Hybrid Systems Biology: Fourth International Workshop, HSB 2015, Madrid, Spain, September 4-5, 2015. Revised Selected Papers PDF
Preview Hybrid Systems Biology: Fourth International Workshop, HSB 2015, Madrid, Spain, September 4-5, 2015. Revised Selected Papers
Alessandro Abate David Šafránek (Eds.) Hybrid Systems 1 7 2 9 I Biology B N L Fourth International Workshop, HSB 2015 Madrid, Spain, September 4–5, 2015 Revised Selected Papers 123 Lecture Notes in Bioinformatics 9271 Subseries of Lecture Notes in Computer Science LNBI Series Editors SorinIstrail BrownUniversity,Providence,RI,USA PavelPevzner UniversityofCalifornia,SanDiego,CA,USA MichaelWaterman UniversityofSouthernCalifornia,LosAngeles,CA,USA LNBI EditorialBoard AlbertoApostolico GeorgiaInstituteofTechnology,Atlanta,GA,USA SørenBrunak TechnicalUniversityofDenmarkKongensLyngby,Denmark MikhailS.Gelfand IITP,ResearchandTrainingCenteronBioinformatics,Moscow,Russia ThomasLengauer MaxPlanckInstituteforInformatics,Saarbrücken,Germany SatoruMiyano UniversityofTokyo,Japan EugeneMyers MaxPlanckInstituteofMolecularCellBiologyandGeneticsDresden,Germany Marie-FranceSagot UniversitéLyon1,Villeurbanne,France DavidSankoff UniversityofOttawa,Canada RonShamir TelAvivUniversity,RamatAviv,TelAviv,Israel TerrySpeed WalterandElizaHallInstituteofMedicalResearchMelbourne,VIC,Australia MartinVingron MaxPlanckInstituteforMolecularGenetics,Berlin,Germany W.EricWong UniversityofTexasatDallas,Richardson,TX,USA More information about this series at http://www.springer.com/series/5381 Š á Alessandro Abate David afr nek (Eds.) (cid:129) Hybrid Systems Biology Fourth International Workshop, HSB 2015 – Madrid, Spain, September 4 5, 2015 Revised Selected Papers 123 Editors Alessandro Abate DavidŠafránek Department ofComputer Science Faculty of Informatics University of Oxford MasarykUniversity Oxford Brno UK Czech Republic ISSN 0302-9743 ISSN 1611-3349 (electronic) Lecture Notesin Computer Science ISBN 978-3-319-26915-3 ISBN978-3-319-26916-0 (eBook) DOI 10.1007/978-3-319-26916-0 LibraryofCongressControlNumber:2015958329 ©SpringerInternationalPublishingSwitzerland2015 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartofthe 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 storageandretrieval,electronicadaptation,computersoftware,orbysimilarordissimilarmethodologynow knownorhereafterdeveloped. Theuseofgeneraldescriptivenames,registerednames,trademarks,servicemarks,etc.inthispublication doesnotimply,evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevant protectivelawsandregulationsandthereforefreeforgeneraluse. Thepublisher,theauthorsandtheeditorsaresafetoassumethattheadviceandinformationinthisbookare believedtobetrueandaccurateatthedateofpublication.Neitherthepublishernortheauthorsortheeditors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissionsthatmayhavebeenmade. Printedonacid-freepaper ThisSpringerimprintispublishedbySpringerNature TheregisteredcompanyisSpringerInternationalPublishingAGSwitzerland Preface The 4th International Workshop on Hybrid Systems Biology (HSB 2015) was held during September 4–5, 2015, at the Facultad de Matemáticas, Universidad Com- plutense de Madrid. HSB2015wasco-locatedwiththeweek-longMadridMeet2015,whichalsohosted CONCUR 2015, QEST 2015, and FORMATS 2015, among other scientific events. PreviouseditionsoftheHSBWorkshopswereheldinNewcastleuponTyne(UK,with CONCUR 2012), Taormina (IT, within ECAL 2013), and Vienna (AT, within VSL 2014). ThescopeoftheHSB2015workshophasbroadenedsincetheearliereditions,and now covers the general area of dynamical models in biology. HSB 2015 retained the emphasis on hybrid approaches – by no means restricted to a narrow class of mathe- matical models – and in particular stressed the importance of taking advantage of techniques developed separately in different areas. Topics featured at the workshop included models of metabolic, signaling, and genetic regulatory networks; models of tissues; biological applications of quantitative and formal analysis techniques; para- metric and non-parametric system identification techniques; efficient techniques for combinedandheterogeneoussimulationsofbiologicalmodels;modelinglanguagesfor biological systems; models coping with incomplete and uncertain biological informa- tion; stochastic and hybrid models in biology; hierarchical approaches for multi-scale, multi-domainanalysis;abstraction,approximation,discretization,andmodelreduction techniques;controlarchitecturesinbiologicalsystems;andmodelingandsynthesisfor synthetic biology. HSB2015wasapackedtwo-dayevent,featuringinvitedtalks,single-trackregular podium sessions, andaninteractive sessionwith postersand software tooldemos.We hostedabout40registeredparticipants,plustwoinvitedspeakers,andaconstantinflow of attendees from other co-located events at Madrid Meet 2015. The 30-minute con- tributed talks were of high quality and the participation lively, interactive, and stimulating. Inall,46ProgramCommittee(PC)membershelpedtoprovideatleastfourreviews (with in some cases up to six) of the submitted contributions, out of which 13 high-qualityarticleswereacceptedtobepresentedduringthesingle-tracksessions,and appear (possibly after further feedback from a shepherding process by the PC mem- bers) as full papers in these proceedings. The articles were bundled in four thematic sessions,whichisreflectedintheorganizationoftheseproceedings:statisticalanalysis; analysis and verification of continuous and hybrid models; quantitative analysis of biological models; and application of advanced models on case studies. In the after- noon of the first day we also hosted a poster/demo session, with 11 presentations, of which five with interactive tool demonstrations. A highlight of HSB 2015 was the presence of two high-profile invited speakers, whom we selected also in view of the breadth of the event: computer sciences and VI Preface control and dynamical systems; theoretical work and laboratory experiments. Luca Cardelli, principal researcher at Microsoft Research Cambridge (UK) and Royal Society research professor at the Department of Computer Science, University of Oxford (UK), gave a seminar titled “Morphisms of Reaction Networks.” Mustafa Khammash, professor of Control Theory and Systems Biology at the Department of Biosystems Science and Engineering at ETH Zürich (CH), gave a talk titled “Cyber- genetics: Synthetic Circuits and Systems for the Precise Control of Living Cells.” Further details on HSB 2015 are featured on the website: http://hsb2015.fi.muni.cz Finally,afewwordsofacknowledgmentaredue.ThankstoDaviddeFrutosEscrig andtoFernandoRosaVelardo(UCM,Spain)forthesupportiveandcan-doattitude,as well as the local seamless organization of the Madrid Meet 2015. Thanks to Springer forhostingtheHSBproceedingsinitsLectureNotesinBioinformatics,asub-seriesof LectureNotesinComputerScience.ThankstoLucaBortolussiandEzioBartoccifrom theSteeringCommitteeofHSBforsupportandencouragement,toallthePCmembers and additional reviewers for their work in ensuring the quality of the contributions to HSB 2015, and to all the participants for contributing to this memorable event. September 2015 Alessandro Abate David Šafránek Organization Program Committee Chairs Alessandro Abate University of Oxford, UK David Šafránek Masaryk University, Czech Republic Program Committee Alessandro Abate University of Oxford, UK Ezio Bartocci Vienna University of Technology, Austria Gregory Batt Inria Paris-Rocquencourt, France Sergiy Bogomolov IST Austria, Austria Luca Bortolussi University of Trieste, Italy Kevin Burrage University of Oxford, UK Luca Cardelli Microsoft Research, Cambridge, UK Pieter Collins Maastricht University, The Netherlands Milan Češka University of Oxford, UK Neil Dalchau Microsoft Research, Cambridge, UK Thao Dang VERIMAG/CNRS, Grenoble, France Hidde De Jong Inria Grenoble - Rhône-Alpes, France Alexandre Donzé University of California, Berkeley, USA François Fages Inria Rocquencourt, France Eric Fanchon TIMC-IMAG Laboratory, Grenoble, France Giancarlo Ferrari-Trecate University of Pavia, Italy Elisa Franco University of California at Riverside/Caltech, USA Sicun Gao MIT CSAIL, USA Radu Grosu Vienna University of Technology, Austria Joao Hespanha University of California, Santa Barbara, USA Jane Hillston University of Edinburgh, UK Agung Julius Rensselaer Polytechnic Institute, USA Heinz Koeppl Technical University Darmstadt, Germany Hillel Kugler Microsoft Research, Cambridge, UK Marta Kwiatkowska University of Oxford, UK Pietro Liò University of Cambridge, UK Oded Maler VERIMAG/CNRS, Grenoble, France Andrzej Mizera University of Luxembourg, Luxembourg Stefan Müller Austrian Academy of Sciences, Vienna, Austria Chris Myers University of Utah, USA Nicola Paoletti University of Oxford, UK Ion Petre Åbo Akademi University, Finland VIII Organization Tatjana Petrov IST Austria, Austria Carla Piazza University of Udine, Italy Nir Piterman University of Leicester, UK Alberto Policriti University of Udine, Italy David Šafránek Masaryk University, Czech Republic Guido Sanguinetti University of Edinburgh, UK Abhyudai Singh University of Delaware, USA Kateřina Staňková Maastricht University, The Netherlands P.S. Thiagarajan National University of Singapore, Singapore Jana Tůmová Royal Institute of Technology, Sweden Aljoscha Wahl Delft University of Technology, The Netherlands Verena Wolf Saarland University, Germany Boyan Yordanov Microsoft Research, Cambridge, UK Paolo Zuliani Newcastle University, UK Additional Reviewers Adimoolam, Arvind Kyriakopoulos, Shmarov, Fedor Daca, Przemyslaw Charalampos Traynard, Pauline Islam, Md. Ariful Milios, Dimitrios Wang, Qinsi Krüger, Thilo Panchal, Charmi Woodhouse, Steven Rogojin, Vladimir Keynote Abstracts
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