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A prototypical non-malignant epithelial model to study genome dynamics and concurrently monitor micro-RNAs and proteins in situ during oncogene-induced senescence

Eirini-Stavroula Komseli, Ioannis S. Pateras, Thorbjørn Krejsgaard, Konrad Stawiski, Sophia V. Rizou, Alexander Polyzos, Fani-Marlen Roumelioti, Maria Chiourea, Ioanna Mourkioti, Eleni Paparouna, Christos P. Zampetidis, Sentiljana Gumeni (+9 others)
2018 BMC Genomics  
in vivo models [100] .  ...  Fig. 9 9 Monitoring concurrently in situ miRs and proteins expression during OIS.  ...  A substantial fraction of miRs may also exist in the cytoplasm in an Ago-free form [141] .  ... 
doi:10.1186/s12864-017-4375-1 pmid:29321003 pmcid:PMC5763532 fatcat:kks4uvvjyrhtpcng3wefxhg7ba

IronFleet

Chris Hawblitzel, Jon Howell, Manos Kapritsos, Jacob R. Lorch, Bryan Parno, Michael L. Roberts, Srinath Setty, Brian Zill
2017 Communications of the ACM  
Verification can, in principle, eliminate these bugs, but it has historically been difficult to apply at full-program scale, much less distributed system scale.  ...  In principle, one can use model checking to reason about the correctness of both protocols 15 and implementations. 17 In practice, however, model checking is incomplete-the accuracy of the results  ...  To manage the subtle concurrency, we keep this layer simple and abstract. In more detail, we formally specify, in Dafny, a distributed system state machine.  ... 
doi:10.1145/3068608 fatcat:tnwzkuonwvahterueljh4axakm

VerifyThis 2015

Marieke Huisman, Vladimir Klebanov, Rosemary Monahan, Michael Tautschnig
2016 International Journal on Software Tools for Technology Transfer (STTT)  
It was the fourth instalment in the VerifyThis competition series.  ...  VerifyThis 2015 was a one-day program verification competition which took place on April 12th, 2015 in London, UK, as part of the European Joint Conferences on Theory and Practice of Software (ETAPS 2015  ...  distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecomm ons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in  ... 
doi:10.1007/s10009-016-0438-x fatcat:7yknibf43nhyzbood4ylzohpyy

IronFleet

Chris Hawblitzel, Jon Howell, Manos Kapritsos, Jacob R. Lorch, Bryan Parno, Michael L. Roberts, Srinath Setty, Brian Zill
2015 Proceedings of the 25th Symposium on Operating Systems Principles - SOSP '15  
Verification can, in principle, eliminate these bugs a priori, but verification has historically been difficult to apply at fullprogram scale, much less distributed-system scale.  ...  learned, we aim to raise the standard for distributed systems from "tested" to "correct." datatype SpecState = SpecState(history:seq) predicate SpecInit(ss:SpecState) { |ss.history|==1 && ss.history[0] in  ...  Acknowledgments We thank Rustan Leino for not just building Dafny but also cheerfully providing ongoing guidance and support in improving it.  ... 
doi:10.1145/2815400.2815428 dblp:conf/sosp/HawblitzelHKLPR15 fatcat:azgftawdt5ffznqstd2zt2ljoa

Formal Verification of the Ethereum 2.0 Beacon Chain [article]

Franck Cassez and Joanne Fuller and Aditya Asgaonkar
2021 arXiv   pre-print
We have formally specified and verified the absence of runtime errors in (a large and critical part of) the Beacon Chain reference implementation using the verification-friendly language Dafny.  ...  Our software artefact is available at https://github.com/ConsenSys/eth2.0-dafny.  ...  This project was supported by an Ethereum Foundation Grant, FY20-285 and we thank Danny Ryan (Ethereum Foundation) and Ben Edgington (ConsenSys) for their help in setting up this project and their support  ... 
arXiv:2110.12909v1 fatcat:76mjydklyvh2thjgmbhx3h4h3m

Komodo

Andrew Ferraiuolo, Andrew Baumann, Chris Hawblitzel, Bryan Parno
2017 Proceedings of the 26th Symposium on Operating Systems Principles - SOSP '17  
Komodo illustrates an alternative approach to attested, on-demand, user-mode, concurrent isolated execution.  ...  We show that the approach is practical and performant with a concrete implementation of a prototype in verified assembly code on ARM TrustZone.  ...  This work was supported in part by the National Science Foundation and VMware under Grant No. CNS-1700521.  ... 
doi:10.1145/3132747.3132782 dblp:conf/sosp/FerraiuoloBHP17 fatcat:wsua4s3a3nb4dcgtyfpzjtbqki

Table of Contents

2021 2021 International Symposium on Theoretical Aspects of Software Engineering (TASE)  
Dafny 95 Hongjian Jiang (vi  ...  Dynamic Verification of C11 Concurrency over Multi Copy Atomics 39 Sanjana Singh (Indian Institute of Technology Delhi), Divyanjali Sharma (Indian Institute of Technology Delhi), and Subodh Sharma (Indian  ...  Model Checking and Logics  ... 
doi:10.1109/tase52547.2021.00004 fatcat:ecupb3l34bbprgwydeg5smtgji

Code generation for Event-B

Víctor Rivera, Néstor Cataño, Tim Wahls, Camilo Rueda
2015 International Journal on Software Tools for Technology Transfer (STTT)  
Modelling relations and sets as datatypes rather than as classes has two main advantages in Dafny.  ...  in Dafny TypeOf(v ) = Type (Var) Dafny(variables v ) = var v : Type;Invariants are modelled as boolean functions with postconditions that can be assumed or asserted.  ...  Chapter 6 -Translating Event-B Machines Proof Obligations to Dafny The Variant Proof Obligation: it states that each convergent event decreases the numeric variant, and each anticipated event does not  ... 
doi:10.1007/s10009-015-0381-2 fatcat:6zktb6u6trhobl4nzqg4rnxca4

Code Generation for Event-B [article]

Victor Rivera
2016 arXiv   pre-print
Stepwise refinement and Design-by-Contract are two formal approaches for modelling systems. These approaches are widely used in the development of systems. Both approaches have (dis-)advantages.  ...  EventB2Java enables users to start the software development process in Event-B, where users can model the system and prove its consistency, to then transition to JML-annotated Java code, where users can  ...  Modelling relations and sets as datatypes rather than as classes has two main advantages in Dafny.  ... 
arXiv:1602.02004v1 fatcat:xxpeia2gpzc5rhckllafzispqm

An Empirical Study on the Correctness of Formally Verified Distributed Systems

Pedro Fonseca, Kaiyuan Zhang, Xi Wang, Arvind Krishnamurthy
2017 Proceedings of the Twelfth European Conference on Computer Systems - EuroSys '17  
Recent advances in formal verification techniques enabled the implementation of distributed systems with machinechecked proofs.  ...  In addition, we are grateful to the authors of the verified systems studied for their help in analyzing our reports and clarifying our questions.  ...  This work was supported in part by DARPA under contract FA8750-16-2-0032.  ... 
doi:10.1145/3064176.3064183 dblp:conf/eurosys/FonsecaZWK17 fatcat:oqryjfoo4zarnbregbo2gk7gzm

Observations of putative pollinators of Hemipilia flabellata Bur. et Franch. (Orchidaceae) in north-west Yunnan Province, China

Y LUO
1999 Botanical journal of the Linnean Society  
The orchid benefits from the great variation of flowers in colour and shape.  ...  Pollinating bees normally sampled only the lowermost flowers in an inflorescence, staying for 1-3 seconds.  ...  The first consists of a tripartite association of model, mimic and dupe (Little, 1983; Dafni, 1984 Dafni, , 1987 Cropper & Calder, 1990; Nilsson, 1992) .  ... 
doi:10.1006/bojl.1999.0245 fatcat:qlfqspch4bffddtx56e6a4glvi

Reproductive biology ofCyrtopodium polyphyllum(Orchidaceae): a Cyrtopodiinae pollinated by deceit

L. M. Pansarin, E. R. Pansarin, M. Sazima
2008 Plant Biology  
models, as already reported by Dafni (1987) for Thelymitra antennifera (Orchidaceae) and its models.  ...  The concurrent flowering of C. polyphyllum with its model plants, as well as the fact that it begins after and ends before their flowering, are constraints that show the dependence of the mimic on its  ... 
doi:10.1111/j.1438-8677.2008.00060.x pmid:18761503 fatcat:jzgtagp6zbf7tpmxili5cbb2ri

Collaborative Verification and Testing with Explicit Assumptions [chapter]

Maria Christakis, Peter Müller, Valentin Wüstholz
2012 Lecture Notes in Computer Science  
An extension to concurrent programs, more advanced properties (such as temporal properties), and the compromises made by model checkers (such as bounding the number of heap objects) are future work.  ...  This compromise cannot be modeled using explicit assumptions alone. For this reason, we implemented a variant of the Dafny verifier that transforms loops as shown in Fig. 3 .  ... 
doi:10.1007/978-3-642-32759-9_13 fatcat:zty4uaxa7rat7aior4prmehgum

Observations of putative pollinators of Hemipilia flabellata Bur. et Franch.(Orchidaceae) in north-west Yunnan Province, China

YI-BO LUO, SING-CHI CHEN
1999 Botanical journal of the Linnean Society  
The orchid benefits from the great variation of flowers in colour and shape.  ...  Pollinating bees normally sampled only the lowermost flowers in an inflorescence, staying for 1-3 seconds.  ...  The first consists of a tripartite association of model, mimic and dupe (Little, 1983; Dafni, 1984 Dafni, , 1987 Cropper & Calder, 1990; Nilsson, 1992) .  ... 
doi:10.1111/j.1095-8339.1999.tb01941.x fatcat:kvkwjpcwcraqtciisgkehjai64

A Parallel Relation-Based Algorithm for Symbolic Bisimulation Minimization [chapter]

Richard Huybers, Alfons Laarman
2019 Lecture Notes in Computer Science  
Symbolic computation using BDDs and bisimulation minimization are alternative ways to cope with the state space explosion in model checking.  ...  Formally, the LTS consists of the following sets: a model checker can handle. For instance, redundant states are frequently present in LTSs which model concurrent systems.  ...  The order in which multiple concurrent events happen usually does not matter for the resulting system state.  ... 
doi:10.1007/978-3-030-11245-5_25 fatcat:dfatb5g53jd3tclhpm4fyxwaay
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