On Non-Parallelizable Deterministic Client Puzzle Scheme with Batch Verification Modes

A (computational) client puzzle scheme enables a client to prove to a server that a certain amount of computing resources (CPU cycles and/or Memory look-ups) has been dedicated to solve a puzzle. Researchers have identified a number of potential applications, such as constructing timed cryptography, fighting junk emails, and protecting critical infrastructure from DoS attacks. In this paper, we first revisit this concept and formally define two properties, namely deterministic computation and parallel computation resistance. Our analysis show that both properties are crucial for the effectiveness of client puzzle schemes in most application scenarios. We prove that the RSW client puzzle scheme, which is based on the repeated squaring technique, achieves both properties. Secondly, we introduce two batch verification modes for the RSW client puzzle scheme in order to improve the verification efficiency of the server, and investigate three methods for handling errors in batch verifications. Lastly, we show that client puzzle schemes can be integrated with reputation systems to further improve the effectiveness in practice

Testing timed systems modeled by stream X-machines

Stream X-machines have been used to specify real systems where complex data structures. They are a variety of extended finite state machine where a shared memory is used to represent communications between the components of systems. In this paper we introduce an extension of the Stream X-machines formalism in order to specify systems that present temporal requirements. We add time in two different ways. First, we consider that (output) actions take time to be performed. Second, our formalism allows to specify timeouts. Timeouts represent the time a system can wait for the environment to react without changing its internal state. Since timeous affect the set of available actions of the system, a relation focusing on the functional behavior of systems, that is, the actions that they can perform, must explicitly take into account the possible timeouts. In this paper we also propose a formal testing methodology allowing to systematically test a system with respect to a specification. Finally, we introduce a test derivation algorithm. Given a specification, the derived test suite is sound and complete, that is, a system under test successfully passes the test suite if and only if this system conforms to the specification

Optimizing Splicing Junction Detection in Next Generation Sequencing Data on a Virtual-GRID Infrastructure

The new protocol for sequencing the messenger RNA in a cell, named RNA-seq produce millions of short sequence fragments. Next Generation Sequencing technology allows more accurate analysis but increase needs in term of computational resources. This paper describes the optimization of a RNA-seq analysis pipeline devoted to splicing variants detection, aimed at reducing computation time and providing a multi-user/multisample environment. This work brings two main contributions. First, we optimized a well-known algorithm called TopHat by parallelizing some sequential mapping steps. Second, we designed and implemented a hybrid virtual GRID infrastructure allowing to efficiently execute multiple instances of TopHat running on different samples or on behalf of different users, thus optimizing the overall execution time and enabling a flexible multi-user environmen

A Modular Formalization of Reversibility for Concurrent Models and Languages

Causal-consistent reversibility is the reference notion of reversibility for concurrency. We introduce a modular framework for defining causal-consistent reversible extensions of concurrent models and languages. We show how our framework can be used to define reversible extensions of formalisms as different as CCS and concurrent X-machines. The generality of the approach allows for the reuse of theories and techniques in different settings.Comment: In Proceedings ICE 2016, arXiv:1608.0313

Trace checking of Metric Temporal Logic with Aggregating Modalities using MapReduce

Modern complex software systems produce a large amount of execution data, often stored in logs. These logs can be analyzed using trace checking techniques to check whether the system complies with its requirements specifications. Often these specifications express quantitative properties of the system, which include timing constraints as well as higher-level constraints on the occurrences of significant events, expressed using aggregate operators. In this paper we present an algorithm that exploits the MapReduce programming model to check specifications expressed in a metric temporal logic with aggregating modalities, over large execution traces. The algorithm exploits the structure of the formula to parallelize the evaluation, with a significant gain in time. We report on the assessment of the implementation - based on the Hadoop framework - of the proposed algorithm and comment on its scalability.Comment: 16 pages, 6 figures, Extended version of the SEFM 2014 pape

Virtual Environment for Next Generation Sequencing Analysis

Next Generation Sequencing technology, on the one hand, allows a more accurate analysis, and, on the other hand, increases the amount of data to process. A new protocol for sequencing the messenger RNA in a cell, known as RNA- Seq, generates millions of short sequence fragments in a single run. These fragments, or reads, can be used to measure levels of gene expression and to identify novel splice variants of genes. The proposed solution is a distributed architecture consisting of a Grid Environment and a Virtual Grid Environment, in order to reduce processing time by making the system scalable and flexibl