CSP design model and tool support

The CSP paradigm is known as a powerful concept for designing and analysing the architectural and behavioural parts of concurrent software. Although the theory of CSP is useful for mathematicians, the programming language occam has been derived from CSP that is useful for any engineering practice. Nowadays, the concept of occam/CSP can be used for almost every object-oriented programming language. This paper describes a tree-based description model and prototype tool that elevates the use of occam/CSP concepts at the design level and performs code generation to Java, C, C++, and machine-readable CSP for the level of implementation. The tree-based description model can be used to browse through the generated source code. The tool is a kind of browser that is able to assist modern workbenches (like Borland Builder, Microsoft Visual C++ and 20-SIM) with coding concurrency. The tool will guide the user through the design trajectory using support messages and several semantic and syntax rule checks. The machine-readable CSP can be read by FDR, enabling more advanced analysis on the design. Early experiments with the prototype tool show that the browser concept, combined with the tree-based description model, enables a user-friendly way to create a design using the CSP concepts and benefits. The design tool is available from our URL, http://www.rt.el.utwente.nl/javapp

Optimization-Based Peptide Mass Fingerprinting for Protein Mixture Identification

*Motivation:* In current proteome research, peptide sequencing is probably the most widely used method for protein mixture identification. However, this peptide-centric method has its own disadvantages such as the immense volume of tandem Mass Spectrometry (MS) data for sequencing peptides. With the fast development of technology, it is possible to investigate other alternative techniques. Peptide Mass Fingerprinting (PMF) has been widely used to identify single purified proteins for more than 15 years. Unfortunately, this technique is less accurate than peptide sequencing method and cannot handle protein mixtures, which hampers the widespread use of PMF technique. If we can remove these limitations, PMF will become a useful tool in protein mixture identification. 
*Results:* We first formulate the problem of PMF protein mixture identification as an optimization problem. Then, we show that the use of some simple heuristics enables us to find good solutions. As a result, we obtain much better identification results than previous methods. Moreover, the result on real MS data can be comparable with that of the peptide sequencing method. Through a comprehensive simulation study, we identify a set of limiting factors that hinder the performance of PMF method in protein mixtures. We argue that it is feasible to remove these limitations and PMF can be a powerful tool in the analysis of protein mixtures

ADL: a graphical design language for real time parallel applications

Designing parallel applications is generally experienced as a tedious and difficult task, especially when hard real-time performance requirements have to be met. This paper discusses on-going work concerning the construction of a Design Entry System which supports the design phase of parallel real-time industrial application development. In particular, in this paper we pay attention to the development and implementation of a graphical Application Design Language. The work is part of the ESPRIT project Hamlet which focuses on industrial application of transputer-based systems for commercially strategic real-time applications

The Hamlet design entry system: an overview of ADL and its environment

Exploiting parallelism for industrial real-time applications has not received much attention compared to scientific applications. The available real-time design methods do not adequately address the issue of parallelism, resulting still in a strong need for low-level tools such as debuggers and monitors. This need illustrates that developing parallel real-time applications is indeed a difficult and tedious task. In this paper we show how problems can be alleviated if an approach is followed that allows for experimentation with designs and implementations. In particular, we discuss a development system that integrates design, implementation, execution, and analysis of real-time applications, putting emphasis on exploitation of parallelism. In the paper we primarily concentrate on the support for application *design*, as we feel that parallelism should essentially be addressed at this level

The Hamlet Application Design Language: introductory definition report

This report provides an introduction to the definition of the Hamlet Application Design Language (ADL). ADL is a graphical-based language and notation supporting the design of parallel real-time applications. Designs expressed in ADL are based on a model of processes that communicate by message-passing. Communication can either be synchronous or asynchronous, and orthogonally, may be subject to blocking, delaying, or nonblocking timing constraints. The language has been devised in such a way that automated (skeletal) code generation can be supported. To this aim, structural aspects are expressed in a notation somewhat similar to data-flow diagrams, whereas behavioral aspects are expressed as state-transition machines following a syntax similar to that of SDL. Exploitation of parallelism is obtained by annotating a design with process replication specifications

A transputer based parallel database system.

A sophisticated database application generation environment known as DB4GL has been developed at Sheffield City Polytechnic. A unique feature of DB4GL is the object-oriented application model used to specify and generate database applications. Although DB4GL has many advanced and powerful features, such as a self-describing data dictionary and extensive integrity rule processing facilities; the system has not been designed for high performance in either the generation tools or the generated database applications. The Parallel-DB4GL (P-DB4GL) project represents an attempt to improve the performance of the generated database applications, by constructing a new concurrent implementation of DB4GL for execution on transputer-based parallel hardware. This thesis describes the DB4GL system as developed to the commencement of the P-DB4GL project. A prototype P-DB4GL system has been implemented that demonstrates how significant performance gains can be obtained from a concurrent implementation on transputer-based parallel hardware. Based on the successful results of this prototype system, designs for a fully functional multiprocessor P-DB4GL system are proposed. The details of this prototype and the fully functional designs are presented in this thesis. The thesis also provides an evaluation of the P-DB4GL project as a whole, and concludes with some suggestions for further research in the areas of parallel databases and object-oriented system implementation

Nonlinear diffusion filtering on surfaces

Nonlinear diffusion filtering is a PDE-based method to remove noise from images that has found much success. This dissertation looks at whether nonlinear diffusion filtering can be combined with the closest point method, a relatively new and novel method for solving partial differential equations on surfaces. The closest point method is an embedding method that uses a simple representation of surfaces. The theory and implementation of for the closest point method is presented. We perform convergence studies that show good agreement with theory.\ud \ud We discuss the use of linear and nonlinear diffusion for image processing, in particular the Perona{Malik and Gaussian schemes. We show that they can be combined with the closest point method to produce impressive results, visualised beautifully using an OpenGL raytracer designed for use with the closest point method. Some surprising and unexpected eects were discovered when moving from a plane to a three-dimensional surface. These effects are described and investigated

A Petri net-occam based methodology for the development of dependable distributed control software.

Analysis of flexible manufacturing cells (FMCs) shows their requirement for flexible, correct, reliable, safe and distributed control. A comparison of the state of the art in software engineering for parallel systems, and an examination of safety related systems, reveal a need for formal and rigorous techniques at all stages in the software life cycle. However, parallel software, safety related software and formal techniques are complex. It is better to avoid faults rather than eliminate or tolerate them, and although less flexible, avoidance is often simpler to implement. There is a need for a tool which overcomes many of these complexities, and this thesis discusses and defines such a tool in the form of a methodology. The novelty of the work is in the combination of the core goals to manage these issues, and how the strategies guide the user to a solution which will not deadlock and which is comprehensible. Place-transition Petri nets are an ideal representation for designing and modelling the interaction of concurrent (and distributed) processes. Occam is a high level real time parallel language designed to execute on one or a network of transputers. Transputers are processing, memory and communication building blocks, and, together with occam, are shown to be suitable for controlling and communicating the control as the DCS in FMCs. The methodology developed in this thesis adopts the mathematically based tools of Petri nets, occam and transputers, and, by exploiting their structural similarities, incorporates them in a steps and tasks to improve the development of correct, reliable and hence safe occam code. The four steps: identify concurrent and sequential operations, produce Petri net graphs for all controllers, combine controller Petri net graphs and translate Petri net graphs into occam; are structured around three core goals: Petri net/occam equivalence, comprehensibility and pro-activity; which are manifest in four strategies: output-work-backwards, concurrent and sequential actions, structuralise and modularise, and deadlock avoidance. The methodology assists in all stages of the software development life cycle, and is applicable to small DCSs such as an FMC. The methodology begins by assisting in the creation of DCS requirements from the manufacturing requirements of the FMC, and guides the user to the production of dependable occam code. Petri nets allow the requirements to be specified as they are created, and the methodology's imposed restrictions enable the final Petri net design to be translated directly into occam. Thus the mathematics behind the formal tools is hidden from the user, which should be attractive to industry.The methodology is successfully applied to the example FMC, and occam code to simulate the FMC is produced. Due to the novelty of the research, many suggestions for further work are given

Dataflow development of medium-grained parallel software

PhD ThesisIn the 1980s, multiple-processor computers (multiprocessors) based on conven- tional processing elements emerged as a popular solution to the continuing demand for ever-greater computing power. These machines offer a general-purpose parallel processing platform on which the size of program units which can be efficiently executed in parallel - the "grain size" - is smaller than that offered by distributed computing environments, though greater than that of some more specialised architectures. However, programming to exploit this medium-grained parallelism remains difficult. Concurrent execution is inherently complex, yet there is a lack of programming tools to support parallel programming activities such as program design, implementation, debugging, performance tuning and so on. In helping to manage complexity in sequential programming, visual tools have often been used to great effect, which suggests one approach towards the goal of making parallel programming less difficult. This thesis examines the possibilities which the dataflow paradigm has to offer as the basis for a set of visual parallel programming tools, and presents a dataflow notation designed as a framework for medium-grained parallel programming. The implementation of this notation as a programming language is discussed, and its suitability for the medium-grained level is examinedScience and Engineering Research Council of Great Britain EC ERASMUS schem

The application of digital techniques to an automatic radar track extraction system

'Modern' radar systems have come in for much criticism in recent years, particularly in the aftermath of the Falklands campaign. There have also been notable failures in commercial designs, including the well-publicised 'Nimrod' project which was abandoned due to persistent inability to meet signal processing requirements. There is clearly a need for improvement in radar signal processing techniques as many designs rely on technology dating from the late 1970's, much of which is obsolete by today’s standards. The Durham Radar Automatic Track Extraction System (RATES) is a practical implementation of current microprocessor technology, applied to plot extraction of surveillance radar data. In addition to suggestions for the design of such a system, results are quoted for the predicted performance when compared with a similar product using 1970's design methodology. Suggestions are given for the use of other VLSI techniques in plot extraction, including logic arrays and digital signal processors. In conclusion, there is an illustrated discussion concerning the use of systolic arrays in RATES and a prediction that this will represent the optimum architecture for future high-speed radar signal processors