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Team:Newcastle University/Modelling
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==Introduction to CellML== | ==Introduction to CellML== | ||
| - | The programming language chosen for modelling was [http://www.cellml.org/ CellML]. CellML has mainly been used to model biological pathways and the molecules involved in these | + | The programming language chosen for modelling was [http://www.cellml.org/ CellML]. CellML has mainly been used to model biological pathways and the molecules involved in these. CellML models are based on a modular structure, which is appropriate when modelling the behaviour of biological parts. CellML seeks to model the mathematics behind biological systems. This is beneficial when capturing information but the implications are that the mathematics behind the behaviour must be clearly defined and understood. |
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| + | Unlike SBML, CellML is good at describing biological entities as components and can also express a wide range of different models. CellML is a modular language, something that is important for this BugBuster project as it enables models of separate components to be built separately and then later be integrated into a single larger model. This is what we have done with models from the parts and constraints repositories, when building the construct. | ||
| + | |||
| + | CellML integrates the language MathML to describe the mathematical relationships between different components and variables within a biological model(Lloyd, et al., 2004). Every variable must have physically defined units. This makes the language more accurate and consistent and should eliminate a large number of errors. The ultimate aim for the CellML language is for the research community to build models and make them freely available for others to build on(Lloyd, et al., 2004). We have used the CellML language in defining all of our part and constraint models. | ||
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==Model generation and simulation== | ==Model generation and simulation== | ||
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* YocG.txt | * YocG.txt | ||
* zapA.txt | * zapA.txt | ||
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| + | ===Further Reading=== | ||
| + | Garny, A. (2003) Cellular Open Resource(COR): A public CellML based environment for modelling biological function, ''International Journal of Bifurcation and Chaos'', '''13''', 3579-3590. | ||
| + | |||
| + | Lloyd, C.M., Halstead, M.D.B. and Nielsen, P.F. (2004) CellML: its future, present and past, ''Progress in Biophysics & Molecular Biology'', '''85''', 433-450. | ||
Revision as of 20:10, 28 October 2008
Newcastle University
GOLD MEDAL WINNER 2008
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Home >> Modelling
Introduction to CellML
The programming language chosen for modelling was [http://www.cellml.org/ CellML]. CellML has mainly been used to model biological pathways and the molecules involved in these. CellML models are based on a modular structure, which is appropriate when modelling the behaviour of biological parts. CellML seeks to model the mathematics behind biological systems. This is beneficial when capturing information but the implications are that the mathematics behind the behaviour must be clearly defined and understood.
Unlike SBML, CellML is good at describing biological entities as components and can also express a wide range of different models. CellML is a modular language, something that is important for this BugBuster project as it enables models of separate components to be built separately and then later be integrated into a single larger model. This is what we have done with models from the parts and constraints repositories, when building the construct.
CellML integrates the language MathML to describe the mathematical relationships between different components and variables within a biological model(Lloyd, et al., 2004). Every variable must have physically defined units. This makes the language more accurate and consistent and should eliminate a large number of errors. The ultimate aim for the CellML language is for the research community to build models and make them freely available for others to build on(Lloyd, et al., 2004). We have used the CellML language in defining all of our part and constraint models.
Model generation and simulation
Modelling in the CellML language was carried out in the [http://cor.physiol.ox.ac.uk/ Cellular Open Resource (COR)] (Garny, et al., 2003). COR is a free resource available in Microsoft Windows. This provides an editor to write in COR language, which has easier readability than the mark-up language. The text is converted into CELLML by the program, which complies and runs models as they are created. Once models were generated in COR, they were loaded into [http://www.cellml.org/tools/pcenv/ PCEnv] for simulation.
Downloads
Download: File:Newcastle-igem2008-CellML-models.zip contains:
- Alt.promoter.constitutive.cellml
- Alt.promoter.constitutiveImport.cellml
- Alt.promoter.inductive.cellml
- Alt.promoter.inductive3.cellml
- Alt.promoter.respressive.cellml
- Alt.protein.cellml
- Alt.RBS.cellml
- Bacillus RBS.cellml
- Basic promoter 2.cellml
- Basic promoter 3.cellml
- Basic Promoter.cellml
- Check comp.cellml
- CodingRegion.cellml
- ComD(NoInducSynthWithComEP).cellml
- ComD.cellml
- ComDAGAIN.cellml
- composite2.cellml
- CompositeModel.cellml
- constitutive promoter.cellml
- DNAa.cellml
- EncodedProtein.cellml
- example tut3main.cellml
- example tut3sub..cellml
- FluxComEP.cellml
- ftsA.cellml
- ftsW.cellml
- HySpank.cellml
- InitialRBS.cellml
- minC.cellml
- NewComD.cellml
- PbofA.cellml
- PcotA.cellml
- Protein.cellml
- proteinCoding.cellml
- PspaS.cellml
- PspollQ.cellml
- Pxyl.cellml
- ResponseRegulator.cellml
- Sensor.cellml
- Tanscription factor.cellml
- To join the components together.doc
- veg.cellml
- XComDP.cellml
- zapA.cellml
File:Newcastle-igem2008-CellML-components.zip contains:
- AgrA.txt
- AgrC.txt
- Bind Components.txt
- CFP.txt
- Cin-box.txt
- ComD.txt
- ComE.txt
- ConstitutivePromoter.txt
- DNAa.txt
- Environment.txt
- Essentials.txt
- Footer.txt
- ftsA.txt
- ftsW.txt
- GFP.txt
- Header.txt
- HySpank.txt
- InducablePromoter.txt
- mCherry.txt
- minC.txt
- OptimalRBS.txt
- P2.txt
- P3.txt
- PbofA.txt
- PbofAmod.txt
- PcotA.txt
- PlcA.txt
- PromoterToRBS.txt
- Protein.txt
- PspaS.txt
- PspollQ.txt
- Pxyl.txt
- RBS.txt
- RBSToCodingRegion.txt
- RepressablePromoter.txt
- ResponseRegulator.txt
- Sensor.txt
- Units.txt
- veg.txt
- XyloseIsomerase.txt
- YFP.txt
- YocF.txt
- YocG.txt
- zapA.txt
Further Reading
Garny, A. (2003) Cellular Open Resource(COR): A public CellML based environment for modelling biological function, International Journal of Bifurcation and Chaos, 13, 3579-3590.
Lloyd, C.M., Halstead, M.D.B. and Nielsen, P.F. (2004) CellML: its future, present and past, Progress in Biophysics & Molecular Biology, 85, 433-450.
