Experimental Biological Protocols with Formal Semantics

Both experimental and computational biology is becoming increasingly automated. Laboratory experiments are now performed automatically on high-throughput machinery, while computational models are synthesized or inferred automatically from data. However, integration between automated tasks in the process of biological discovery is still lacking, largely due to incompatible or missing formal representations. While theories are expressed formally as computational models, existing languages for encoding and automating experimental protocols often lack formal semantics. This makes it challenging to extract novel understanding by identifying when theory and experimental evidence disagree due to errors in the models or the protocols used to validate them. To address this, we formalize the syntax of a core protocol language, which provides a unified description for the models of biochemical systems being experimented on, together with the discrete events representing the liquid-handling steps of biological protocols. We present both a deterministic and a stochastic semantics to this language, both defined in terms of hybrid processes. In particular, the stochastic semantics captures uncertainties in equipment tolerances, making it a suitable tool for both experimental and computational biologists. We illustrate how the proposed protocol language can be used for automated verification and synthesis of laboratory experiments on case studies from the fields of chemistry and molecular programming

Handling Data-Based Concurrency in Context-Aware Service Protocols

Dependency analysis is a technique to identify and determine data dependencies between service protocols. Protocols evolving concurrently in the service composition need to impose an order in their execution if there exist data dependencies. In this work, we describe a model to formalise context-aware service protocols. We also present a composition language to handle dynamically the concurrent execution of protocols. This language addresses data dependency issues among several protocols concurrently executed on the same user device, using mechanisms based on data semantic matching. Our approach aims at assisting the user in establishing priorities between these dependencies, avoiding the occurrence of deadlock situations. Nevertheless, this process is error-prone, since it requires human intervention. Therefore, we also propose verification techniques to automatically detect possible inconsistencies specified by the user while building the data dependency set. Our approach is supported by a prototype tool we have implemented.Comment: In Proceedings FOCLASA 2010, arXiv:1007.499

Model checking probabilistic and stochastic extensions of the pi-calculus

We present an implementation of model checking for probabilistic and stochastic extensions of the pi-calculus, a process algebra which supports modelling of concurrency and mobility. Formal verification techniques for such extensions have clear applications in several domains, including mobile ad-hoc network protocols, probabilistic security protocols and biological pathways. Despite this, no implementation of automated verification exists. Building upon the pi-calculus model checker MMC, we first show an automated procedure for constructing the underlying semantic model of a probabilistic or stochastic pi-calculus process. This can then be verified using existing probabilistic model checkers such as PRISM. Secondly, we demonstrate how for processes of a specific structure a more efficient, compositional approach is applicable, which uses our extension of MMC on each parallel component of the system and then translates the results into a high-level modular description for the PRISM tool. The feasibility of our techniques is demonstrated through a number of case studies from the pi-calculus literature

EXACT2: the semantics of biomedical protocols

© 2014 Soldatova et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.This article has been made available through the Brunel Open Access Publishing Fund.Background: The reliability and reproducibility of experimental procedures is a cornerstone of scientific practice. There is a pressing technological need for the better representation of biomedical protocols to enable other agents (human or machine) to better reproduce results. A framework that ensures that all information required for the replication of experimental protocols is essential to achieve reproducibility. Methods: We have developed the ontology EXACT2 (EXperimental ACTions) that is designed to capture the full semantics of biomedical protocols required for their reproducibility. To construct EXACT2 we manually inspected hundreds of published and commercial biomedical protocols from several areas of biomedicine. After establishing a clear pattern for extracting the required information we utilized text-mining tools to translate the protocols into a machine amenable format. We have verified the utility of EXACT2 through the successful processing of previously ‘unseen’ (not used for the construction of EXACT2) protocols. Results: The paper reports on a fundamentally new version EXACT2 that supports the semantically-defined representation of biomedical protocols. The ability of EXACT2 to capture the semantics of biomedical procedures was verified through a text mining use case. In this EXACT2 is used as a reference model for text mining tools to identify terms pertinent to experimental actions, and their properties, in biomedical protocols expressed in natural language. An EXACT2-based framework for the translation of biomedical protocols to a machine amenable format is proposed. Conclusions: The EXACT2 ontology is sufficient to record, in a machine processable form, the essential information about biomedical protocols. EXACT2 defines explicit semantics of experimental actions, and can be used by various computer applications. It can serve as a reference model for for the translation of biomedical protocols in natural language into a semantically-defined format.This work has been partially funded by the Brunel University BRIEF award and a grant from Occams Resources

Comparing BDD and SAT based techniques for model checking Chaum's Dining Cryptographers Protocol

We analyse different versions of the Dining Cryptographers protocol by means of automatic verification via model checking. Specifically we model the protocol in terms of a network of communicating automata and verify that the protocol meets the anonymity requirements specified. Two different model checking techniques (ordered binary decision diagrams and SAT-based bounded model checking) are evaluated and compared to verify the protocols

Partial Order Reduction for Security Protocols

Security protocols are concurrent processes that communicate using cryptography with the aim of achieving various security properties. Recent work on their formal verification has brought procedures and tools for deciding trace equivalence properties (e.g., anonymity, unlinkability, vote secrecy) for a bounded number of sessions. However, these procedures are based on a naive symbolic exploration of all traces of the considered processes which, unsurprisingly, greatly limits the scalability and practical impact of the verification tools. In this paper, we overcome this difficulty by developing partial order reduction techniques for the verification of security protocols. We provide reduced transition systems that optimally eliminate redundant traces, and which are adequate for model-checking trace equivalence properties of protocols by means of symbolic execution. We have implemented our reductions in the tool Apte, and demonstrated that it achieves the expected speedup on various protocols

Verification of the TESLA protocol in MCMAS-X

We present MCMAS-X, an extension of the OBDD-based model checker MCMAS for multi-agent systems, to explicit and deductive knowledge. We use MCMAS-X to verify authentication properties in the TESLA secure stream protocol