Mike Holcombe - MSc Projects 2005-6

WMLH-1. Simple Formal Methods tool – Eclipse plug-ins.

Key words: Eclipse, formal methods


This is a series of related projects to develop further the ADEPT environment which has been funded by IBM and is used within Genesys. The tool will also be used in the Eclipse environment for the Crossover (1st year undergraduate) and Software Hut (2nd year undergraduate) projects.

Eclipse is an international movement, strongly supported by many large companies such as IBM, which develops and promotes an open source IDE. This has the facility for incorporating plug ins to support various types of design, program and test activities in a coherent manner.

See http://www.genesys.shef.ac.uk/eclipse


and http://www.eclipse.org/

The concept is to allow users to build a simple editor for formal specifications which will connect with the X-machine editor that already exists as an Eclipse plug-in. Simple basic types will be combined using constructors into more complex types. Functions and relations suitable for using as transitions in X-machines will be included.

The key aspect is that it should be flexible and easy to use.


No specific requirements other than access to PCs, eclipse and Java.


Start with the Eclipse pages on Genesys.

Module Links


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Project description.

WMLH-2: Computational Systems Biology. A model of Candida albicans the most frequent fungal pathogen of humans

Key words: Agent based modelling, X-machine framework

Key words: C programming language


Candida albicans is the most frequently isolated fungal pathogen of humans, affecting immuocompromised patients ranging from premature infants to AIDS sufferers. Systemic infections have an attributed mortality of 30-50%. Although many properties have been shown to contribute to virulence in animal studies, its pathogenesis is not well understood. Analysis of the genome has been undertaken to provide researchers with more tools to investigate Candidiasis.

We will be collaborating with the Department of Infectious Diseases, Imperial College, London.


We will build a detailed model of this organisms using the successful approach that has already been carried out in the Computational Systems Biology group


Our approach to this is to use a framework based on the XMML language for describing the behaviour of the agents – which could be the complete organism or key aspects of some of the molecular pathways involved in it – and to use the X-Machine Agents Framework





Start with papers from supervisor

Module Links 3D Computer graphics

Prerequisites - Good programming skills

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Project description.

WMLH-3: easyTest. SSIT, ISS

Testing is the most expensive part  of the software development process consuming at least 50% of time and money in any typical project. Yet,
despite this, testing is rarely dealt with in any detail, if at all, in programming courses. New approaches to software development, such as
eXtreme Programming (XP) require you to write your tests FIRST, before starting to code and to run these tests regularly on the code as you
develop it. This gives you much more confidence that your code is good. However, it is not easy to write tests and if the tests are poor the
code will also be poor (buggy).

This project will create an on-line test support system, easyTest, which will be both a learning tool and a practical test tool. The focus is a
'learn and do' approach for use in a first Java programming course.

Part of the tool will be some simple pages of information and guidance on how to write simple tests with many examples and a practical and
structured approach to thinking about simple programs and classes in order to create tests. The second part will be an integrated tool which
will store tests and provide a mechanism for applying these to the developing code with minimal effort.

There is already a popular program for running tests in this way – Junit - and we will build on this. This is available from: 

The final product should be a powerful aid to novice programmers that will guide them in writing tests and provide a friendly environment so
that they can do their testing as they try to develop their code. The tool must support programmer activity and not 'get in the way'

K. Beck, "eXtreme programming explained - embrace change" Addison-Wesley.
M. Holcombe, Notes on XP - from supervisor.

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Project description.

WMLH-4 Software Hut resource and publicity page. SST, ISS

The Software Hut is an innovative project carried out by all 2nd year undergraduates in the Department. It is similar in concept to the Maxi project in that there are real clients, usually from local businesses and other organisations. The project is to construct a web page which will present some of the achievements of the software hut, examples of systems built and clients, a facility for prospective clients to send in project requests and as much good marketing content as we can find.


Information Provided by supervisor.

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