307 research outputs found
Testing data types implementations from algebraic specifications
Algebraic specifications of data types provide a natural basis for testing
data types implementations. In this framework, the conformance relation is
based on the satisfaction of axioms. This makes it possible to formally state
the fundamental concepts of testing: exhaustive test set, testability
hypotheses, oracle. Various criteria for selecting finite test sets have been
proposed. They depend on the form of the axioms, and on the possibilities of
observation of the implementation under test. This last point is related to the
well-known oracle problem. As the main interest of algebraic specifications is
data type abstraction, testing a concrete implementation raises the issue of
the gap between the abstract description and the concrete representation. The
observational semantics of algebraic specifications bring solutions on the
basis of the so-called observable contexts. After a description of testing
methods based on algebraic specifications, the chapter gives a brief
presentation of some tools and case studies, and presents some applications to
other formal methods involving datatypes
Spin canting in a Dy-based Single-Chain Magnet with dominant next-nearest neighbor antiferromagnetic interactions
We investigate theoretically and experimentally the static magnetic
properties of single crystals of the molecular-based Single-Chain Magnet (SCM)
of formula [Dy(hfac)NIT(CHOPh)] comprising
alternating Dy and organic radicals. A peculiar inversion between maxima
and minima in the angular dependence of the magnetic molar susceptibility
occurs on increasing temperature. Using information regarding the
monomeric building block as well as an {\it ab initio} estimation of the
magnetic anisotropy of the Dy ion, this anisotropy-inversion phenomenon
can be assigned to weak one-dimensional ferromagnetism along the chain axis.
This indicates that antiferromagnetic next-nearest-neighbor interactions
between Dy ions dominate, despite the large Dy-Dy separation, over the
nearest-neighbor interactions between the radicals and the Dy ions.
Measurements of the field dependence of the magnetization, both along and
perpendicularly to the chain, and of the angular dependence of in a
strong magnetic field confirm such an interpretation. Transfer matrix
simulations of the experimental measurements are performed using a classical
one-dimensional spin model with antiferromagnetic Heisenberg exchange
interaction and non-collinear uniaxial single-ion anisotropies favoring a
canted antiferromagnetic spin arrangement, with a net magnetic moment along the
chain axis. The fine agreement obtained with experimental data provides
estimates of the Hamiltonian parameters, essential for further study of the
dynamics of rare-earths based molecular chains.Comment: 11 pages, 8 figure
Delays in Biological Regulatory Networks
International audienceIn this article, we propose a refinement of the modeling of genetic regulatory networks based on the approach of René Thomas. The notion of delays of activation/inhibition are added in order to specify which variable is faster affected by a change of its regulators. The formalism of linear hybrid automata is well suited to allow such refinement. We then use HyTech for two purposes: (1) to find automatically all paths from a specified initial state to another one and (2) to synthesize co nstraints on the delay parameters in order to follow any specific path
Synchronous versus asynchronous modeling of gene regulatory networks
Motivation: In silico modeling of gene regulatory networks has gained some momentum recently due to increased interest in analyzing the dynamics of biological systems. This has been further facilitated by the increasing availability of experimental data on geneâgene, proteinâprotein and geneâprotein interactions. The two dynamical properties that are often experimentally testable are perturbations and stable steady states. Although a lot of work has been done on the identification of steady states, not much work has been reported on in silico modeling of cellular differentiation processes
A general computational method for robustness analysis with applications to synthetic gene networks
Motivation: Robustness is the capacity of a system to maintain a function in the face of perturbations. It is essential for the correct functioning of natural and engineered biological systems. Robustness is generally defined in an ad hoc, problem-dependent manner, thus hampering the fruitful development of a theory of biological robustness, recently advocated by Kitano
JWalk: a tool for lazy, systematic testing of java classes by design introspection and user interaction
Popular software testing tools, such as JUnit, allow frequent retesting of modified code; yet the manually created test scripts are often seriously incomplete. A unit-testing tool called JWalk has therefore been developed to address the need for systematic unit testing within the context of agile methods. The tool operates directly on the compiled code for Java classes and uses a new lazy method for inducing the changing design of a class on the fly. This is achieved partly through introspection, using Javaâs reflection capability, and partly through interaction with the user, constructing and saving test oracles on the fly. Predictive rules reduce the number of oracle values that must be confirmed by the tester. Without human intervention, JWalk performs bounded exhaustive exploration of the classâs method protocols and may be directed to explore the space of algebraic constructions, or the intended design state-space of the tested class. With some human interaction, JWalk performs up to the equivalent of fully automated state-based testing, from a specification that was acquired incrementally
Modeling stochasticity and robustness in gene regulatory networks
Motivation: Understanding gene regulation in biological processes and modeling the robustness of underlying regulatory networks is an important problem that is currently being addressed by computational systems biologists. Lately, there has been a renewed interest in Boolean modeling techniques for gene regulatory networks (GRNs). However, due to their deterministic nature, it is often difficult to identify whether these modeling approaches are robust to the addition of stochastic noise that is widespread in gene regulatory processes. Stochasticity in Boolean models of GRNs has been addressed relatively sparingly in the past, mainly by flipping the expression of genes between different expression levels with a predefined probability. This stochasticity in nodes (SIN) model leads to over representation of noise in GRNs and hence non-correspondence with biological observations
On the complexity of acyclic modules in automata networks
Modules were introduced as an extension of Boolean automata networks. They
have inputs which are used in the computation said modules perform, and can be
used to wire modules with each other. In the present paper we extend this new
formalism and study the specific case of acyclic modules. These modules prove
to be well described in their limit behavior by functions called output
functions. We provide other results that offer an upper bound on the number of
attractors in an acyclic module when wired recursively into an automata
network, alongside a diversity of complexity results around the difficulty of
deciding the existence of cycles depending on the number of inputs and the size
of said cycle.Comment: 21 page
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