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Towards Quantitative Verification of Reaction Systems [chapter]

Artur Męski, Maciej Koutny, Wojciech Penczek
2016 Lecture Notes in Computer Science  
This paper introduces reaction systems with discrete concentrations which are an extension of reaction systems allowing for quantitative modelling.  ...  We then define the problem of reachability for reaction systems with discrete concentrations, and provide its suitable encoding in smt, together with a verification method (bounded model checking) for  ...  Acknowledgements The study is cofounded by the European Union from resources of the European Social Fund.  ... 
doi:10.1007/978-3-319-41312-9_12 fatcat:gnpoewg5tnh53n7fakghinzpkq

Self-adaptive software needs quantitative verification at runtime

Radu Calinescu, Carlo Ghezzi, Marta Kwiatkowska, Raffaela Mirandola
2012 Communications of the ACM  
Quantitative Verification at Runtime Quantitative verification is a math-ematically based technique for analyzing the correctness, performance, and reliability of systems exhibiting stochastic behavior  ...  In contrast, runtime use of quantitative verification also supports fine-grain adaptation of system parameters (such as by continually adjusting the amount of CPU allocated to the services of a software  ... 
doi:10.1145/2330667.2330686 fatcat:s75xkr5oejcr5cch27mezzm5my

Advances and challenges of quantitative verification and synthesis for cyber-physical systems

Marta Kwiatkowska
2016 2016 Science of Security for Cyber-Physical Systems Workshop (SOSCYPS)  
This paper gives an overview of quantitative verification and synthesis techniques developed for cyber-physical systems, summarising recent achievements and future challenges in this important field.  ...  We are witnessing a huge growth of cyber-physical systems, which are autonomous, mobile, endowed with sensing, controlled by software, and often wirelessly connected and Internet-enabled.  ...  CHALLENGES Clearly, there has been much progress towards quantitative verification and aspects of quantitative synthesis for CPS, with a wide variety of relevant case studies serving as proof of concept  ... 
doi:10.1109/soscyps.2016.7579999 dblp:conf/cpsweek/Kwiatkowska16 fatcat:ugbkizf4xrcgzjvgtutecnepuu

Query-based verification of qualitative trends and oscillations in biochemical systems

Paolo Ballarini, Maria Luisa Guerriero
2010 Theoretical Computer Science  
Qualitative/quantitative analysis of biochemical systems a b s t r a c t We investigate the application of query-based verification to the analysis of behavioural trends of stochastic models of biochemical  ...  We introduce a specific modelling convention through which stochastic models of biochemical systems are made suitable to verification of the behavioural queries we define.  ...  The Centre for Systems Biology at Edinburgh is a Centre for Integrative Systems Biology (CISB) funded by the BBSRC and EPSRC in 2006.  ... 
doi:10.1016/j.tcs.2010.02.010 fatcat:5erppsuuanaz5bwy5qywep3zma

From software verification to 'everyware' verification

Marta Kwiatkowska
2013 Computer Science - Research and Development  
The research involves investigating the fundamentals of quantitative verification, development of algorithms and prototype implementations, and experimenting with case studies.  ...  In this paper we describe the objectives and initial progress of the research aimed at extending the capabilities of quantitative, probabilistic verification to challenging ubiquitous computing scenarios  ...  ' verification through a shift towards employing the following: • Agent-based frameworks.  ... 
doi:10.1007/s00450-013-0249-1 fatcat:yijv5tfqwjb5rlopsnmy6gpsf4

Multi-Level Security for Internet Banking Services

Sowjanya V.L., Mrs. K. Santosh Jhansi
2017 IJARCCE  
This paper proposing an alternate method by applying authentication via multi-level user verification by applying biometrics an application in the service of sessions. 627 CASHMA authentication server  ...  In case of successful user verification, the CASHMA authentication server releases an authentication certificate to the client, proving its identity to third parties, and includes a timeout that sets the  ...  This paper explores multi-level user verification in order to provide more security for internet banking services.  ... 
doi:10.17148/ijarcce.2017.65120 fatcat:zoanhr77ibb3jgpoz3oygtptte

Quantitative evaluation in embedded system design

Joost-Pieter Katoen
2008 Proceedings of the conference on Design, automation and test in Europe - DATE '08  
The evaluation of extra-functional properties of embedded systems, such as reliability, timeliness, and energy consumption, as well as dealing with uncertainty, e.g., in the timing of events, is getting  ...  We survey some main developments and trends in the modeling, and the analysis of these aspects and stress the importance of approaches that tackle both extrafunctional, as well as correctness aspects.  ...  Reactions to the stimuli provided by the environment should be prompt (responsiveness), i.e., the system has to "keep up" with the speed of the processes with which it interacts.  ... 
doi:10.1145/1403375.1403398 fatcat:ts74r2e2hneqjbruqoldevkv6a

UP Finder: A COBRA toolbox extension for identifying gene overexpression strategies for targeted overproduction

Xi Wang, Liang Yu, Shulin Chen
2017 Metabolic Engineering Communications  
The outputs are also quantitatively ranked to show the preference for determining overexpression strategies in pathway design.  ...  All the key gene/pathway targets are identified in one click after simply loading a Systems Biology Markup Language model and specifying a metabolite as the targeted product.  ...  Acknowledgement The authors thank Lengge Se (University of New Mexico, NM) to assist in the UP Finder code making.  ... 
doi:10.1016/j.meteno.2017.08.001 pmid:29188184 pmcid:PMC5699525 fatcat:p4vbvi7lfvgxxlmizyvkcabs6a

A Simulation Model For The Whole Life Cycle Of The Slime Mold Dictyostelium Discoideum

Matthias Becker
2010 ECMS 2010 Proceedings edited by A Bargiela S A Ali D Crowley E J H Kerckhoffs  
Slime molds are fascinating organisms, they can either live as an organism consisting out of a single cell or they can form a multi-cellular organism.  ...  Therefore from the biological point of view, the slime molds are studied in order to understand the evolutionary step from a single cell organism to a multi-cellular organism. Studies have  ...  Quantitative Verification After comparing the real and simulated behavior mainly by sight, we now do detailed measurements of the timing of the development of Dictyostelium discoideum.  ... 
doi:10.7148/2010-0247-0252 dblp:conf/ecms/Becker10 fatcat:brfd2qj7org3liepr2q2ajtygu

Page 69 of Journal of Chemical Education Vol. 30, Issue 2 [page]

1953 Journal of Chemical Education  
A comparison of the distribution curves obtained from several different temperatures (amplitudes of vibration) points toward a verification of the Arrhenius equation for the energy of activation.  ...  Since it was not possible to quantitatively observe the temper- ature (amplitude of vibration), except to note the most probable velocity which was based upon arbitrary units, the verification of the Arrhenius  ... 

Metabolic network analysis integrated with transcript verification for sequenced genomes

Ani Manichaikul, Lila Ghamsari, Erik F Y Hom, Chenwei Lin, Ryan R Murray, Roger L Chang, S Balaji, Tong Hao, Yun Shen, Arvind K Chavali, Ines Thiele, Xinping Yang (+6 others)
2009 Nature Methods  
Using Chlamydomonas reinhardtii as a model, we describe a systems-level methodology bridging metabolic network reconstruction with experimental verification of enzyme encoding open reading frames.  ...  Our quantitative and predictive metabolic model and its associated cloned open reading frames provide useful resources for metabolic engineering.  ...  Finally, we may look beyond metabolic network modeling toward reconstruction of regulatory 13 and signaling 14 networks as alternative systems-level frameworks to guide future efforts.  ... 
doi:10.1038/nmeth.1348 pmid:19597503 pmcid:PMC3139173 fatcat:myvp7ezpifhtjcmhezcryrglsi

A Safety Analysis Approach to Clinical Workflows: Application and Evaluation

Lamis Al-Qora'n, Neil Gordon, Martin Walker, Septavera Sharvia, Sohag Kabir
2014 International Journal of Advanced Computer Science and Applications  
The outcomes of using this approach include identification of the root causes of hazardous workflow failures that may put patients' lives at risk.  ...  harmful failures of the system's output.  ...  backwards from the top level of the system towards the basic component level.  ... 
doi:10.14569/specialissue.2014.040310 fatcat:vhjw6ddiybhhljnwbqngwpwi4a

Towards modular verification of pathways: fairness and assumptions

Peter Drábik, Andrea Maggiolo-Schettini, Paolo Milazzo
2012 Electronic Proceedings in Theoretical Computer Science  
We view biochemical pathways as concurrent systems of reactions competing for molecular resources.  ...  Modular verification is a technique used to face the state explosion problem often encountered in the verification of properties of complex systems such as concurrent interactive systems.  ...  We motivate it by considering a quantitative system consisting of four reactions A 3 and k 4 are the reaction rates.  ... 
doi:10.4204/eptcs.100.5 fatcat:u4o3hvznkve5vjtbomszwmknlu

Taming the complexity of biological pathways through parallel computing

P. Ballarini, R. Guido, T. Mazza, D. Prandi
2008 Briefings in Bioinformatics  
Biological systems are characterised by a large number of interacting entities whose dynamics is described by a number of reaction equations.  ...  His research interests are in formal techniques for systems' verification/ specification, probabilistic model-checking, stochastic Petri nets and temporal logic reasoning.  ...  of model-checking verification to systems biology.  ... 
doi:10.1093/bib/bbp020 pmid:19339382 fatcat:5yzyzsjbjvd2hb5rxufpg6hube

Quantitative reactive modeling and verification

Thomas A. Henzinger
2013 Computer Science - Research and Development  
The theory will be evaluated not only in the context of software and hardware engineering, but also in the context of systems biology.  ...  Formal verification aims to improve the quality of software by detecting errors before they do harm.  ...  Above all, the author thanks his many wonderful collaborators on the topic of this project.  ... 
doi:10.1007/s00450-013-0251-7 pmid:27069511 pmcid:PMC4811300 fatcat:cimfqu272beijj6dgqpvsz7koy
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