Robert Kukla

Scientific names are ambiguous as identifiers for biological taxa: their context and definition are required for accurate data integration

Biologists use scientific names to label the organisms described in their data; however, these names are not unique identifiers for taxonomic entities. Alternative taxonomic classifications may apply the same name, associated with alternative definition or circumscription. Consequently, labelling data with scientific names alone does not unambiguously distinguish between taxon concepts. Accurate integration and comparison of biological data is required on taxon concepts, as defined in alternative taxonomic classifications. We have derived an abstract, inclusive model for the diverse representations of taxonomic concepts used by taxonomists and in taxonomic databases. This model has been implemented as a proposed standard XML schema for the exchange and comparison of taxonomic concepts between data providers and users. The representation and exchange of taxon definitions conformant with this schema will facilitate the development of taxonomic name/concept resolution services, allowing the meaningful integration and comparison of biological datasets, with greater accuracy than on the basis of name alone.

PEDFLOW: Development of an Autonomous Agent Model of Pedestrian Flow

The need for an autonomous agent approach for the modeling of pedestrians in urban environments is discussed, and PEDFLOW is placed in the context of existing models. PEDFLOW is a microscopic model of pedestrians’ movement; each pedestrian is represented as an agent capable of making its own decisions on the basis of a part of the observable scene local to that pedestrian. The model, implemented in Java, provides a framework in which agents are visualized as squares in a grid and movement is modeled as a change of grid position with a delay that characterizes the speed of the agent. A single rule set that is made specific to each agent by the incorporation of parameters characterizing types of pedestrians is used. The rules originate from computer-aided analysis of video footage and are transformed into a form that can be efficiently processed by the agent. By adding tools to extract measures of pedestrian flow, the PEDFLOW model will be made useful to urban planners to evaluate infrastructural changes intended to promote walking in the urban environment.

MaTSE: the gene expression time-series explorer

BackgroundHigh throughput gene expression time-course experiments provide a perspective on biological functioning recognized as having huge value for the diagnosis, treatment, and prevention of diseases. There are however significant challenges to properly exploiting this data due to its massive scale and complexity. In particular, existing techniques are found to be ill suited to finding patterns of changing activity over a limited interval of an experiments time frame. The Time-Series Explorer (TSE) was developed to overcome this limitation by allowing users to explore their data by controlling an animated scatter-plot view. MaTSE improves and extends TSE by allowing users to visualize data with missing values, cross reference multiple conditions, highlight gene groupings, and collaborate by sharing their findings.ResultsMaTSE was developed using an iterative software development cycle that involved a high level of user feedback and evaluation. The resulting software combines a variety of visualization and interaction techniques which work together to allow biologists to explore their data and reveal temporal patterns of gene activity. These include a scatter-plot that can be animated to view different temporal intervals of the data, a multiple coordinated view framework to support the cross reference of multiple experimental conditions, a novel method for highlighting overlapping groups in the scatter-plot, and a pattern browser component that can be used with scatter-plot box queries to support cooperative visualization. A final evaluation demonstrated the tools effectiveness in allowing users to find unexpected temporal patterns and the benefits of functionality such as the overlay of gene groupings and the ability to store patterns.ConclusionsWe have developed a new exploratory analysis tool, MaTSE, that allows users to find unexpected patterns of temporal activity in gene expression time-series data. Overall, the study acted well to demonstrate the benefits of an iterative software development life cycle and allowed us to investigate some visualization problems that are likely to be common in the field of bioinformatics. The subjects involved in the final evaluation were positive about the potential of MaTSE to help them find unexpected patterns in their data and characterized MaTSE as an exploratory tool valuable for hypothesis generation and the creation of new biological knowledge.

Intelligent storage devices for scalable information management systems

Abstract For most large commercial organisations the ability to store and manipulate massive volumes of data is a key operational requirement. Database systems are fundamental to the efficient provision of a range of business tasks from on-line transaction processing, decision support and enterprise information systems. High performance multiprocessor database servers open up new possibilities for the realisation of these commercial requirements. If these opportunities are to be realised intelligent storage devices will be required to provide a uniform interface regardless of implementation and which also directly supports the basic need of scalability. In this paper we explore some of the issues for such a device.

Intelligent Storage Devices for Scalable Information Management Systems

For most large commercial organisations the ability to store and manipulate massive volumes of data is a key operational requirement. Database systems are now fundamental to the efficient provision of a range of business tasks from on-line transaction processing through to decision support and enterprise information systems. High performance multi-processor database servers open up new possibilities for the realisation of these commercial requirements. However, if these opportunities are to be realised some form of fundamental intelligent storage device will be required which provides a uniform interface regardless of implementation and which also directly supports the basic need of scalability. In this paper we explore some of the issues for such a device.

A Comparison of Video and Infrared Based Tracking of Pedestrian Movements

We provide a comparison of the relative merits of video and infrared based methods for collecting pedestrian movements from the real world and also from experimental environments. We describe the underlying technological basis of both methods and the tools we have developed to help in collection and analysis of the data. The desire to collect such data is driven by the need of modellers and simulation packages to use base data that is founded in valid empirical evidence, rather than some form of inspired supposition, as is the case with many of the current systems. In addition to the collection of speeds we are also interested in understanding and quantifying the ranges of distances people deviate from a straight-on path when confronted by some obstruction in front of them.