SimTK: Whole-Cell Computational Model of Mycoplasma genitalium: Downloads

Downloads

M. genitalium whole-cell model

Code update

Dec 03, 2012

Updates to publication releaseNotes View License

Download Package

Download Links

Model code (current)

WholeCell-Git-repo.html (URL)

May 23, 2013

Any

Source code

WholeCell code (current) (Git repo)

Model and knowledge base code & data (old)

allcode.zip

Dec 03, 2012

140 MB

Any

Source code

Provides all whole-cell model code, training data, and knowledge base browser code.

Model code (old)

Simulation.zip

Dec 03, 2012

78 MB

Any

Source code

Provides all whole-cell model code.

Example code to edit network and training data

editKB.m

Dec 03, 2012

6 KB

Any

Source code

Example code to edit network and training data

2012b MCR Linux binaries

McrBinaries.zip

Jun 07, 2013

283 MB

Linux

Application/binary

Whole-cell model binaries for use with 2012b Linux MCR

Virtual machine

VirtualMachine.ova (URL)

Mar 20, 2014

Any

Application/binary

Ubuntu (Mint 14) virtual machine (10.5 GB). See instructions for username and password.

Documentation Links

Frequently asked questions

FAQ.html (URL)

Jun 16, 2014

Frequently asked questions

Parameter table

Parameters.xlsx

May 30, 2013

Table of the model's parameters

Metabolic reactions table

Metabolism.xlsx

May 30, 2013

Table of the model's metabolic reactions

State properties table

StateProperties.xlsx

May 31, 2013

Table of the model's state properties

State property row and column IDs

StatePropertyRowColIDs.xlsx

May 31, 2013

Table of the row and column labels of model's state properties

Virtual machine instructions

VirtualMachineInstructions.txt

May 24, 2013

Virtual machine instructions

Detailed installation instructions

InstallationInstructions.zip

May 24, 2013

Contains detailed instructions for installing whole-cell code on Mint Linux 14

FBA metabolic sub-model

Metabolism.lp

Jul 23, 2013

Metabolic sub-model (FBA linear programming problem in Gurobi .lp format)

FBA metabolic sub-model

Metabolism.lpsolve.lp

Jul 23, 2013

Metabolic sub-model (FBA linear programming problem in lpsolve .lp format)

FBA metabolic sub-model

Metabolism.lpt

Jul 23, 2013

Metabolic sub-model (FBA linear programming problem in cplex .lpt format)

FBA metabolic sub-model

Metabolism.lpx

Jul 23, 2013

Metabolic sub-model (FBA linear programming problem in Xpress .lpx format)

FBA metabolic sub-model

Metabolism.mod

Jul 23, 2013

Metabolic sub-model (FBA linear programming problem in MathProg .mod format)

FBA metabolic sub-model

Metabolism.sbml

Jul 23, 2013

Metabolic sub-model (SBML format)

FBA metabolic sub-model

Metabolism.xml

Jul 23, 2013

Metabolic sub-model (FBA linear programming problem in LPFML .xml format)

FBA metabolic sub-model

Metabolism.zpl

Jul 23, 2013

Metabolic sub-model (FBA linear programming problem in ZIMPL .zpl format)

FBA metabolic sub-model

Metabolism.ltx

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. View License

Download Package

Download Links

Model and knowledge base code & data

allcode.zip

Nov 20, 2012

137 MB

Any

Source code

Provides all whole-cell model code, training data, and knowledge base browser code.

Model code

Simulation.zip

Nov 20, 2012

75 MB

Any

Source code

Provides all whole-cell model code.

Model linux binaries

Simulation.bin.zip

Nov 20, 2012

218 MB

Linux

Application/binary

Provides linux binaries of whole-cell model for use with MATLAB MCR R2011b.

Simulations

Simulations.html (URL)

Jun 16, 2014

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

KnowledgeBase.zip

Aug 03, 2012

40 MB

Any

Source code

Provides all whole-cell training data and interactive browser code.

Knowledge base interactive browser

KnowledgeBase.html (URL)

Jun 16, 2014

Any

Data/images/video

Interactive web interface to the M. genitalium knowledge base

Knowledge base data (xlsx)

KnowledgeBase.xlsx

Aug 03, 2012

1 MB

Any

Data/images/video

Provides all whole-cell training data in Excel format.

Knowledge base data (sql)

KnowledgeBase.sql.zip

Aug 03, 2012

1 MB

Any

Data/images/video

Provides all whole-cell training data in MySQL format.

Documentation Links

User guide

UserGuide.pdf

Aug 03, 2012

Guide to installing and using the M. genitalium knowledge base and whole-cell model

User guide

UserGuide.m

Aug 03, 2012

User guide example code

Publication

Paper.html (URL)

Jul 19, 2012

Publication supplementary text

SupplementaryText.pdf

Jun 21, 2013

Whole-Cell model publication supplementary text

Supplementary Table S1

tableS1.xlsx

Aug 03, 2012

Supplementary Table S1

Supplementary Table S2

tableS2.xls

Aug 03, 2012

Supplementary Table S2

Supplementary Table S3

tableS3.xlsx

Aug 15, 2012

Supplementary Table S3

Model-driven drug reposition..

Publication release

Mar 04, 2015

This package provides all code for the publication. View License

Download Package

Download Links

WholeCellModelSourceCodeV1.1.zip

Mar 04, 2015

82 MB

Any

Source code

CalculateGrowthEnzymeSensitivities.m

May 04, 2015

11 KB

Any

Source code

CalculateGrowthRateWithModifiedEnzymeExpression.m

Mar 04, 2015

460

Any

Source code

Mycoplasma genitalium Tmk.pdb

Mar 04, 2015

131 KB

Any

Data/images/video

Mycoplasma genitalium Tmk.0YB.pdb

Mar 04, 2015

149 KB

Any

Data/images/video

Mycoplasma genitalium Tmk.13Y.pdb

Mar 04, 2015

148 KB

Any

Data/images/video

Mycoplasma genitalium Tmk.16T.pdb

Mar 03, 2015

144 KB

Any

Data/images/video

Mycoplasma genitalium Tmk.31Z.pdb

Mar 04, 2015

168 KB

Any

Data/images/video

Mycoplasma genitalium Tmk.32E.pdb

Mar 04, 2015

149 KB

Any

Data/images/video

Mycoplasma genitalium Tmk.32K.pdb

Mar 04, 2015

70 KB

Any

Data/images/video

Mycoplasma genitalium Tmk.T05.pdb

Mar 04, 2015

145 KB

Any

Data/images/video

Staphylococcus aureus Tmk.0YB.pdb

Mar 04, 2015

144 KB

Any

Data/images/video

Staphylococcus aureus Tmk.13Y.pdb

Mar 04, 2015

143 KB

Any

Data/images/video

Staphylococcus aureus Tmk.16T.pdb

Mar 04, 2015

139 KB

Any

Data/images/video

Staphylococcus aureus Tmk.31Z.pdb

Mar 04, 2015

139 KB

Any

Data/images/video

Staphylococcus aureus Tmk.32E.pdb

Mar 04, 2015

144 KB

Any

Data/images/video

Staphylococcus aureus Tmk.32K.pdb

Mar 04, 2015

135 KB

Any

Data/images/video

Staphylococcus aureus Tmk.T05.pdb

Mar 04, 2015

140 KB

Any

Data/images/video

Homo sapiens Tmk.0YB.pdb

Mar 04, 2015

173 KB

Any

Data/images/video

Homo sapiens Tmk.13Y.pdb

Mar 04, 2015

172 KB

Any

Data/images/video

Homo sapiens Tmk.16T.pdb

Mar 04, 2015

168 KB

Any

Data/images/video

Homo sapiens Tmk.31Z.pdb

Mar 04, 2015

168 KB

Any

Data/images/video

Homo sapiens Tmk.32E.pdb

Mar 04, 2015

173 KB

Any

Data/images/video

Homo sapiens Tmk.32K.pdb

Mar 04, 2015

164 KB

Any

Data/images/video

Homo sapiens Tmk.T05.pdb

Mar 04, 2015

169 KB

Any

Data/images/video

Documentation Links

SupplementaryTablesAndFigures.pdf

Mar 04, 2015

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)

Parameter est. DREAM Challenge

Code for 2013 whole-cell model parameter estimation DREAM challenge

Competition release

May 23, 2013

View License

Download Links

Challenge code (Git repo DREAM challenge branch)

WholeCell-Git-repo.html (URL)

Mar 22, 2014

Any

Source code

Challenge code (Git repo DREAM challenge branch)

Perturbation data

Perturbation data.html (URL)

Mar 23, 2014

Any

Data/images/video

Perturbation data

Documentation Links

Challenge home page

Challenge.html (URL)

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)

Synthetic networks

Publication release

May 23, 2013

This package provides all code for the publication. View License

Download Package

Download Links

Whole-cell synthetic networks code

Whole-cell-Git-repo.html (URL)

Apr 07, 2014

Any

Source code

Whole-cell synthetic networks code (Git repo synthetic networks branch)

Figure 1a code

figure1a.m

Apr 07, 2014

1 KB

Any

Source code

Figure 1a code

Figure 1b code

figure1b.m

Apr 07, 2014

1 KB

Any

Source code

Figure 1b code

Figure 2 code

figure2.m

Apr 07, 2014

1 KB

Any

Source code

Figure 2 code

Figure 3 code

figure3.m

Apr 07, 2014

1 KB

Any

Source code

Figure 3 code

Figure S2 code

figureS2.m

Apr 07, 2014

838

Any

Source code

Figure S2 code

Figure S5 code

figureS5.m

Apr 07, 2014

749

Any

Source code

Figure S5 code

Individual model predictions (.mat)

Model predictons.html (URL)

Apr 07, 2014

Any

Data/images/video

Model predictions (.mat)

All model predictions (.mat)

Model predictions.zip

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

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

Download Package

Download Links

WholeCellKB

WholeCellKB.html (URL)

Jun 16, 2014

Any

Application/binary

WholeCellKB

Source code (current)

WholeCellKB-Git-repo.html (URL)

Mar 09, 2014

Any

Source code

WholeCellKB code (latest) (Git repository)

Source code (publication release)

WholeCellKB-code.zip

May 23, 2013

6 MB

Any

Source code

Source code (publication release)

Data

WholeCellKB-data.zip

Oct 01, 2012

2 MB

Any

Data/images/video

Data

Documentation Links

Getting started guide

Tutorial.html (URL)

Jun 16, 2014

Tutorial

User guide

UserGuide.html (URL)

Jun 16, 2014

User guide

Developer guide

DevelopersGuide.pdf

Sep 28, 2012

Developer's guide

Source code documentation

Documentation.html (URL)

Jun 16, 2014

Source code documentation

Data model documentation

DataModelDocumentation.svg (URL)

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

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