Chen, C

Clack, C

Nagl, SB

BMC Systems Biology

UCL Discovery

BioMed CentralBMC Systems BiologyssOpen AccePoster presentationContext sensitivity in individual-based modelingChih-Chun Chen*1, Christopher D Clack1 and Sylvia B Nagl2Address: 1Department of Computer Science, University College London, London, WC1E 6BT, UK and 2Department of Oncology and Biochemistry, University College London, London, WC1E 6BT, UKEmail: Chih-Chun Chen* - c.chen@cs.ucl.ac.uk* Corresponding author    The function of many bio-molecules and biological enti-ties is dependent on their context. We can define contextas anything influencing the molecule but which is not themolecule itself. For example, 'moonlighting' proteins [1]use various molecular mechanisms to switch betweenfunctions, such as differential localisation, complex for-mation and substrate formation; these can all be classifiedas context-dependent mechanisms. Cell function is alsohighly dependent on external signals and local environ-ment e.g. [2]. Context sensitivity implies the following:1. Biological function can not be deduced purely froman entity's type or species. Role and species need to berepresented as distinct aspects of an entity.2. An entity can play several different roles during itslifetime and some of these can be simultaneous.A biological system can be seen to consist of a largenumber of individual entities e.g. molecules, cells. Indi-vidual-Based modelling techniques are those that modelfrom the 'bottom up', taking the behaviour of these enti-ties as their starting point. Simulations run from thesemodels can reveal emergent phenomena and structuresthat would not be easy to predict from analysis alone.Context sensitive multifunctionality in Biology poses achallenge in individual-based modelling because contextconditions often need to be represented at higher levels ofabstraction. For example, complex formation depends onthe collective behaviour of several different molecules.However, we can reduce the representation of context toan interaction between an individual and its environ-ment, where its environment is anything that affects theentity's behaviour or function but that is not internal tothe entity itself. Context sensitive multifunctionality canthen be represented in terms of different state transforma-tions for different individual-environment combinations.Process algebras such as the π-calculus [3], bioambientcalculus [4] and brane calculus [5] can be used to describeinteractions between entities in biological systems. In gen-eral, they consist of (i) a language for describing systems(ii) a behavioural equivalence or inequivalence thatallows comparison of system behaviours and (iii) axiomsthat allow for proofs for equivalence between systems [6].A biological entity is represented by a process and a hand-shake mechanism between processes via a channel is usu-ally used to represent interactions between entities. Oncethe data are exchanged, both processes continue. Sincecontext-sensitive multi-functionality can be seen simplyas interactions between entities, process algebras can beused to formally represent these models.References1. Jeffrey CJ: Molecular mechanisms for multitasking: recentcrystal structures of moonlighting proteins.  Current Opinion inStructural Biology 2004, 14:663-668.2. Barcellos-Hoff MH, Costes SV: A systems biology approach tomulticellular and multi-generational radiation responses.Mutation Research 2006, 597:32-38.3. Regev A, Silverman W, Shapiro E: Representation and simulationof biochemical processes using the pi-calculus process alge-from BioSysBio 2007: Systems Biology, Bioinformatics and Synthetic BiologyManchester, UK. 11–13 January 2007Published: 8 May 2007BMC Systems Biology 2007, 1(Suppl 1):P44 doi:10.1186/1752-0509-1-S1-P44<supplement> <title> <p>BioSysBio 2007: Systems Biology, Bioinformatics, Synthetic Biology</p> </title> <editor>John Cumbers, Xu Gu, Jong Sze Wong</editor> <note>Meeting abstracts – A single PDF containing all abstracts in this Supplement is available <a href="www.biomedcentral.com/content/files/pdf/1752-0509-1-S1-full.pdf">here</a>.</note> <url>http://www.biomedcentral.com/content/pdf/1752-0509-1-S1-info.pdf</url> </supplement>This abstract is available from: http://www.biomedcentral.com/1752-0509/1?issue=S1© 2007 Chen et al; licensee BioMed Central Ltd. Page 1 of 2(page number not for citation purposes)BMC Systems Biology 2007, 1(Suppl 1):P44 http://www.biomedcentral.com/1752-0509/1?issue=S1Publish with BioMed Central   and  every scientist can read your work free of charge"BioMed Central will be the most significant development for disseminating the results of biomedical research in our lifetime."Sir Paul Nurse, Cancer Research UKYour research papers will be:available free of charge to the entire biomedical communitypeer reviewed and published immediately upon acceptancecited in PubMed and archived on PubMed Central yours — you keep the copyrightSubmit your manuscript here:http://www.biomedcentral.com/info/publishing_adv.aspBioMedcentralbra.  In Pacific Symposium on Biocomputing, Singapore Volume 6. Editedby: Altman RB, Dunker AK, Hunter L, Klein TE. ; 2001:459-470. 4. Regev A, Panina EM, Silverman W, Cardelli L, Shapiro E: Bioambi-ents: an abstraction for biological compartments.  TheoreticalComputer Science 2004, 325:141-167.5. Cardelli L: Brane calculi.  CMSB 2004, LNBI 2005, 3082:.6. Hinchey M, Bowen JP, Rouff CA: Introduction to Formal Meth-ods.  In Agent Technology from a Formal Perspective Edited by: Rouff CA,Hinchey M, Rash J, Truszkowski W, Gordon-Spears D. Springer; 2006. Page 2 of 2(page number not for citation purposes)

Context sensitivity in individual-based modeling

Chih-Chun Chen

Christopher D Clack

Sylvia B Nagl

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http://discovery.ucl.ac.uk/124671/1/1752-0509-1-S1-P44.pdf

Context sensitivity in individual-based modeling

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