Process Oriented Design for Java: Concurrency for All

Welch, Peter H.

doi:10.1007/3-540-46080-2_72

Cited by 29 publications

(20 citation statements)

References 7 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Erlang [80], Go [81] and Scala [82] are examples of languages designed to support message-passing. Alternatively, a general-purpose language can be used in conjunction with libraries such as JCSP [83] or MPI [84].…”

Section: Scalable Simulationmentioning

confidence: 99%

Engineering Simulations for Cancer Systems Biology

Bown¹,

Andrews²,

Deeni³

et al. 2012

CDT

View full text Add to dashboard Cite

Abstract: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.

show abstract

Section: Scalable Simulationmentioning

confidence: 99%

Engineering Simulations for Cancer Systems Biology

Bown¹,

Andrews²,

Deeni³

et al. 2012

CDT

View full text Add to dashboard Cite

show abstract

“…A number of software libraries and specialised programming languages are available to support process-oriented programming in a safe, efficient way; in particular, the CoSMoS project makes use of occam-π [8] and JCSP [9]. occam-π is a concurrent procedural language with support for extremely lightweight communication and synchronisation between processes; the occam-π compiler performs a variety of static checks to detect common concurrency errors at compile time.…”

Section: Process-oriented Programmingmentioning

confidence: 99%

Birds on the wall: Distributing a process-oriented simulation

Sampson

Bjørndalen

Andrews

2009

2009 IEEE Congress on Evolutionary Computation

View full text Add to dashboard Cite

Abstract-The CoSMoS project aims to develop reusable tools and techniques for complex systems modelling and simulation. Using process-oriented software design techniques, we have built a concurrent model of continuous space, usable in a variety of complex systems simulations. In this paper, we describe how we refactored our space model to allow our simulations to run in an efficient and highly-scalable manner across clusters of commodity machines-and, in particular, to support distributed simulation and visualisation on the Tromsø Display Wall.

show abstract

“…Nevertheless, CSP is a process algebra that enables the definition of channels and datatypes, along with flexible and elegant parallel operators. In addition, the CSP notation is supported by a refinement theory, refinement checkers, such as FDR [17], animators [28], and implementations, such as JCSP [43,42] and OCCAM [16].…”

Section: Some Considerationsmentioning

confidence: 99%