERS

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

Previous Releases


Publication release

Jan 24, 2012

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.

Download Links

Model and knowledge base code & data

Nov 20, 2012
137 MB
Any
Source code
Provides all whole-cell model code, training data, and knowledge base browser code.

Model code

Nov 20, 2012
75 MB
Any
Source code
Provides all whole-cell model code.

Model linux binaries

Nov 20, 2012
218 MB
Linux
Application/binary
Provides linux binaries of whole-cell model for use with MATLAB MCR R2011b.

Simulations

Jun 16, 2014
0
Any
Data/images/video
Provides summaries of each simulation reported in Karr et al., 2012 as well as links to download the results of each simulation.

Knowledge base code & data

Aug 03, 2012
40 MB
Any
Source code
Provides all whole-cell training data and interactive browser code.

Knowledge base interactive browser

Jun 16, 2014
0
Any
Data/images/video
Interactive web interface to the M. genitalium knowledge base

Knowledge base data (xlsx)

Aug 03, 2012
1 MB
Any
Data/images/video
Provides all whole-cell training data in Excel format.

Knowledge base data (sql)

Aug 03, 2012
1 MB
Any
Data/images/video
Provides all whole-cell training data in MySQL format.

Documentation Links

User guide

Aug 03, 2012
Guide to installing and using the M. genitalium knowledge base and whole-cell model

User guide

Aug 03, 2012
User guide example code

Publication

Jul 19, 2012

Publication supplementary text

Jun 21, 2013
Whole-Cell model publication supplementary text

Supplementary Table S1

Aug 03, 2012
Supplementary Table S1

Supplementary Table S2

Aug 03, 2012
Supplementary Table S2

Supplementary Table S3

Aug 15, 2012
Supplementary Table S3


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

This package provides all code for the publication.

Download Links

Mar 04, 2015
82 MB
Any
Source code

May 04, 2015
11 KB
Any
Source code

Mar 04, 2015
460
Any
Source code

Mar 04, 2015
131 KB
Any
Data/images/video

Mar 04, 2015
149 KB
Any
Data/images/video

Mar 04, 2015
148 KB
Any
Data/images/video

Mar 03, 2015
144 KB
Any
Data/images/video

Mar 04, 2015
168 KB
Any
Data/images/video

Mar 04, 2015
149 KB
Any
Data/images/video

Mar 04, 2015
70 KB
Any
Data/images/video

Mar 04, 2015
145 KB
Any
Data/images/video

Mar 04, 2015
144 KB
Any
Data/images/video

Mar 04, 2015
143 KB
Any
Data/images/video

Mar 04, 2015
139 KB
Any
Data/images/video

Mar 04, 2015
139 KB
Any
Data/images/video

Mar 04, 2015
144 KB
Any
Data/images/video

Mar 04, 2015
135 KB
Any
Data/images/video

Mar 04, 2015
140 KB
Any
Data/images/video

Mar 04, 2015
173 KB
Any
Data/images/video

Mar 04, 2015
172 KB
Any
Data/images/video

Mar 04, 2015
168 KB
Any
Data/images/video

Mar 04, 2015
168 KB
Any
Data/images/video

Mar 04, 2015
173 KB
Any
Data/images/video

Mar 04, 2015
164 KB
Any
Data/images/video

Mar 04, 2015
169 KB
Any
Data/images/video

PLEASE CITE THESE PAPERS

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

Download Links

Challenge code (Git repo DREAM challenge branch)

Mar 22, 2014
0
Any
Source code
Challenge code (Git repo DREAM challenge branch)

Perturbation data

Mar 23, 2014
0
Any
Data/images/video
Perturbation data

Documentation Links

Challenge home page

Mar 22, 2014
Challenge home page

PLEASE CITE THESE PAPERS

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.

Download Links

Whole-cell synthetic networks code

Apr 07, 2014
0
Any
Source code
Whole-cell synthetic networks code (Git repo synthetic networks branch)

Figure 1a code

Apr 07, 2014
1 KB
Any
Source code
Figure 1a code

Figure 1b code

Apr 07, 2014
1 KB
Any
Source code
Figure 1b code

Figure 2 code

Apr 07, 2014
1 KB
Any
Source code
Figure 2 code

Figure 3 code

Apr 07, 2014
1 KB
Any
Source code
Figure 3 code

Figure S2 code

Apr 07, 2014
838
Any
Source code
Figure S2 code

Figure S5 code

Apr 07, 2014
749
Any
Source code
Figure S5 code

Individual model predictions (.mat)

Apr 07, 2014
0
Any
Data/images/video
Model predictions (.mat)

All model predictions (.mat)

Apr 07, 2014
116 MB
Any
Data/images/video
All model predictions (.mat)

PLEASE CITE THESE PAPERS

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.

Download Links

WholeCellKB

Jun 16, 2014
0
Any
Application/binary
WholeCellKB

Source code (current)

Mar 09, 2014
0
Any
Source code
WholeCellKB code (latest) (Git repository)

Source code (publication release)

May 23, 2013
6 MB
Any
Source code
Source code (publication release)

Data

Oct 01, 2012
2 MB
Any
Data/images/video
Data

Documentation Links

Getting started guide

Jun 16, 2014
Tutorial

User guide

Jun 16, 2014
User guide

Developer guide

Sep 28, 2012
Developer's guide

Source code documentation

Jun 16, 2014
Source code documentation

Data model documentation

Sep 24, 2012
Data model documentation

PLEASE CITE THESE PAPERS

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.

Download Links

WholeCellDB

Jun 16, 2014
0
Any
Application/binary
WholeCellSimDB

Source code

Jun 16, 2014
0
Any
Source code
WholeCellSimDB code (Git repository)

Documentation Links

User tutorial

Jun 16, 2014
User tutorial

Developer's guide

Jun 16, 2014
Developer's guide

Source code documentation

Jun 16, 2014
Source code documentation

Data model

Mar 20, 2014
Data model

PLEASE CITE THESE PAPERS

Karr JR*, Phillips NC*, Covert MW. WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions. Database. (2014) View


Image not available
WholeCellViz
Publication release
Sep 06, 2012

WholeCellViz is a web-based software program for visually analyzing whole-cell simulations.

Download Links

WholeCellViz

Jun 16, 2014
0
Any
Application/binary
WholeCellViz

Source code (current)

May 23, 2013
0
Any
Source code
WholeCellViz code (current) (Git repo)

Source code (publication release)

Jul 26, 2013
8 MB
Any
Source code
Source code (publication release)

Documentation Links

Tutorial

Jun 16, 2014
Tutorial

Developers' guide

Jan 25, 2013
Developers' guide

MIT license

Jul 18, 2013
MIT license

PLEASE CITE THESE PAPERS

Lee R*, Karr JR*, Covert MW. WholeCellViz: Data visualization for whole-cell models. BMC Bioinformatics 14, 253 (2013) View


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