Engineering simulations for cancer systems biology

Computer simulation can be used to inform in vivo and in vitro experimentation, enabling rapid, low-cost hypothesis generation and directing experimental design in order to test those hypotheses. In this way, in silico models become a scientific instrument for investigation, and so should be developed to high standards, be carefully calibrated and their findings presented in such that they may be reproduced. Here, we outline a framework that supports developing simulations as scientific instruments, and we select cancer systems biology as an exemplar domain, with a particular focus on cellular signalling models. We consider the challenges of lack of data, incomplete knowledge and modelling in the context of a rapidly changing knowledge base. Our framework comprises a process to clearly separate scientific and engineering concerns in model and simulation development, and an argumentation approach to documenting models for rigorous way of recording assumptions and knowledge gaps. We propose interactive, dynamic visualisation tools to enable the biological community to interact with cellular signalling models directly for experimental design. There is a mismatch in scale between these cellular models and tissue structures that are affected by tumours, and bridging this gap requires substantial computational resource. We present concurrent programming as a technology to link scales without losing important details through model simplification. We discuss the value of combining this technology, interactive visualisation, argumentation and model separation to support development of multi-scale models that represent biologically plausible cells arranged in biologically plausible structures that model cell behaviour, interactions and response to therapeutic interventions

Towards an Open Set of Real-World Benchmarks for Model Queries and Transformations

International audienceWith the growing size and complexity of systems under design, industry needs a generation of Model-Driven Engineering (MDE) tools, especially model query and transformation, with the proven capability to handle large-scale scenarios. While researchers are proposing several technical solutions in this sense, the community lacks a set of shared scalability benchmarks, that would simplify quantitative assessment of advancements and enable cross-evaluation of different proposals. Benchmarks in previous work have been synthesized to stress specific features of model management, lacking both generality and industrial validity. In this paper, we initiate an effort to define a set of shared benchmarks, gathering queries and transformations from real-world MDE case studies. We make these case available to community evaluation via a public MDE benchmark repository

Agent-based models and individualism: is the world agent-based?

Agent-based models (ABMs) are an increasingly popular tool in the social sciences. This trend seems likely to continue, so that they will become widely used in geography and in urban and regional planning. We present an overview of examples of these models in the life sciences, economics, planning, sociology, and archaeology. We conclude that ABMs strongly tend towards an individualist view of the social world. This point is reinforced by closer consideration of particular examples. This discussion pays attention to the inadequacy of an individualist model of society with reference to debates in social theory. We argue that because models are closed representations of an open world it is important that institutions and other social structures be explicitly included, or that their omission be explained. A tentative explanation for the bias of ABMs is offered, based on an examination of early research in artificial intelligence and distributed artificial intelligence from which disciplines the approach is derived. Some implications of these findings are discussed. We indicate some useful research directions which are beginning to tackle the individualism issue directly. We further note that the underlying assumptions of ABMs are often hidden in the implementation details. We conclude that such models must be subject to critical examination of their assumptions, and that model builders should engage with social theory if the approach is to realise its full potential

A modern approach to computer systems for linear programming

At head of title: Center for Computational Research in Economics and Management Science

Code coverage measurement framework for android devices

Software testing is a very important activity in the software development life cycle. Numerous general black- and white-box techniques exist to achieve different goals and there are a lot of practices for different kinds of software. The testing of embedded systems, however, raises some very special constraints and requirements in software testing. Special solutions exist in this field, but there is no general testing methodology for embedded systems. One of the goals of the CIRENE project was to fill this gap and define a general testing methodology for embedded systems that could be specialized to different environments. The project included a pilot implementation of this methodology in a specific environment: an Android-based Digital TV receiver (Set-Top-Box). In this pilot, we implemented method level code coverage measurement of Android applications. This was done by instrumenting the applications and creating a framework for the Android device that collected basic information from the instrumented applications and communicated it through the network towards a server where the data was finally processed. The resulting code coverage information was used for many purposes according to the methodology: test case selection and prioritization, traceability computation, dead code detection, etc. The resulting methodology and toolset were reused in another project where we investigated whether the coverage information can be used to determine locations to be instrumented in order to collect relevant information about software usability. In this paper, we introduce the pilot implementation and, as a proof-of-concept, present how the coverage results were used for different purposes

The 1993 Goddard Conference on Space Applications of Artificial Intelligence

This publication comprises the papers presented at the 1993 Goddard Conference on Space Applications of Artificial Intelligence held at the NASA/Goddard Space Flight Center, Greenbelt, MD on May 10-13, 1993. The purpose of this annual conference is to provide a forum in which current research and development directed at space applications of artificial intelligence can be presented and discussed

A study of turbulent flows about oscillating airfoils

Issued as Progress reports [1-6], and Technical report, Project no. E-16-66