Temporal Multivariate Networks. (2014)
Book Chapter
Archambault, D., Abello, J., Kennedy, J., Kobourov, S., Ma, K.-L., Miksch, S., Muelder, C., & Telea, A. C. (2014). Temporal Multivariate Networks. In A. Kerren, H. Purchase, & M. Ward (Eds.), Multivariate Network Visualization (151-175). Springer-Verlag. https://doi.org/10.1007/978-3-319-06793-3_8

In this chapter, we define, characterize, and summarize the data and visualization techniques relating to temporal multivariate networks. Section 2.1.1 provides definitions and examples that characterize the networks we address in this chapter. We fu... Read More about Temporal Multivariate Networks..

Vesper: Visualising species archives (2014)
Journal Article
Graham, M., & Kennedy, J. (2014). Vesper: Visualising species archives. Ecological Informatics, 24, 132-147. https://doi.org/10.1016/j.ecoinf.2014.08.004

Vesper (Visual Exploration of SPEcies-referenced Repositories) is a tool that visualises Darwin Core Archive (DwC-A) datasets, and is aimed at reducing the amount of time and effort expended by biologists to ascertain the quality of data they are gen... Read More about Vesper: Visualising species archives.

VIPER: a visualisation tool for exploring inheritance inconsistencies in genotyped pedigrees (2012)
Journal Article
Paterson, T., Graham, M., Kennedy, J., & Law, A. (2012). VIPER: a visualisation tool for exploring inheritance inconsistencies in genotyped pedigrees. BMC Bioinformatics, 13(Suppl 8), S5. https://doi.org/10.1186/1471-2105-13-S8-S5

Pedigree genotype datasets are used for analysing genetic inheritance and to map genetic markers and traits. Such datasets consist of hundreds of related animals genotyped for thousands of genetic markers and invariably contain multiple errors in bot... Read More about VIPER: a visualisation tool for exploring inheritance inconsistencies in genotyped pedigrees.

A comparison of techniques for name matching (2012)
Journal Article
Peng, T., Li, L., & Kennedy, J. (2012). A comparison of techniques for name matching. GSTF journal on computing, 2,

Information explosion is a problem for everyone nowadays. It is a great challenge to all kinds of businesses to maintain high quality of data in their information applications, such as data integration, text and web mining, information retrieval, sea... Read More about A comparison of techniques for name matching.

MaTSE: The microarray time-series explorer (2012)
Presentation / Conference Contribution
Craig, P., Cannon, A., Kukla, R., & Kennedy, J. (2012, October). MaTSE: The microarray time-series explorer. Presented at 2012 IEEE Symposium on Biological Data Visualization (BioVis)

This paper describes the design, development and evaluation of the Microarray Time-Series Explorer (MaTSE), a novel information visualization application for the exploratory analysis of large scale microarray timeseries data. The software combines a... Read More about MaTSE: The microarray time-series explorer.

Form (2009)
Book Chapter
Kennedy, J., & Cannon, A. (2009). Form. In L. Liu, & M. T. Özsu (Eds.), Encyclopedia of Database Systems. Springer-Verlag

Refactoring data transforms in MaTSE for flexibility. (2009)
Presentation / Conference Contribution
Craig, P., & Kennedy, J. (2009, October). Refactoring data transforms in MaTSE for flexibility

In early prototypes of the Microarray Time-series Explorer
(MaTSE) data transforms were tightly coupled with visualisation components. While this allowed us to achieve our initial objective of developing the application to the level where we were ab... Read More about Refactoring data transforms in MaTSE for flexibility..

Re-architecting Visualizations to Java Swing. (2009)
Presentation / Conference Contribution
Graham, M., & Kennedy, J. (2009, October). Re-architecting Visualizations to Java Swing. Paper presented at REVISE: Refactoring Visualization from Experience, VizWeek Workshop

Standard Data Model Representation for Taxonomic Information (2006)
Journal Article
Kennedy, J., Hyam, R., Kukla, R., & Paterson, T. (2006). Standard Data Model Representation for Taxonomic Information. OMICS, 10(2), 220-230. https://doi.org/10.1089/omi.2006.10.220

The names used by biologists to label the observations they make are imprecise. This is an issue as workers increasingly seek to exploit data gathered from multiple, unrelated sources on line. Even when the international codes of nomenclature are fol... Read More about Standard Data Model Representation for Taxonomic Information.

Scientific names are ambiguous as identifiers for biological taxa: their context and definition are required for accurate data integration (2005)
Presentation / Conference Contribution
Kennedy, J., Kukla, R., & Paterson, T. (2005, July). Scientific names are ambiguous as identifiers for biological taxa: their context and definition are required for accurate data integration. Presented at Second International Workshop, DILS 2005, San Diego, CA, USA

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 defi... Read More about Scientific names are ambiguous as identifiers for biological taxa: their context and definition are required for accurate data integration.

Time-series Explorer: An Animated Information Visualisation for Microarray Time-course Data (2005)
Journal Article
Craig, P., Kennedy, J., & Cumming, A. (2005). Time-series Explorer: An Animated Information Visualisation for Microarray Time-course Data. BMC Bioinformatics, 6(Suppl 3), P8. https://doi.org/10.1186/1471-2105-6-S3-P8

Microarray technologies are a relatively new development that allow biologists to monitor the activity of thousands of genes (normally around 8,000) in parallel across multiple stages of a biological process. While this new perspective on biological... Read More about Time-series Explorer: An Animated Information Visualisation for Microarray Time-course Data.

Extending Taxonomic Visualisation to Incorporate Synonymy and Structural Markers (2005)
Journal Article
Graham, M., & Kennedy, J. (2005). Extending Taxonomic Visualisation to Incorporate Synonymy and Structural Markers. Information Visualization, 4(3), 206-223. https://doi.org/10.1057/palgrave.ivs.9500096

The visualisation of taxonomic hierarchies has evolved from indented lists of names to techniques that can display thousands of nodes and onto hundreds of thousands of nodes over multiple taxonomies. However, challenges remain within multiple hierarc... Read More about Extending Taxonomic Visualisation to Incorporate Synonymy and Structural Markers.

The Prometheus Description Model: an examination of the taxonomic description-building process and its representation (2005)
Journal Article
Pullan, M. R., Armstrong, K. E., Paterson, T., Cannon, A., Kennedy, J. B., Watson, M. F., McDonald, S. M., & Raguenaud, C. (2005). The Prometheus Description Model: an examination of the taxonomic description-building process and its representation. Taxon, 54(3), 751-765. https://doi.org/10.2307/25065431

A model for representing taxonomic descriptive data is presented. The model has been developed in response to the growing requirement for the global exchange of descriptive data. Meaningful exchange of data requires that data be represented in a form... Read More about The Prometheus Description Model: an examination of the taxonomic description-building process and its representation.

Animated interval scatter-plot views for the exploratory analysis of large scale microarray time-course data. (2005)
Journal Article
Craig, P., Kennedy, J., & Cumming, A. (2005). Animated interval scatter-plot views for the exploratory analysis of large scale microarray time-course data. Information Visualization, 4(3), 149-163. https://doi.org/10.1057/palgrave.ivs.9500101

Microarray technologies are a relatively new development that allow biologists to monitor the activity of thousands of genes (normally around 8,000) in parallel across multiple stages of a biological process. While this new perspective on biological... Read More about Animated interval scatter-plot views for the exploratory analysis of large scale microarray time-course data..

Coordinated parallel views for the exploratory analysis of microarray time-course data. (2005)
Presentation / Conference Contribution
Craig, P., Kennedy, J., & Cumming, A. (2005, July). Coordinated parallel views for the exploratory analysis of microarray time-course data. Presented at Third International Conference on Coordinated & Multiple Views in Exploratory Visualization

Microarray time-course data relate to the recorded activity of thousands of genes, in parallel, over multiple discrete points in time during a biological process. Existing techniques that attempt to support the exploratory analysis of this data rely... Read More about Coordinated parallel views for the exploratory analysis of microarray time-course data..

Exploring and examining assessment data via a matrix visualisation (2004)
Presentation / Conference Contribution
Graham, M., & Kennedy, J. (2004, May). Exploring and examining assessment data via a matrix visualisation. Presented at Proceedings of the working conference on Advanced visual interfaces - AVI '04, Gallipoli, Italy

OPAL (Online PArtner Lens) is an application designed to match project requirements with suitable teams and individuals, and as part of its matching process features an evaluation mechanism designed to elicit measures of trust between potential partn... Read More about Exploring and examining assessment data via a matrix visualisation.

A universal character model and ontology of defined terms for taxonomic description. (2004)
Presentation / Conference Contribution
Paterson, T., Kennedy, J., Pullan, M. R., Cannon, A., Armstrong, K. E., Watson, M. F., Raguenaud, C., McDonald, S. M., & Russell, G. (2004, March). A universal character model and ontology of defined terms for taxonomic description. Presented at Data Integration in the Life Sciences. First International Workshop, DILS 2004

Taxonomists classify biological specimens into groups (taxa) on the basis of similarities between their observed features (characters). The description of these characters is therefore central to taxonomy, but there is currently no agreed model, defi... Read More about A universal character model and ontology of defined terms for taxonomic description..

Coordinated graph and scatter-plot views for the visual exploration of microarray time-series data (2003)
Presentation / Conference Contribution
Craig, P., & Kennedy, J. (2003, October). Coordinated graph and scatter-plot views for the visual exploration of microarray time-series data. Presented at IEEE Symposium on Information Visualization 2003 (IEEE Cat. No.03TH8714), Seattle WA

Microarrays are a relatively new, high-throughput data acquisition technology for investigating biological phenomena at the micro-level. The product of microarray experiments is large-scale time-series data, which subject to proper analysis has the p... Read More about Coordinated graph and scatter-plot views for the visual exploration of microarray time-series data.

A methodology for composing well-defined character descriptions. (2003)
Report
Paterson, T., Cannon, A., Raguenaud, C., Russell, G., Armstrong, K. E., MacDonald, S. M., Pullan, M. R., Watson, M. F., & Kennedy, J. (2003). A methodology for composing well-defined character descriptions

Taxonomy has been described as “the science of documenting biodiversity”, which involves collecting, naming, describing, identifying and classifying specimens of organisms (Keogh, 1995). Descriptions are the fundamental information units used in the... Read More about A methodology for composing well-defined character descriptions..

Using curves to enhance parallel coordinate visualisations (2003)
Presentation / Conference Contribution
Graham, M., & Kennedy, J. (2003, July). Using curves to enhance parallel coordinate visualisations. Presented at Seventh International Conference on Information Visualization, 2003. IV 2003., London, UK

This paper introduces a number of refinements to the Parallel Coordinates visualisation metaphor for multi-dimensional data. Firstly, the traditional set of poly-lines are replaced with a collection of smooth curves across the attribute axes, allowin... Read More about Using curves to enhance parallel coordinate visualisations.