Team:Newcastle University/Modelling

From 2008.igem.org

(Difference between revisions)
Line 4: Line 4:
==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 (CellML model repository, 2008).  CellML models are based on a modular structure, which is appropriate when modelling the behaviour of biological parts (Rouilly, et al., 2007).  CellML is accepted as a standard by members of the Physiome project (The Physiome Project, 2006).
+
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. 
-
CellML looks to model the mathematics behind this system (Schilstra, et al., 2006).  This is beneficial when capturing information but the implications are that the mathematics behind the behaviour must be clearly defined and understood. An aim of CellML was to overcome some of the limitations of SBML (Lloyd, et al., 2004). Particularly, the modularity of CellML allows it to be utilised on a large scale.  Whole models or components of parts of models can be integrated successfully to produce larger models whilst maintaining the language structure (Lloyd, et al., 2004).
 
==Model generation and simulation==
==Model generation and simulation==
Line 106: Line 109:
* YocG.txt
* YocG.txt
* zapA.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.

Revision as of 20:10, 28 October 2008

Bugbuster-logo-red.png
Ncl uni logo.jpg


Newcastle University

GOLD MEDAL WINNER 2008

Home Team Original Aims Software Modelling Proof of Concept Brick Wet Lab Conclusions


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.