Tony Griffiths

Teallach: a model-based user interface development environment for object databases

Abstract Model-based user interface development environments show promise for improving the productivity of user interface developers, and possibly for improving the quality of developed interfaces. While model-based techniques have previously been applied to the area of database interfaces, they have not been specifically targeted at the important area of object database applications. Such applications make use of models that are semantically richer than their relational counterparts in terms of both data structures and application functionality. In general, model-based techniques have not addressed how the information referenced in such applications is manifested within the described models, and is utilised within the generated interface itself. This lack of experience with such systems has led to many model-based projects providing minimal support for certain features that are essential to such data intensive applications, and has prevented object database interface developers in particular from benefiting from model-based techniques. This paper presents the Teallach model-based user interface development environment for object databases, describing the models it supports, the relationships between these models, the tool used to construct interfaces using the models and the generation of Java programs from the declarative models. Distinctive features of Teallach include comprehensive facilities for linking models, a flexible development method, an open architecture, and the generation of running applications based on the models constructed by designers.

Automated tracking of gene expression in individual cells and cell compartments

Many intracellular signal transduction processes involve the reversible translocation from the cytoplasm to the nucleus of transcription factors. The advent of fluorescently tagged protein derivatives has revolutionized cell biology, such that it is now possible to follow the location of such protein molecules in individual cells in real time. However, the quantitative analysis of the location of such proteins in microscopic images is very time consuming. We describe CellTracker, a software tool designed for the automated measurement of the cellular location and intensity of fluorescently tagged proteins. CellTracker runs in the MS Windows environment, is freely available (at http://www.dbkgroup.org/celltracker/), and combines automated cell tracking methods with powerful image-processing algorithms that are optimized for these applications. When tested in an application involving the nuclear transcription factor NF-κB, CellTracker is competitive in accuracy with the manual human analysis of such images but is more than 20 times faster, even on a small task where human fatigue is not an issue. This will lead to substantial benefits for time-lapse-based high-content screening.

Generating user interface code in a model based user interface development environment

Declarative models play an important role in most software design activities, by allowing designs to be constructed that selectively abstract over complex implementation details. In the user interface setting, Model-Based User Interface Development Environments (MB-UIDEs) provide a context within which declarative models can be constructed and related, as part of the interface design process. However, such declarative models are not usually directly executable, and may be difficult to relate to existing software components. It is therefore important that MB-UIDEs both fit in well with existing software architectures and standards, and provide an effective route from declarative interface specification to running user interfaces. This paper describes how user interface software is generated from declarative descriptions in the Teallach MB-UIDE. Distinctive features of Teallach include its open architecture, which connects directly to existing applications and widget sets, and the generation of executable interface applications in Java. This paper focuses on how Java programs, organized using the model-view-controller pattern (MVC), are generated from the task, domain and presentation models of Teallach.

The Tripod spatio-historical data model

The storage and analysis of large amounts of time-varying spatial and aspatial data is becoming an important feature of many application domains. This has fuelled the need for spatio-temporal extensions to data models and their associated querying facilities. To date, much of this work has focused on the relational data model, with object data models receiving far less consideration. Where descriptions of such object models do exist, these models fail to fully integrate their spatial, aspatial and temporal dimensions into a uniform and coherent model. In addition, there is currently a lack of systems which build upon these models to produce database architectures that address the broad spectrum of issues related to the delivery of a fully functional spatio-temporal DBMS. This paper presents a foundation for the development of such a system, called Tripod, by describing a spatio-historical object model based on a specialized mechanism, called a history, for maintaining knowledge about entities that change over time. Key features of the resulting model include: (i) consistent representations of primitive spatial and timestamp types; (ii) a component-based design in which spatial, timestamp and historical extensions are formalized incrementally, for subsequent use together or separately; (iii) compatibility with mainstream query processing frameworks for object databases; and (iv) the integration of the spatio-temporal proposal with the ODMG object database standard. The paper presents a comprehensive formal characterization of the model and illustrates its capabilities in a crime data management application. It is also shown how the model can be programmed using an extension to the ODMG language bindings. The model and language bindings have been fully implemented.

The Teallach tool: using models for flexible user interface design

Model-based user interface development environments aim to provide designers with a more systematic approach to user interface development using a particular design method. This method is realised through tools which support the construction and linkage of the supported models. This paper presents the tools which support the construction of the Teallach models in the context of the Teallach design method. Distinctive features of the Teallach tool include comprehensive facilities for relating the different models, and the provision of a flexible design method in which models can be constructed and related by designers in different orders and in different ways.

Tripod: a comprehensive system for the management of spatial and aspatial historical objects

Spatio-temporal databases have been the focus of considerable research attention in recent years. To date, much of this work has focused on the relational data model, with object data models receiving far less consideration. Where descriptions of such object models do exist, there is currently a lack of systems that build upon these models to produce database architectures that address the broad spectrum of issues related to the delivery for a fully fuctional spatio-temporal DBMS. This paper presents an overview of such a system by describing a spatio-historical object DBMS that utilises a specialised mechanism, called a history, for maintaining knowledge about entities that change over time. Key features of the resulting proposal include: (i) consistent representations of primitive spatial and temporal types; (ii) a component-based design in which spatial, temporal and historical extensions are formalised incrementally, for subsequent use together or separately; (iii) compatibility with mainstream query processing frameworks for object databases; and (iv) the integration of the spatio-temporal proposal with the ODMG standard.

Exploiting Model-based Techniques for User Interfaces to Databases

Model-based systems provide methods for supporting the systematic and efficient development of application interfaces. This paper examines how model-based technologies can be exploited to develop user interfaces to databases. To this end five model-based systems, namely Adept, HUMANOID, Mastermind, TADEUS and DRIVE are discussed through the use of a unifying case study which allows the examination of the approaches followed by the different systems.

Teallach — a flexible user-interface development environment for object database applications

The Teallach project has adapted model-based user-interface development techniques to the systematic creation of user-interfaces for object-oriented database applications. Model-based approaches aim to provide designers with a more principled approach to user-interface development using a variety of underlying models, and tools which manipulate these models. Here we present the results of the Teallach project, describing the tools developed and the flexible design method supported. Distinctive features of the Teallach system include provision of database-specific constructs, comprehensive facilities for relating the different models, and support for a flexible design method in which models can be constructed and related by designers in different orders and in different ways, to suit their particular design rationales. The system then creates the desired user-interface as an independent, fully functional Java application, with automatically generated help facilities.

Spatio-temporal evolution: querying patterns of change in databases

This paper contributes a general approach to characterizing patterns of change in a spatio-temporal database.While there is a particular interest in modelling and querying how spatio-temporal entities evolve, the approach contributed by the paper is distinctive in being applicable without modification to aspatial entities as well. The paper uses the Tripod spatio-temporal model to describe and instantiate in detail the contributed approach. After briefly describing a typical application and providing basic knowledge about Tripod, the paper characterizes and classifies evolution queries and describes in detail how they are evaluated.

A query calculus for spatio-temporal object databases

The development of any comprehensive proposal for spatio-temporal databases involves significant extensions to many aspects of a non-spatio-temporal architecture. One aspect that has received less attention than most is the development of a query calculus that can be used to provide a semantics for spatio-temporal queries and underpin an effective query optimization and evaluation framework. We show how a query calculus for spatio-temporal object databases that builds upon the monoid calculus proposed by Fegaras and Maier (2000) for ODMG-compliant database systems can be developed. The paper shows how an extension of the ODMG type system with spatial and temporal types can be accommodated into the monoid approach. It uses several queries over historical (possibly spatial) data to illustrate how, by mapping them into monoid comprehensions, the way is open for the application of a logical optimizer based on the normalization algorithm proposed by Fegaras and Maier.