Principled Simulation of Cell Proliferation Dynamics using the CoSMoS Approach

Fiona A C Polack; Alastair Philip Droop

doi:10.1007/s11047-014-9468-z

Principled Simulation of Cell Proliferation Dynamics using the CoSMoS Approach

Fiona A C Polack, Alastair Philip Droop

Computer Science

Research output: Contribution to journal › Article › peer-review

Abstract

A collaboration between cancer biologists and
academic software engineers has been exploring the
development of an agent-based simulator to inform and
support work on the dynamics of cell proliferation in the
study of prostate disorders. The research has influenced and
been informed by the CoSMoS project. This paper presents
the simulation project (which is not yet complete). We
reflect on the reality of following CoSMoS principles; we
describe the domain exploration and show how software
modelling approaches (here, Petri nets, state diagrams) can
be used to express both biological and software models.
We explore fitness for purpose and consider ways to
present a fitness argument. We consider issues in choosing
simulation media and mapping from domain models
through to code. The implementation emphasis is on
traceability to support reuse and extension of the simulator,
as well as demonstrable fitness for purpose. Initial work on
calibration is presented. We discuss the calibration results,
that both support and challenge the design and assumptions
captured in the domain modelling and development
activities.

Original language	English
Pages (from-to)	63-82
Number of pages	20
Journal	Natural Computing
Volume	14
Issue number	1
Early online date	17 Oct 2014
DOIs	https://doi.org/10.1007/s11047-014-9468-z
Publication status	Published - Mar 2015

Keywords

Cell proliferation Agent-based simulation CoSMoS Modelling and simulation 1

Access to Document

10.1007/s11047-014-9468-z

1 Finished

C2D2 research 1a - Data and simulation of the dynamics of stem cell amplification in prostate disease development and control (Benign Prostatic Hyperplasia)
Polack, F. A. C. (Principal investigator), Maitland, N. J. (Co-investigator) & Stepney, S. (Co-investigator)
1/03/12 → 30/09/12
Project: Other project › Other internal award

Cite this

@article{0b3528f6ea8d49a789ca7854f86dd326,

title = "Principled Simulation of Cell Proliferation Dynamics using the CoSMoS Approach",

abstract = "A collaboration between cancer biologists andacademic software engineers has been exploring thedevelopment of an agent-based simulator to inform andsupport work on the dynamics of cell proliferation in thestudy of prostate disorders. The research has influenced andbeen informed by the CoSMoS project. This paper presentsthe simulation project (which is not yet complete). Wereflect on the reality of following CoSMoS principles; wedescribe the domain exploration and show how softwaremodelling approaches (here, Petri nets, state diagrams) canbe used to express both biological and software models.We explore fitness for purpose and consider ways topresent a fitness argument. We consider issues in choosingsimulation media and mapping from domain modelsthrough to code. The implementation emphasis is ontraceability to support reuse and extension of the simulator,as well as demonstrable fitness for purpose. Initial work oncalibration is presented. We discuss the calibration results,that both support and challenge the design and assumptionscaptured in the domain modelling and developmentactivities.",

keywords = "Cell proliferation Agent-based simulation CoSMoS Modelling and simulation 1",

author = "Polack, {Fiona A C} and Droop, {Alastair Philip}",

year = "2015",

month = mar,

doi = "10.1007/s11047-014-9468-z",

language = "English",

volume = "14",

pages = "63--82",

journal = "Natural Computing",

issn = "1567-7818",

publisher = "Springer",

number = "1",

}

TY - JOUR

T1 - Principled Simulation of Cell Proliferation Dynamics using the CoSMoS Approach

AU - Polack, Fiona A C

AU - Droop, Alastair Philip

PY - 2015/3

Y1 - 2015/3

N2 - A collaboration between cancer biologists andacademic software engineers has been exploring thedevelopment of an agent-based simulator to inform andsupport work on the dynamics of cell proliferation in thestudy of prostate disorders. The research has influenced andbeen informed by the CoSMoS project. This paper presentsthe simulation project (which is not yet complete). Wereflect on the reality of following CoSMoS principles; wedescribe the domain exploration and show how softwaremodelling approaches (here, Petri nets, state diagrams) canbe used to express both biological and software models.We explore fitness for purpose and consider ways topresent a fitness argument. We consider issues in choosingsimulation media and mapping from domain modelsthrough to code. The implementation emphasis is ontraceability to support reuse and extension of the simulator,as well as demonstrable fitness for purpose. Initial work oncalibration is presented. We discuss the calibration results,that both support and challenge the design and assumptionscaptured in the domain modelling and developmentactivities.

AB - A collaboration between cancer biologists andacademic software engineers has been exploring thedevelopment of an agent-based simulator to inform andsupport work on the dynamics of cell proliferation in thestudy of prostate disorders. The research has influenced andbeen informed by the CoSMoS project. This paper presentsthe simulation project (which is not yet complete). Wereflect on the reality of following CoSMoS principles; wedescribe the domain exploration and show how softwaremodelling approaches (here, Petri nets, state diagrams) canbe used to express both biological and software models.We explore fitness for purpose and consider ways topresent a fitness argument. We consider issues in choosingsimulation media and mapping from domain modelsthrough to code. The implementation emphasis is ontraceability to support reuse and extension of the simulator,as well as demonstrable fitness for purpose. Initial work oncalibration is presented. We discuss the calibration results,that both support and challenge the design and assumptionscaptured in the domain modelling and developmentactivities.

KW - Cell proliferation Agent-based simulation CoSMoS Modelling and simulation 1

U2 - 10.1007/s11047-014-9468-z

DO - 10.1007/s11047-014-9468-z

M3 - Article

SN - 1567-7818

VL - 14

SP - 63

EP - 82

JO - Natural Computing

JF - Natural Computing

IS - 1

ER -

Principled Simulation of Cell Proliferation Dynamics using the CoSMoS Approach

Abstract

Keywords

Access to Document

Projects

C2D2 research 1a - Data and simulation of the dynamics of stem cell amplification in prostate disease development and control (Benign Prostatic Hyperplasia)

Cite this