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Introduction to CellML

The programming language chosen for modelling was 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 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 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

File:ProofConcept gfp.zip

Team:Newcastle University/Modelling

From 2008.igem.org

Newcastle University

Introduction to CellML

Model generation and simulation

Downloads

Further Reading