KInNeSS: A Modular Framework for Computational Neuroscience

Making use of very detailed neurophysiological, anatomical, and behavioral data to build biologically-realistic computational models of animal behavior is often a difficult task. Until recently, many software packages have tried to resolve this mismatched granularity with different approaches. This paper presents KInNeSS, the KDE Integrated NeuroSimulation Software environment, as an alternative solution to bridge the gap between data and model behavior. This open source neural simulation software package provides an expandable framework incorporating features such as ease of use, scalability, an XML based schema, and multiple levels of granularity within a modern object oriented programming design. KInNeSS is best suited to simulate networks of hundreds to thousands of branched multi-compartmental neurons with biophysical properties such as membrane potential, voltage-gated and ligand-gated channels, the presence of gap junctions or ionic diffusion, neuromodulation channel gating, the mechanism for habituative or depressive synapses, axonal delays, and synaptic plasticity. KInNeSS outputs include compartment membrane voltage, spikes, local-field potentials, and current source densities, as well as visualization of the behavior of a simulated agent. An explanation of the modeling philosophy and plug-in development is also presented. Further development of KInNeSS is ongoing with the ultimate goal of creating a modular framework that will help researchers across different disciplines to effectively collaborate using a modern neural simulation platform.

Parallel Programming of General-Purpose Programs Using Task-Based Programming Models

The prevalence of multicore processors is bound to drive most kinds of software development towards parallel programming. To limit the difficulty and overhead of parallel software design and maintenance, it is crucial that parallel programming models allow an easy-to-understand, concise and dense representation of parallelism. Parallel programming models such as Cilk++ and Intel TBBs attempt to offer a better, higher-level abstraction for parallel programming than threads and locking synchronization. It is not straightforward, however, to express all patterns of parallelism in these models. Pipelines are an important parallel construct, although difficult to express in Cilk and TBBs in a straightfor- ward way, not without a verbose restructuring of the code. In this paper we demonstrate that pipeline parallelism can be easily and concisely expressed in a Cilk-like language, which we extend with input, output and input/output dependency types on procedure arguments, enforced at runtime by the scheduler. We evaluate our implementation on real applications and show that our Cilk-like scheduler, extended to track and enforce these dependencies has performance comparable to Cilk++.

PLUMED 2: New feathers for an old bird

Enhancing sampling and analyzing simulations are central issues in molecular simulation. Recently, we introduced PLUMED, an open-source plug-in that provides some of the most popular molecular dynamics (MD) codes with implementations of a variety of different enhanced sampling algorithms and collective variables (CVs). The rapid changes in this field, in particular new directions in enhanced sampling and dimensionality reduction together with new hardware, require a code that is more flexible and more efficient. We therefore present PLUMED 2 here a,complete rewrite of the code in an object-oriented programming language (C++). This new version introduces greater flexibility and greater modularity, which both extends its core capabilities and makes it far easier to add new methods and CVs. It also has a simpler interface with the MD engines and provides a single software library containing both tools and core facilities. Ultimately, the new code better serves the ever-growing community of users and contributors in coping with the new challenges arising in the field.

Program summary

Program title: PLUMED 2

Catalogue identifier: AEEE_v2_0

Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEEE_v2_0.html

Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland

Licensing provisions: Yes

No. of lines in distributed program, including test data, etc.: 700646

No. of bytes in distributed program, including test data, etc.: 6618136

Distribution format: tar.gz

Programming language: ANSI-C++.

Computer: Any computer capable of running an executable produced by a C++ compiler.

Operating system: Linux operating system, Unix OSs.

Has the code been vectorized or parallelized?: Yes, parallelized using MPI.

RAM: Depends on the number of atoms, the method chosen and the collective variables used.

Classification: 3, 7.7, 23. Catalogue identifier of previous version: AEEE_v1_0.

Journal reference of previous version: Comput. Phys. Comm. 180 (2009) 1961.

External routines: GNU libmatheval, Lapack, Bias, MPI. (C) 2013 Elsevier B.V. All rights reserved.

Desenvolvimento de Frameworks de Testes Automáticos de Software

O objetivo deste trabalho é o desenvolvimento de frameworks de testes automáticos de software. Este tipo de testes normalmente está associado ao modelo evolucionário e às metodologias ágeis de desenvolvimento de software, enquanto que os testes manuais estão relacionados com o modelo em cascata e as metodologias tradicionais. Como tal foi efetuado um estudo comparativo sobre os tipos de metodologias e de testes existentes, para decidir quais os que melhor se adequavam ao projeto e dar resposta à questão "Será que realmente compensa realizar testes (automáticos)?". Finalizado o estudo foram desenvolvidas duas frameworks, a primeira para a implementação de testes funcionais e unitários sem dependências a ser utilizada pelos estagiários curriculares da LabOrders, e a segunda para a implementação de testes unitários com dependências externas de base de dados e serviços, a ser utilizada pelos funcionários da empresa. Nas últimas duas décadas as metodologias ágeis de desenvolvimento de software não pararam de evoluir, no entanto as ferramentas de automação não conseguiram acompanhar este progresso. Muitas áreas não são abrangidas pelos testes e por isso alguns têm de ser feitos manualmente. Posto isto foram criadas várias funcionalidades inovadoras para aumentar a cobertura dos testes e tornar as frameworks o mais intuitivas possível, nomeadamente: 1. Download automático de ficheiros através do Internet Explorer 9 (e versões mais recentes). 2. Análise do conteúdo de ficheiros .pdf (através dos testes). 3. Obtenção de elementos web e respetivos atributos através de código jQuery utilizando a API WebDriver com PHP bindings. 4. Exibição de mensagens de erro personalizadas quando não é possível encontrar um determinado elemento. As frameworks implementadas estão também preparadas para a criação de outros testes (de carga, integração, regressão) que possam vir a ser necessários no futuro. Foram testadas em contexto de trabalho pelos colaboradores e clientes da empresa onde foi realizado o projeto de mestrado e os resultados permitiram concluir que a adoção de uma metodologia de desenvolvimento de software com testes automáticos pode aumentar a produtividade, reduzir as falhas e potenciar o cumprimento de orçamentos e prazos dos projetos das organizações.

Timing verification in transaction modeling

Les systèmes Matériels/Logiciels deviennent indispensables dans tous les aspects de la vie quotidienne. La présence croissante de ces systèmes dans les différents produits et services incite à trouver des méthodes pour les développer efficacement. Mais une conception efficace de ces systèmes est limitée par plusieurs facteurs, certains d'entre eux sont: la complexité croissante des applications, une augmentation de la densité d'intégration, la nature hétérogène des produits et services, la diminution de temps d’accès au marché. Une modélisation transactionnelle (TLM) est considérée comme un paradigme prometteur permettant de gérer la complexité de conception et fournissant des moyens d’exploration et de validation d'alternatives de conception à des niveaux d’abstraction élevés. Cette recherche propose une méthodologie d’expression de temps dans TLM basée sur une analyse de contraintes temporelles. Nous proposons d'utiliser une combinaison de deux paradigmes de développement pour accélérer la conception: le TLM d'une part et une méthodologie d’expression de temps entre différentes transactions d’autre part. Cette synergie nous permet de combiner dans un seul environnement des méthodes de simulation performantes et des méthodes analytiques formelles. Nous avons proposé un nouvel algorithme de vérification temporelle basé sur la procédure de linéarisation des contraintes de type min/max et une technique d'optimisation afin d'améliorer l'efficacité de l'algorithme. Nous avons complété la description mathématique de tous les types de contraintes présentées dans la littérature. Nous avons développé des méthodes d'exploration et raffinement de système de communication qui nous a permis d'utiliser les algorithmes de vérification temporelle à différents niveaux TLM. Comme il existe plusieurs définitions du TLM, dans le cadre de notre recherche, nous avons défini une méthodologie de spécification et simulation pour des systèmes Matériel/Logiciel basée sur le paradigme de TLM. Dans cette méthodologie plusieurs concepts de modélisation peuvent être considérés séparément. Basée sur l'utilisation des technologies modernes de génie logiciel telles que XML, XSLT, XSD, la programmation orientée objet et plusieurs autres fournies par l’environnement .Net, la méthodologie proposée présente une approche qui rend possible une réutilisation des modèles intermédiaires afin de faire face à la contrainte de temps d’accès au marché. Elle fournit une approche générale dans la modélisation du système qui sépare les différents aspects de conception tels que des modèles de calculs utilisés pour décrire le système à des niveaux d’abstraction multiples. En conséquence, dans le modèle du système nous pouvons clairement identifier la fonctionnalité du système sans les détails reliés aux plateformes de développement et ceci mènera à améliorer la "portabilité" du modèle d'application.

Identification et localisation des préoccupations fonctionnelles dans un code légataire Java

Traditionnellement, les applications orientées objets légataires intègrent différents aspects fonctionnels. Ces aspects peuvent être dispersés partout dans le code. Il existe différents types d’aspects : • des aspects qui représentent des fonctionnalités métiers ; • des aspects qui répondent à des exigences non fonctionnelles ou à d’autres considérations de conception comme la robustesse, la distribution, la sécurité, etc. Généralement, le code qui représente ces aspects chevauche plusieurs hiérarchies de classes. Plusieurs chercheurs se sont intéressés à la problématique de la modularisation de ces aspects dans le code : programmation orientée sujets, programmation orientée aspects et programmation orientée vues. Toutes ces méthodes proposent des techniques et des outils pour concevoir des applications orientées objets sous forme de composition de fragments de code qui répondent à différents aspects. La séparation des aspects dans le code a des avantages au niveau de la réutilisation et de la maintenance. Ainsi, il est important d’identifier et de localiser ces aspects dans du code légataire orienté objets. Nous nous intéressons particulièrement aux aspects fonctionnels. En supposant que le code qui répond à un aspect fonctionnel ou fonctionnalité exhibe une certaine cohésion fonctionnelle (dépendances entre les éléments), nous proposons d’identifier de telles fonctionnalités à partir du code. L’idée est d’identifier, en l’absence des paradigmes de la programmation par aspects, les techniques qui permettent l’implémentation des différents aspects fonctionnels dans un code objet. Notre approche consiste à : • identifier les techniques utilisées par les développeurs pour intégrer une fonctionnalité en l’absence des techniques orientées aspects • caractériser l’empreinte de ces techniques sur le code • et développer des outils pour identifier ces empreintes. Ainsi, nous présentons deux approches pour l’identification des fonctionnalités existantes dans du code orienté objets. La première identifie différents patrons de conception qui permettent l’intégration de ces fonctionnalités dans le code. La deuxième utilise l’analyse formelle de concepts pour identifier les fonctionnalités récurrentes dans le code. Nous expérimentons nos deux approches sur des systèmes libres orientés objets pour identifier les différentes fonctionnalités dans le code. Les résultats obtenus montrent l’efficacité de nos approches pour identifier les différentes fonctionnalités dans du code légataire orienté objets et permettent de suggérer des cas de refactorisation.

Desenvolupament d’una biblioteca per a la generació de diagrames vectorials basat en l’entorn gràfic de JAVA2D i aplicació d’aquesta biblioteca per a la implementació d’una eina per al desenvolupament de diagrames d’E/R

En aquest projecte es vol implementar una llibreria en Java, que proporcioni les eines necessàries per a crear diagrames i esquemes. Es vol proporcionar a la llibreria un conjunt d’objectes bàsics, també mètodes i funcionalitats suficients per a gestionar aquests objectes. Per altra part, es vol implementar una aplicació per a dissenyar diagrames Entitat-Relació que utilitzi aquesta llibreria

Model-based objects recognition in man-made environments

We describe a model-based objects recognition system which is part of an image interpretation system intended to assist autonomous vehicles navigation. The system is intended to operate in man-made environments. Behavior-based navigation of autonomous vehicles involves the recognition of navigable areas and the potential obstacles. The recognition system integrates color, shape and texture information together with the location of the vanishing point. The recognition process starts from some prior scene knowledge, that is, a generic model of the expected scene and the potential objects. The recognition system constitutes an approach where different low-level vision techniques extract a multitude of image descriptors which are then analyzed using a rule-based reasoning system to interpret the image content. This system has been implemented using CEES, the C++ embedded expert system shell developed in the Systems Engineering and Automatic Control Laboratory (University of Girona) as a specific rule-based problem solving tool. It has been especially conceived for supporting cooperative expert systems, and uses the object oriented programming paradigm

Programming Principles: Super and Sub-classes

In this session we introduce inheritance - one of the cornerstone concepts of object oriented programming. We look at how to define super and sub-classes, how to maintain encapsulation using the super() constructor, and why it is useful to use substitution to hold references to sub-classes in references typed as their super-class.

Dynamic programming for stochastic target problems, Viscosity solutions and hedging in markets with Portfolio constraints and large investors

The purpose of this expository arti le is to present a self- ontained overview of some results on the hara terization of the optimal value fun tion of a sto hasti target problem as (dis ontinuous) vis osity solution of a ertain dynami programming PDE and its appli ation to the problem of hedging ontingent laims in the presen e of portfolio onstraints and large investors

The effectiveness of assessment learning objects produced using pair programming

Pair Programming is a technique from the software development method eXtreme Programming (XP) whereby two programmers work closely together to develop a piece of software. A similar approach has been used to develop a set of Assessment Learning Objects (ALO). Three members of academic staff have developed a set of ALOs for a total of three different modules (two with overlapping content). In each case a pair programming approach was taken to the development of the ALO. In addition to demonstrating the efficiency of this approach in terms of staff time spent developing the ALOs, a statistical analysis of the outcomes for students who made use of the ALOs is used to demonstrate the effectiveness of the ALOs produced via this method.

The constrained compartmentalized knapsack problem: mathematical models and solution methods

The constrained compartmentalized knapsack problem can be seen as an extension of the constrained knapsack problem. However, the items are grouped into different classes so that the overall knapsack has to be divided into compartments, and each compartment is loaded with items from the same class. Moreover, building a compartment incurs a fixed cost and a fixed loss of the capacity in the original knapsack, and the compartments are lower and upper bounded. The objective is to maximize the total value of the items loaded in the overall knapsack minus the cost of the compartments. This problem has been formulated as an integer non-linear program, and in this paper, we reformulate the non-linear model as an integer linear master problem with a large number of variables. Some heuristics based on the solution of the restricted master problem are investigated. A new and more compact integer linear model is also presented, which can be solved by a branch-and-bound commercial solver that found most of the optimal solutions for the constrained compartmentalized knapsack problem. On the other hand, heuristics provide good solutions with low computational effort. (C) 2011 Elsevier BM. All rights reserved.

Fault Coverage-Driven Incremental Test Generation

In this paper, we consider a classical problem of complete test generation for deterministic finite-state machines (FSMs) in a more general setting. The first generalization is that the number of states in implementation FSMs can even be smaller than that of the specification FSM. Previous work deals only with the case when the implementation FSMs are allowed to have the same number of states as the specification FSM. This generalization provides more options to the test designer: when traditional methods trigger a test explosion for large specification machines, tests with a lower, but yet guaranteed, fault coverage can still be generated. The second generalization is that tests can be generated starting with a user-defined test suite, by incrementally extending it until the desired fault coverage is achieved. Solving the generalized test derivation problem, we formulate sufficient conditions for test suite completeness weaker than the existing ones and use them to elaborate an algorithm that can be used both for extending user-defined test suites to achieve the desired fault coverage and for test generation. We present the experimental results that indicate that the proposed algorithm allows obtaining a trade-off between the length and fault coverage of test suites.

A transformational language for mutant description

Mutation testing has been used to assess the quality of test case suites by analyzing the ability in distinguishing the artifact under testing from a set of alternative artifacts, the so-called mutants. The mutants are generated from the artifact under testing by applying a set of mutant operators, which produce artifacts with simple syntactical differences. The mutant operators are usually based on typical errors that occur during the software development and can be related to a fault model. In this paper, we propose a language-named MuDeL (MUtant DEfinition Language)-for the definition of mutant operators, aiming not only at automating the mutant generation, but also at providing precision and formality to the operator definition. The proposed language is based on concepts from transformational and logical programming paradigms, as well as from context-free grammar theory. Denotational semantics formal framework is employed to define the semantics of the MuDeL language. We also describe a system-named mudelgen-developed to support the use of this language. An executable representation of the denotational semantics of the language is used to check the correctness of the implementation of mudelgen. At the very end, a mutant generator module is produced, which can be incorporated into a specific mutant tool/environment. (C) 2008 Elsevier Ltd. All rights reserved.