Revision as of 15:54, 29 October 2008

Newcastle University

GOLD MEDAL WINNER 2008

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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

File:Newcastle-igem2008-CellML-models.zip	Contains the CellML models created as part of the Parts Repository. See Team:Newcastle University/Parts Repository for more information.
File:Newcastle-igem2008-CellML-components.zip	Contains the individual component text files, containing CellML, from the Parts Repository. See Team:Newcastle University/Parts Repository for more information.
File:ProofConcept gfp.zip	Contains: The CellML model of the proof of concept BioBrick. See Proof of Concept Brick for more information.

@@ Line 17: / Line 17: @@
 ==Downloads==
-Download:
+<table border="1"><tr><td valign="top">
-[[Image:Newcastle-igem2008-CellML-models.zip]] contains:
+[[Image:Newcastle-igem2008-CellML-models.zip]]
-* Alt.promoter.constitutive.cellml
+<td valign="top">
-* Alt.promoter.constitutiveImport.cellml
+Contains the CellML models created as part of the Parts Repository. See [[Team:Newcastle University/Parts Repository]] for more information.
-* Alt.promoter.inductive.cellml
+<tr><td valign="top">
-* Alt.promoter.inductive3.cellml
+[[Image:Newcastle-igem2008-CellML-components.zip]]
-* Alt.promoter.respressive.cellml
+<td valign="top">
-* Alt.protein.cellml
+Contains the individual component text files, containing CellML, from the Parts Repository. See [[Team:Newcastle University/Parts Repository]] for more information.
-* Alt.RBS.cellml
+<tr><td valign="top">
-* 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
-[[Image: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
 [[Image:ProofConcept gfp.zip]]
+</td><td valign="top">
+Contains: The CellML model of the proof of concept BioBrick. See [[Team:Newcastle University/ProofOfConceptBrick|Proof of Concept Brick]] for more information.
+<html></td></tr></table></html>
 ===Further Reading===

Team:Newcastle University/Modelling

From 2008.igem.org

Revision as of 15:54, 29 October 2008

Newcastle University

Introduction to CellML

Model generation and simulation

Downloads

Further Reading