Computational Methods in Systems Biology: 13th International Conference, CMSB 2015, Nantes, France, September 16-18, 2015, Proceedings PDF
Preview Computational Methods in Systems Biology: 13th International Conference, CMSB 2015, Nantes, France, September 16-18, 2015, Proceedings
Olivier Roux · Jérémie Bourdon (Eds.) 8 0 Computational Methods 3 9 I B in Systems Biology N L 13th International Conference, CMSB 2015 Nantes, France, September 16–18, 2015 Proceedings 123 Lecture Notes in Bioinformatics 9308 Subseries of Lecture Notes in Computer Science LNBI Series Editors Sorin Istrail Brown University, Providence, RI, USA Pavel Pevzner University of California, San Diego, CA, USA Michael Waterman University of Southern California, Los Angeles, CA, USA LNBI Editorial Board Alberto Apostolico Georgia Institute of Technology, Atlanta, GA, USA Søren Brunak Technical University of Denmark, Kongens Lyngby, Denmark Mikhail S. Gelfand IITP, Research and Training Center on Bioinformatics, Moscow, Russia Thomas Lengauer Max Planck Institute for Informatics, Saarbrücken, Germany Satoru Miyano University of Tokyo, Tokyo, Japan Eugene Myers Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany Marie-France Sagot Université Lyon 1, Villeurbanne, France David Sankoff University of Ottawa, Ottawa, Canada Ron Shamir Tel Aviv University, Ramat Aviv, Tel Aviv, Israel Terry Speed WalterandElizaHallInstituteofMedicalResearch,Melbourne,VIC,Australia Martin Vingron Max Planck Institute for Molecular Genetics, Berlin, Germany W. Eric Wong University of Texas at Dallas, Richardson, TX, USA More information about this series at http://www.springer.com/series/5381 é é Olivier Roux J r mie Bourdon (Eds.) (cid:129) Computational Methods in Systems Biology 13th International Conference, CMSB 2015 – Nantes, France, September 16 18, 2015 Proceedings 123 Editors Olivier Roux Jérémie Bourdon ÉcoleCentrale deNantes UniversitédeNantes Nantes Nantes France France ISSN 0302-9743 ISSN 1611-3349 (electronic) Lecture Notesin Bioinformatics ISBN 978-3-319-23400-7 ISBN978-3-319-23401-4 (eBook) DOI 10.1007/978-3-319-23401-4 LibraryofCongressControlNumber:2015947797 LNCSSublibrary:SL8 – Bioinformatics SpringerChamHeidelbergNewYorkDordrechtLondon ©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 SpringerInternationalPublishingAGSwitzerlandispartofSpringerScience+BusinessMedia (www.springer.com) Preface This volume contains the articles presented at CMSB 2015. The 13th International Conference on Computational Methods in Systems Biology (CMSB) was held during September 16–18, 2015, at La Cité - Nantes Event Center in Nantes, France. The CMSB annual conference series, created in 2003, provides a unique forum of discussion for computer scientists, biologists, mathematicians, engineers, and physi- cists interested in a system-level understanding of biological processes. Topicsofinterestincludeformalismsformodelingbiologicalprocesses;modelsand their biological applications; frameworks for model verification, validation, analysis, andsimulationofbiologicalsystems;high-performancecomputationalsystemsbiology and parallel implementations; model inference from experimental data; model inte- gration from biological databases; multi-scale modeling and analysis methods; and computationalapproachesforsyntheticbiology.Casestudiesinsystemsandsynthetic biology were especially encouraged. The 2015 conference was an opportunity to hear about research on the analysis of biological systems, networks, and data ranging from intercellular to multi-scale. This year, keyword lists often contain such words as: model checking, stochastic analysis, hybrid systems, circadian clock, time series data, logic programming, constraints solving. . . emphazing the wide spectrum of interests of the CMSB community. The2015editionofCMSBreceived48regularsubmissions.Amongstthem,5were withdrawn by the authors for various reasons, so 43 complete submissions were reviewed by the Program Committee, each submission being reviewed by 3 Program Committee members. In the end, 20 articles were selected for presentation at the conference and publication in the proceedings (acceptance rate: 46 %). This volume contains in addition the abstracts of four invited speakers: Marta Kwiatkowska,DavidHarel,GillesBernot,andDavidFell.Moreover,thereare2short papers selected out of 4 submitted, and several posters were presented at the conference. As program co-chairs,we havemany people tothank. Wewould first liketothank theProgramCommitteemembersandtheexternalreviewersfortheirpeerreviewsand thevaluablefeedbacktheyprovidedtotheauthors.OurspecialthanksgoestoFrançois Fages and Pedro Mendes for their useful advice on matters related to the organization of the conference. We acknowledge the support of the EasyChair conference system during the reviewing process and the production of these proceedings (http://www. easychair.org). We also thank Kaushik Chowdhury and the IEEE Computer Society Technical Committee on Simulation for supporting the best student paper award. Our gratitudegoestoallmembersoftheOrganizingCommitteefortheirhelp,support,and spiritedparticipationbefore,during,andaftertheconference.Itisourpleasantdutyto VI Preface acknowledge the financial support from our sponsors. Finally, we would like to thank alltheparticipantsoftheconference.Itwasthequalityoftheirpresentationsandtheir contributions to the discussions that made the meeting a scientific success. July 2015 Olivier Roux Jérémie Bourdon Organization Program Committee Tatsuya Akutsu Kyoto University, Japan Julio Banga IIM-CSIC, Spain Gregory Batt INRIA Paris-Rocquencourt, France Gilles Bernot University of Nice Sophia Antipolis, France AlexanderBockmayr Freie Universität Berlin, Germany Jérémie Bourdon LINA, France Luca Cardelli Microsoft Research, UK Hidde De Jong Inria, France Diego Di Bernardo Telethon Institute of Genetics and Medicine, Italy Finn Drablos NTNU, Norway François Fages Inria Paris-Rocquencourt, France David Fell Oxford Brookes University, UK Radu Grosu Stony Brook University, USA Calin Guet IST, Austria Ashutosh Gupta TIFR, India Monika Heiner Brandenburg University at Cottbus, Germany Heinz Koeppl TU Darmstadt, Germany Marta Kwiatkowska University of Oxford, UK Pietro Lio’ University of Cambridge, UK Wolfgang Marwan Otto-von-Guericke-Universität Magdeburg, Germany Hiroshi Matsuno Yamaguchi University, Japan Tommaso Mazza IRCCS Casa Sollievo della Sofferenza - Mendel, Italy Pedro Mendes The University of Manchester, UK and University of Connecticut Health Center, USA Stéphane Minvielle CRCNA (UMR 892 INSERM/6299 CNRS), France Satoru Miyano University of Tokyo, Japan Zoran Nikoloski Max-PlanckInstituteofMolecularPlantPhysiology,Germany Loïc Paulevé CNRS/LRI, France Alberto Policriti University of Udine, Italy Ovidiu Radulescu University of Montpellier 2, France Olivier Roux IRCCyN (UMR 6597 Ecole Centrale de Nantes, CNRS), France Heike Siebert Freie Universität Berlin, Germany Anne Siegel IRISA – CNRS, France Evangelos Luxembourg Centre for Systems Biomedicine, Luxembourg Simeonidis Joerg Stelling ETH Zurich, Switzerland VIII Organization Carolyn Talcott SRI International, USA P.S. Thiagarajan National University of Singapore, Singapore Denis Thieffry IBEns (UMR CNRS 8197 - INSERM 1024), France Adelinde Uhrmacher Universität Rostock, Germany Jose Vilar Biophysics Unit (CSIC-UPV/EHU), Spain Verena Wolf Saarland University, Germany Steering Committee Finn Drablos NTNU, Norway François Fages Inria Paris-Rocquencourt, France David Harel Weizmann Institute of Science, Israel Monika Heiner Brandenburg University at Cottbus, Germany Thomas Henzinger IST Austria (Institute of Science and Technology Austria) Tommaso Mazza IRCCS Casa Sollievo della Sofferenza - Mendel, Italy Pedro Mendes The University of Manchester, UK and University of Connecticut Health Center, USA Satoru Miyano University of Tokyo, Japan Gordon Plotkin University of Edinburgh, UK Corrado Priami University of Trento, Italy Carolyn Talcott SRI International, USA Adelinde Uhrmacher Universität Rostock, Germany Organizing Committee Michèle-Anne Audrain, IRCCyN Elodie Guidon, LINA Audrey Bihouée, BIRD Carito Guziolowski, IRCCyN Jérémie Bourdon, LINA Abdelhalim Larhlimi, LINA Virginie Dupont, IRCCyN Morgan Magnin, IRCCyN Damien Eveillard, LINA Olivier Roux, IRCCyN Julien Gras, LINA & BIRD Additional Reviewers Akshay, S. Gyori, Benjamin Basset, Nicolas Helms, Tobias Bing, Liu Klarner, Hannes Ceska, Milan Koch, Ina Cinquemani, Eugenio Köksal, Ali Sinan Donzé, Alexandre Llamosi, Artemis Fauré, Adrien Lukina, Anna Gonzalez, Aitor Monteiro, Pedro T. Organization IX Naldi, Aurélien Rodionova, Alena Napolitano, Francesco Rohr, Christian Ono, Hiromasa Sandmann, Werner Pagliarini, Roberto Stoll, Gautier Paoletti, Nicola Streck, Adam Parvu, Ovidiu Tamura, Takeyuki Peng, Danhua Traynard, Pauline Petrov, Tatjana Videla, Santiago Remy, Elisabeth
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