Engineering Simulations as Scientific Instruments: A Pattern Language: With Kieran Alden, Paul S. Andrews, James L. Bown, Alastair Droop, Richard B. Greaves, Mark Read, Adam T. Sampson, Jon Timmis, Alan F.T. Winfield PDF
Preview Engineering Simulations as Scientific Instruments: A Pattern Language: With Kieran Alden, Paul S. Andrews, James L. Bown, Alastair Droop, Richard B. Greaves, Mark Read, Adam T. Sampson, Jon Timmis, Alan F.T. Winfield
Susan Stepney · Fiona A.C. Polack Engineering Simulations as Scientifi c Instruments: A Pattern Language With Kieran Alden, Paul S. Andrews, James L. Bown, Alastair Droop, Richard B. Greaves, Mark Read, Adam T. Sampson, Jon Timmis, Alan F.T. Winfi eld Engineering Simulations as Scientific Instruments: A Pattern Language Susan Stepney • Fiona A.C. Polack Engineering Simulations as Scientific Instruments: A Pattern Language With Kieran Alden, Paul S. Andrews, James L. Bown, Alastair Droop, Richard B. Greaves, Mark Read, Adam T. Sampson, Jon Timmis, Alan F.T. Winfield Susan Stepney Fiona A.C. Polack Dept. of Computer Science School of Computing and Mathematics University of York Keele University York, UK Newcastle-under-Lyme, UK Written in collaboration with Kieran Alden, Paul S. Andrews, James L. Bown, Alastair Droop, Richard B. Greaves, Mark Read, Adam T. Sampson, Jon Timmis and Alan F.T. Winfield. ISBN 978-3-030-01937-2 ISBN 978-3-030-01938-9 (eBook) https://doi.org/10.1007/978-3-030-01938-9 Library of Congress Control Number: 2018961032 © Springer Nature Switzerland AG 2018 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made. The publisher remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. This Springer imprint is published by the registered company Springer Nature Switzerland AG The registered company address is: Gewerbestrasse 11, 6330 Cham, Switzerland Preface Computer-basedsimulationisakeytoolinmanyfieldsofscientificresearch. In silico experiments can be used to explore and understand complex pro- cesses,toguideandcomplementinvitroandinvivoexperiments,tosuggest newhypothesestoinvestigate,andtopredictresultswhereexperimentsare infeasible.Simulationisanattractive,accessibletool:producingnewsimu- lations of simple systems is relatively easy. But it is also a dangerous one: simulations (and their underlying models) are often complex, buggy, and difficulttorelatetotherealworldsystem. ArecentUKGovernmentreportoncomputationalmodelling([95],con- densedas[44])makesseveralrecommendations,including Decision-makersneedtobeintelligentcustomersformodels,andthosethatsup- plymodelsshouldprovideappropriateguidancetomodeluserstosupportproper useandinterpretation.Thisincludesprovidingsuitablemodeldocumentationde- tailingmodelpurpose,assumptions,sensitivities,andlimitations,andevidenceof appropriatequalityassurance. InthisbookwedescribetheCoSMoS(ComplexSystemsModellingand Simulation)approach,apattern-basedapproachtoengineeringtrustworthy simulations:simulationsthatarebothscientificallyusefultotheresearcher, and scientifically credible to third parties. The CoSMoS approach emphas- isesthreekeyaspectstothisdevelopmentofasimulationasascientificinstru- ment: the use of models to capture the scientific domain and the simulation platform;theuseofargumentstoprovideevidencethatthescientificinstru- ment is fit for purpose; and the close co-working of domain scientists and simulationsoftwareengineers. TheCoSMoSapproachisgeneric:itdoesnotmandateaparticularmod- ellingtechnique,aparticularimplementationlanguage,oraparticularreal world application domain. What it does mandate is the careful and struc- v vi Preface tured use of models and arguments, to ensure that the simulation is both well-engineered,andseentobewell-engineered. Thebookisusefulfordomainscientistswhowishtoseewhatisneeded tobuildandusescientificallycrediblesimulations,andforsoftwareengin- eerswhowishtobuildscientificsimulationsthatareusefulandusable.The examplesinthebookfocusmainlyonbiologicalsimulations,toexploitthe specificexperienceoftheauthors,buttheCoSMoSapproachisnotrestricted tothisdomain.Theapproachwedescribeisalsousefulforbuildingsimula- tionsaspartoftheprocessofbuildingengineeredsystems.Therearesome differences between scientific simulation (crudely, simulating the world as it is) and engineering design simulation (simulating the world as we wish ittobe),butmuchoftheapproachiscommon.Thesedifferencesarenoted whentheyoccur. Whatthisbookisnot Thisisnotabookaboutsoftwareengineering.Whereweadvocateparticu- larsoftwareengineeringapproachesandgoodpracticesforbuildingsimu- lations, we mention them in the endnotes1 and refer to standard literature discussingthem. Neitheristhisabookaboutspecificmodellingapproachesornotations2, whether mathematical, computational, or otherwise. Again, there is much excellentliteratureavailableonspecificmodellingtechniques,towhichwe refer. Nor is it a book about experimental methods, although the simulations areusedtoperform(numerical,virtual)experimentsinawayanalogousto realworldexperiments. Norisitabookaboutdevelopingbio-inspiredalgorithms(whichareab- stractionsofbiology,butnotsimulationsofbiology). Whatthisbookis This is a book about how to combine well-established approaches in a manner that leads to a robust and argued-trustworthy simulation: how to combine modelling to build an appropriate scientific instrument, software engineering to build the instrument appropriately, and experimental tech- niquestousetheinstrumentappropriatelyforscientificinvestigation. Preface vii Part I provides a managerial overview: the rationale for and benefits of using the CoSMoS approach, and a small worked example to demonstrate theapproachinaction. PartIIisacatalogueofthecoreCoSMoSpatterns.Startyourprojectatthe CoSMoS Simulation Project (92) pattern, and follow the guidance, using the other referenced patterns as your specific context demands. The develop- mentanduseofasimulationasascientificinstrumentwillprobablyinclude mostofthesecorepatterns. Part III is a catalogue of “helper” patterns. These are more specific pat- terns of use only in certain domains, for certain purposes, or with certain modelling and implementation approaches. Use of these is not required to develop a CoSMoS simulation, but they provide possible routes for doing so. PartIVdocumentsCellBranch,asubstantialcasestudydevelopedusing theCoSMoSapproach. Acknowledgements The original CoSMoS (Complex Systems Modelling and Simulation) re- search project (2007–2012) was funded by the UK’s Engineering and Phys- icalSciencesResearchCouncil(EPSRC),grantnumbersEP/E053505/1and EP/E049419/1,withadditionalsupportfromMicrosoftResearchandCelox- ica. The CellBranch research project (2014–2015) was funded by the UK’s Biotechnology and Biological Sciences Research Council (BBSRC), grant numberBB/L018705/1. AlistofCoSMoSpublicationsandassociatedtoolsisavailableintheend- notes3. The York Computational Immunology Lab (YCIL) is using CoSMoS for manyofitsprojects.Ithasmadeextensivematerialavailable,includingsim- ulations, simulation analysis tools, and fitness-for-purpose argumentation tools,availableatwww.york.ac.uk/computational-immunology/software/. Theauthorteamhavemadesubstantialandvariouscontributionstothe CoSMoSproject,totheCellBranchproject,toYCILprojects,andduringall stagesofthedevelopmentofthisbook.Inadditiontotheiroverallworkon thestructure,writing,andeditingofthisbook,theyhavehadthefollowing specific roles on the projects, and, as far as can be determined from such a jointeffort,havemadethefollowingspecificcontributionstothebook: • Susan Stepney (Principal Investigator of CoSMoS and CellBranch): de- veloperofthedetailedpatternlanguagestructure viii Preface • FionaPolack(Co-InvestigatorofCoSMoS):developerofthedetailedar- gumentationpatternsuite • KieranAlden(ResearchAssociateapplyingCoSMoSinYCIL):contrib- utortoCalibrationandSensitivity Analysispatterns • PaulAndrews(ResearchAssociateonCoSMoS):developeroftheinitial CoSMoS philosophy, process, phases, and high-level models: contrib- utortoChapter1 • JamesBown(advisorymemberofCoSMoS):contributortoChapter2 • AlastairDroop(owneroftheAlKanworkedexampleinChapter3):con- tributortoChapter3 • RichardGreaves(ResearchAssociateonCellBranch):developerofPart IV • Mark Read (then PhD student applying CoSMoS in YCIL): contributor toCalibrationandSensitivity Analysispatterns • AdamSampson(ResearchAssociateonCoSMoS):contributortodocu- mentationandrealworldpatterns • Jon Timmis (Co-Investigator of CoSMoS; applying CoSMoS in YCIL): contributortoChapter1 • AlanWinfield(advisorymemberofCoSMoS):contributortoChapter2, embodiedsimulationpattern,andseveralantipatterns We thank all our other CoSMoS project partners, CoSMoS workshop con- tributors, CoSMoS case study domain scientists and simulation engineers, and in particular Christopher Alexander, Frederick Barnes, Sabine Diet- mann,FionaFrame,PhilipGarnett,TeodorGhetiu,JulianneD.Halley,Tim Hoverd, Norman J. Maitland, Carl G. Ritson, Austin Smith, and Peter H. Welch. SusanStepney,FionaPolack York,UK,2018 Contents PartI OverviewoftheCoSMoSapproach 1 CoSMoS:rationaleandconcepts ............................... 3 1.1 WhyCoSMoS ............................................ 3 1.2 Complexsystemssimulation .............................. 4 1.3 Simulationasascientificinstrument........................ 5 1.4 Simulationsinengineering ................................ 8 1.5 Workingtogether ......................................... 11 1.6 Patternlanguage.......................................... 13 1.7 TheCoSMoSconcepts..................................... 16 2 What’sinitforme? ........................................... 25 2.1 Whythischapter,andwhyus?............................. 25 2.2 Whatchallengesdoweface................................ 26 2.3 WhatcantheCoSMoSapproachdotohelp? ................ 29 2.4 Summaryandfutureperspectives.......................... 39 3 TheCoSMoSapproachinminiature ........................... 43 3.1 Introduction–arunningexample .......................... 43 3.2 TheCoSMoSSimulationProject............................ 44 3.3 Discoveryphase .......................................... 45 3.4 Developmentphase....................................... 70 3.5 Explorationphase ........................................ 80 3.6 Argueinstrumentfitforpurpose........................... 83 3.7 Realworldsimulation..................................... 88 ix x Contents PartII TheCoreCoSMoSPatternLanguage 4 TheCoSMoSsimulationpattern ............................... 91 4.1 Catalogueoftoplevelpatterns............................. 91 4.2 Phasepatterns............................................ 92 4.3 Rolepatterns ............................................. 99 4.4 Genericpatterns ..........................................108 4.5 Antipatterns..............................................114 5 Discoveryphasepatterns:buildingthedomainmodel ..........117 5.1 Catalogueofdiscoveryphasepatterns......................117 5.2 Contextsettingpatterns ...................................119 5.3 Domainmodellingpatterns................................128 5.4 Antipatterns..............................................137 6 Developmentphasepatterns:developingtheplatform ..........147 6.1 Catalogueofdevelopmentphasepatterns ..................147 6.2 Platformmodellingpatterns ...............................148 6.3 Implementationpatterns ..................................160 6.4 Antipatterns..............................................169 7 Explorationphasepatterns:usingtheplatform .................173 7.1 Catalogueofexplorationphasepatterns ....................173 7.2 Modelandusagepatterns .................................174 7.3 Antipatterns..............................................182 8 Structuredargumentationpatterns.............................185 8.1 Catalogueofargumentationpatterns .......................185 8.2 Argumentpatterns........................................186 8.3 Basicstructuredargumentpatterns.........................190 8.4 Genericargumentpatterns ................................200 PartIII TheCoSMoSHelperPatterns 9 ModellingandDocumentationPatterns........................207 9.1 Catalogueofpatterns .....................................207 9.2 Modellingapproaches.....................................208 9.3 Communicationanddocumentation .......................217 10 Realworldsimulationpatterns ................................227 10.1 Catalogueofpatterns .....................................227 10.2 Developmentprocess .....................................228 10.3 Engineeredsystems.......................................238
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