A single-code software model for multiphysics analysis-engine on parallel and distributed computers with the PHYSICA toolkit

Abstract not available

A signaling visualization toolkit to support rational design of combination therapies and biomarker discovery: SiViT

Targeted cancer therapy aims to disrupt aberrant cellular signalling pathways. Biomarkers are surrogates of pathway state, but there is limited success in translating candidate biomarkers to clinical practice due to the intrinsic complexity of pathway networks. Systems biology approaches afford better understanding of complex, dynamical interactions in signalling pathways targeted by anticancer drugs. However, adoption of dynamical modelling by clinicians and biologists is impeded by model inaccessibility. Drawing on computer games technology, we present a novel visualisation toolkit, SiViT, that converts systems biology models of cancer cell signalling into interactive simulations that can be used without specialist computational expertise. SiViT allows clinicians and biologists to directly introduce for example loss of function mutations and specific inhibitors. SiViT animates the effects of these introductions on pathway dynamics, suggesting further experiments and assessing candidate biomarker effectiveness. In a systems biology model of Her2 signalling we experimentally validated predictions using SiViT, revealing the dynamics of biomarkers of drug resistance and highlighting the role of pathway crosstalk. No model is ever complete: the iteration of real data and simulation facilitates continued evolution of more accurate, useful models. SiViT will make accessible libraries of models to support preclinical research, combinatorial strategy design and biomarker discovery.

Technology for employability toolkit

This toolkit distills the ideas and guidance from the Jisc ‘Technology for employability’ http://bit.ly/technology_for_employability report into a useful and usable toolkit that can be used by Higher Education (HE) and Further Education (FE) educational providers to aid dialogue, decision-making and planning in respect of developing student employability and use of technology for employability.

The PROSPER Toolkit

The PROSPER (Proof and Specification Assisted Design Environments) project advocates the use of toolkits which allow existing verification tools to be adapted to a more flexible format so that they may be treated as components. A system incorporating such tools becomes another component that can be embedded in an application. This paper describes the PROSPER Toolkit which enables this. The nature of communication between components is specified in a language-independent way. It is implemented in several common programming languages to allow a wide variety of tools to have access to the toolkit.

Integrating SVC and HOL with the PROSPER Toolkit

We describe an integration of the SVC decision procedure with the HOL theorem prover. This integration was achieved using the PROSPER toolkit. The SVC decision procedure operates on rational numbers, an axiomatic theory for which was provided in HOL. The decision procedure also returns counterexamples and a framework has been devised for handling counterexamples in a HOL setting.

Degradation toolkit for predicting the amount of degradation of particulate solids in lean phase pneumatic conveyors

Abstract not available

Response toolkit to provide an active response against intrusions using Ontology-Based IRS

Los sistemas de respuesta activa tienen por objetivo ejecutar una respuesta en contra de una intrusión de forma automática. Sin embargo, ejecutar una respuesta automáticamente no es una tarea trivial ya que el costo de ejecutar una respuesta podría ser más grande que el efecto que cause la intrusión propiamente dicha. También, el sistema debe contar con un amplio conjunto de acciones de respuesta y un algoritmo que seleccione la respuesta óptima. Este artículo propone un toolkit de respuestas que será integrado a un IRS basado en Ontologías para permitir la ejecución automática de la mejor respuesta cuando una intrusión es detectada. Se presenta un conjunto de respuestas basadas en host y basadas en red que pueden ser ejecutadas por el IRS, dicha ejecución es llevada a cabo mediante agentes basados en plugins que han sido distribuidos en la red. Finalmente, se realiza la verificación del sistema propuesto, tomando como caso de uso un ataque de defacement obteniéndose resultados satisfactorios.

EasyInterface: a toolkit for the rapid development of GUIs for research prototype tools

During the lifetime of a research project, different partners develop several research prototype tools that share many common aspects. This is equally true for researchers as individuals and as groups: during a period of time they often develop several related tools to pursue a specific research line. Making research prototype tools easily accessible to the community is of utmost importance to promote the corresponding research, get feedback, and increase the tools’ lifetime beyond the duration of a specific project. One way to achieve this is to build graphical user interfaces (GUIs) that facilitate trying tools; in particular, with web-interfaces one avoids the overhead of downloading and installing the tools. Building GUIs from scratch is a tedious task, in particular for web-interfaces, and thus it typically gets low priority when developing a research prototype. Often we opt for copying the GUI of one tool and modifying it to fit the needs of a new related tool. Apart from code duplication, these tools will “live” separately, even though we might benefit from having them all in a common environment since they are related. This work aims at simplifying the process of building GUIs for research prototypes tools. In particular, we present EasyInterface, a toolkit that is based on novel methodology that provides an easy way to make research prototype tools available via common different environments such as a web-interface, within Eclipse, etc. It includes a novel text-based output language that allows to present results graphically without requiring any knowledge in GUI/Web programming. For example, an output of a tool could be (a structured version of) “highlight line number 10 of file ex.c” and “when the user clicks on line 10, open a dialog box with the text ...”. The environment will interpret this output and converts it to corresponding visual e_ects. The advantage of using this approach is that it will be interpreted equally by all environments of EasyInterface, e.g., the web-interface, the Eclipse plugin, etc. EasyInterface has been developed in the context of the Envisage [5] project, and has been evaluated on tools developed in this project, which include static analyzers, test-case generators, compilers, simulators, etc. EasyInterface is open source and available at GitHub2.

Atratividade de projetos de software livre: importância teórica e estratégias para administração

Thousands of Free and Open Source Software Projects (FSP) were, and continually are, created on the Internet. This scenario increases the number of opportunities to collaborate to the same extent that it promotes competition for users and contributors, who can guide projects to superior levels, unachievable by founders alone. Thus, given that the main goal of FSP founders is to improve their projects by means of collaboration, the importance to understand and manage the capacity of attracting users and contributors to the project is established. To support researchers and founders in this challenge, the concept of attractiveness is introduced in this paper, which develops a theoretical-managerial toolkit about the causes, indicators and consequences of attractiveness, enabling its strategic management.

E-contracting with price configuration for Web services and QoS

The large amount of information in electronic contracts hampers their establishment due to high complexity. An approach inspired in Software Product Line (PL) and based on feature modelling was proposed to make this process more systematic through information reuse and structuring. By assessing the feature-based approach in relation to a proposed set of requirements, it was showed that the approach does not allow the price of services and of Quality of Services (QoS) attributes to be considered in the negotiation and included in the electronic contract. Thus, this paper also presents an extension of such approach in which prices and price types associated to Web services and QoS levels are applied. An extended toolkit prototype is also presented as well as an experiment example of the proposed approach.

Extension of the core map of common bean with EST-SSR, RGA, AFLP, and putative functional markers

Microsatellites and gene-derived markers are still underrepresented in the core molecular linkage map of common bean compared to other types of markers. In order to increase the density of the core map, a set of new markers were developed and mapped onto the RIL population derived from the `BAT93` x `Jalo EEP558` cross. The EST-SSR markers were first characterized using a set of 24 bean inbred lines. On average, the polymorphism information content was 0.40 and the mean number of alleles per locus was 2.7. In addition, AFLP and RGA markers based on the NBS-profiling method were developed and a subset of the mapped RGA was sequenced. With the integration of 282 new markers into the common bean core map, we were able to place markers with putative known function in some existing gaps including regions with QTL for resistance to anthracnose and rust. The distribution of the markers over 11 linkage groups is discussed and a newer version of the common bean core linkage map is proposed.

Thermal effects in the evolution of initially layered mantle material

A simplified model for anisotropic mantle convection based on a novel class of rheologies, originally developed for folding instabilities in multilayered rock (MUHLHAUS et al., 2002), is extended ¨ through the introduction of a thermal anisotropy dependent on the local layering. To examine the effect of the thermal anisotropy on the evolution of mantle material, a parallel implementation of this model was undertaken using the Escript modelling toolkit and the Finley finite-element computational kernel (DAVIES et al., 2004). For the cases studied, there appears too little if any effect. For comparative purposes, the effects of anisotropic shear viscosity and the introduced thermal anisotropy are also presented. These results contribute to the characterization of viscous anisotropic mantle convection subject to variation in thermal conductivities and shear viscosities.

Eco-efficiency for the Dairy Processing Industry - Fact Sheet Sumary

This Toolkit was developed for the Australian dairy processing industry on behalf of Dairy Australia. At the conclusion of the project, industry participants gained exclusive access to a comprehensive Eco-Efficiency Manual, which outlined many of the opportunities available to the industry. Summary fact sheets were also prepared as publicly available resources and these are available for download below