Location: Bugbuster Standard Virtual Biological Machine @ 81668aa7b2db / index.html

Author:
mcoo001 <devnull@localhost>
Date:
2010-01-11 13:58:23+13:00
Desc:
Added a title to description index.html
Permanent Source URI:
https://models.cellml.org/workspace/bugbuster/rawfile/81668aa7b2dbffdcb448f7969caa5040e701a999/index.html
Compare... Download Source

Model Overview

This is a Systems Model for the gold medal-winning machine 'Bugbuster' produced by the team from Newcastle University for the iGEM 2008 competition. Details about the project can be found here: http://2008.igem.org/Team:Newcastle_University.

A constitutive promoter leads to the production of proteins spaK and spaR. Subtilin activates spaK which in turn activates spaR. Activated spaR is a transcriptional regulator for GFP. The system senses and reports subtilin concentrations via GFP.

Model Output

The Figure below shows the GFP time-course for the model, for various concentrations of initial Subtilin.

 

Model Files

Two variants of the model are available here:

·         1. An online version, linking to SVPs and Templates in the CellML Model Repository, that can be run from any browser with an appropriate simulator registered can be found here.

·         2. All the files needed for the Systems Model encapsulated into a ZIP file, suitable for downloading and simulating in an appropriate locally-installed simulator can be found here.

Model Architecture

The numbers on the schematic above relate to imported components. A map of the imported component architecture is as follows:

 

BugbusterModel.BugbusterModel_SVBM[

 BugbusterModel.ChassisBacillus(Chassis_Bacillus(Template_Chassis_WellStirredBag))

 BugbusterModel.Time(Time)

 BugbusterModel.SpeciesInitialConcentrations

1. BugbusterModel.Bugbuster_Promoter1(Bugbuster_Promoter1(Template_Promoter_Constitutive))

2. BugbusterModel.RNA1(Template_Species)

3. BugbusterModel.RNA1_interface

4. BugbusterModel.Bioenvironment_Degradation_RNA1(Bioenvironment_Degradation_BugbusterRNA1(Template_RxR1P1))

5. BugbusterModel.Bugbuster_RBS_spaR_1(Bugbuster_RBS_spaR(Template_RBS))

6. BugbusterModel.Bugbuster_ProteinCDS_spaR_1(Bugbuster_ProteinCDS_spaR(Template_ProteinCDS))

7. BugbusterModel.Bugbuster_RBS_spaK(Bugbuster_RBS_spaK(Template_RBS))

8. BugbusterModel.Bugbuster_ProteinCDS_spaK(Bugbuster_ProteinCDS_spaK(Template_ProteinCDS))

9. BugbusterModel.spaK(Template_Species)

10.BugbusterModel.spaK_interface

11.BugbusterModel.Bioenvironment_Degradation_spaK(Bioenvironment_Degradation_spaK(Template_RxR1P1))

12.BugbusterModel.Subtilin

13.BugbusterModel.spaKActivation(Bioenvironment_RxR2P1_spaKActivation(Template_RxR2P1)

14.BugbusterModel.spaKactive(Template_Species)

15.BugbusterModel.spaKactive_interface

16.BugbusterModel.Bioenvironment_Dephosphorylation_spaKactive(Bioenvironment_Dephosphorylation_spaKactive(Template_RxR1P1))

17.BugbusterModel.Bioenvironment_Degradation_spaKactive(Bioenvironment_Degradation_spaKactive(Template_RxR1P1))

18.BugbusterModel.spaR(Template_Species)

19.BugbusterModel.spaR_interface

20.BugbusterModel.Bioenvironment_Degradation_spaR(Bioenvironment_Degradation_spaR(Template_RxR1P1))

21.BugbusterModel.spaRActivation(Bioenvironment_RxR2P1_spaRActivation(Template_RxR2P1)

22.BugbusterModel.spaRactive(Template_Species)

23.BugbusterModel.spaRactive_interface

24.BugbusterModel.Bioenvironment_Dephosphorylation_spaRactive(Bioenvironment_Dephosphorylation_spaRactive(Template_RxR1P1))

25.BugbusterModel.Bioenvironment_Degradation_spaRactive(Bioenvironment_Degradation_spaRactive(Template_RxR1P1))

26.BugbusterModel.Bugbuster_Promoter2(Bugbuster_Promoter2(Template_Promoter_Inducible))

27.BugbusterModel.RNA2(Template_Species)

28.BugbusterModel.RNA2_interface

29.BugbusterModel.Bioenvironment_Degradation_RNA2(Bioenvironment_Degradation_BugbusterRNA2(Template_RxR1P1))

30.BugbusterModel.Bugbuster_RBS_GFP(Bugbuster_RBS_GFP(Template_GFP))

31.BugbusterModel.Bugbuster_ProteinCDS_GFP(Bugbuster_ProteinCDS_GFP(Template_ProteinCDS))

32.BugbusterModel.GFP(Template_Species)

33.BugbusterModel.GFP_interface

34.BugbusterModel.Bioenvironment_Degradation_GFP(Bioenvironment_Degradation_GFP(Template_RxR1P1))

]

 
where the following code is used:

 M[A] Model M contains A

A(B)  A imports a component that is referred to as B

F.S Component or model is named S, held in file named F

D Component is named D, held in file name D (i.e. shorthand for D.D)

Physical Implementation

Several of the Parts used in this model have their DNA stored in the Repository of Standard Biological Parts. They are as follows:

The promoter for spaR and spaK  (number 1. above): Part BBa_K104002.

The RBS for spaR  (number 5. above): Part BBa_K104003.

The CDS for the spaR protein (number 6. above): Part BBa_K104004.

The RBS for spaK (number 7. above): Part BBa_K104005.

The CDS for the spaK protein (number 8. above): Part BBa_K104006.

The promoter for GFP (number 26. above): Part BBa_K104008.

The RBS for GFP (number 30. above): Part BBa_K104009.