Capybara: equivalence ClAss enumeration of coPhylogenY event-BAsed ReconciliAtions

International audienceMotivation: Phylogenetic tree reconciliation is the method of choice in analysing host-symbiont systems. Despite the many reconciliation tools that have been proposed in the literature, two main issues remain unresolved: (i) listing suboptimal solutions (i.e. whose score is "close" to the optimal ones) and (ii) listing only solutions that are biologically different "enough". The first issue arises because the optimal solutions are not always the ones biologically most significant; providing many suboptimal solutions as alternatives for the optimal ones is thus very useful. The second one is related to the difficulty to analyse an often huge number of optimal solutions. In this paper, we propose Capybara that addresses both of these problems in an efficient way. Furthermore, it includes a tool for visualising the solutions that significantly helps the user in the process of analysing the results. Availability and implementation: The source code, documentation, and binaries for all platforms ar

Stream Differential Equations: Specification Formats and Solution Methods

Streams, or innite sequences, are innite objects of a very simple type, yet they have a rich theory partly due to their ubiquity in mathematics and computer science. Stream dierential equations are a coinductive method for specifying streams and stream operations, and their theory has been developed in many papers over the past two decades. In this paper we present a survey of the many results in this area. Our focus is on the classication of dierent formats of stream dierential equations, their solution methods, and the classes of streams they can dene. Moreover, we describe in detail the connection between the so-called syntactic solution method and abstract GSOS

Stream differential equations: Specification formats and solution methods

Streams, or infinite sequences, are infinite objects of a very simple type, yet they have a rich theory partly due to their ubiquity in mathematics and computer science. Stream differential equations are a coinductive method for specifying streams and stream operations, and their theory has been developed in many papers over the past two decades. In this paper we present a survey of the many results in this area. Our focus is on the classification of different formats of stream differential equations, their solution methods, and the classes of streams they can define. Moreover, we describe in detail the connection between the so-called syntactic solution method and abstract GSOS

Proceedings of the First NASA Formal Methods Symposium

Topics covered include: Model Checking - My 27-Year Quest to Overcome the State Explosion Problem; Applying Formal Methods to NASA Projects: Transition from Research to Practice; TLA+: Whence, Wherefore, and Whither; Formal Methods Applications in Air Transportation; Theorem Proving in Intel Hardware Design; Building a Formal Model of a Human-Interactive System: Insights into the Integration of Formal Methods and Human Factors Engineering; Model Checking for Autonomic Systems Specified with ASSL; A Game-Theoretic Approach to Branching Time Abstract-Check-Refine Process; Software Model Checking Without Source Code; Generalized Abstract Symbolic Summaries; A Comparative Study of Randomized Constraint Solvers for Random-Symbolic Testing; Component-Oriented Behavior Extraction for Autonomic System Design; Automated Verification of Design Patterns with LePUS3; A Module Language for Typing by Contracts; From Goal-Oriented Requirements to Event-B Specifications; Introduction of Virtualization Technology to Multi-Process Model Checking; Comparing Techniques for Certified Static Analysis; Towards a Framework for Generating Tests to Satisfy Complex Code Coverage in Java Pathfinder; jFuzz: A Concolic Whitebox Fuzzer for Java; Machine-Checkable Timed CSP; Stochastic Formal Correctness of Numerical Algorithms; Deductive Verification of Cryptographic Software; Coloured Petri Net Refinement Specification and Correctness Proof with Coq; Modeling Guidelines for Code Generation in the Railway Signaling Context; Tactical Synthesis Of Efficient Global Search Algorithms; Towards Co-Engineering Communicating Autonomous Cyber-Physical Systems; and Formal Methods for Automated Diagnosis of Autosub 6000

Programming Languages and Systems

This open access book constitutes the proceedings of the 31st European Symposium on Programming, ESOP 2022, which was held during April 5-7, 2022, in Munich, Germany, as part of the European Joint Conferences on Theory and Practice of Software, ETAPS 2022. The 21 regular papers presented in this volume were carefully reviewed and selected from 64 submissions. They deal with fundamental issues in the specification, design, analysis, and implementation of programming languages and systems

Tools and Algorithms for the Construction and Analysis of Systems

This open access two-volume set constitutes the proceedings of the 26th International Conference on Tools and Algorithms for the Construction and Analysis of Systems, TACAS 2020, which took place in Dublin, Ireland, in April 2020, and was held as Part of the European Joint Conferences on Theory and Practice of Software, ETAPS 2020. The total of 60 regular papers presented in these volumes was carefully reviewed and selected from 155 submissions. The papers are organized in topical sections as follows: Part I: Program verification; SAT and SMT; Timed and Dynamical Systems; Verifying Concurrent Systems; Probabilistic Systems; Model Checking and Reachability; and Timed and Probabilistic Systems. Part II: Bisimulation; Verification and Efficiency; Logic and Proof; Tools and Case Studies; Games and Automata; and SV-COMP 2020