hosted by
publicationslist.org    
Kieran O'Neill    - research student - 




 kierano [rollmop] gmail [period] com










Kieran O'Neill is a Masters student studying at the University of KwaZulu-Natal in Pietermaritzburg, South Africa. For the majority of his masters, he has been funded by and worked with the central node of the National Bioinformatics Network, based in Cape Town. 

Kieran's background is primarily in computer science, although he has a second undergraduate major in biochemistry. Kieran's research interests lie in the field of bioinformatics, most recently in bio-ontologies, information integration and the application of HCI to bioinformatics, including participatory design and information visualisation. For his Masters project, Kieran has developed OntoDas, a tool for visually supporting the construction of ontology-based biological queries.

From September to December 2007, Kieran will be embarking on a student internship at the EBI, where he will work further on OntoDas, integrating it more with the ontology lookup service, and with the new DAS ontology.

							 

































Conference papers




2007















 

K M O’Neill,  A  Garcia-Castro,  D  Jacobson    (2007)   Knowledge Driven User Interfaces for Complex Biological Queries   In: Proceedings of the First Southern African Bioinformatics Workshop   Edited by:, S Hazelhurst, M Ramsay.      Johannesburg, South Africa:     
Abstract: With the explosion of biological data in the postgenomic era, there has been a growing need for semantic data integration, supported
by ontologies. Semantic integration techniques enable biologists to construct complex biological queries. However, the construction
of these queries and analysis of their results can place a high cognitive load on biologists. This paper presents a proposed information
visualisation tool, Digr, to aid biologists in these processes within the context of DigraBase, a graph database for semantic data
integration. A working example of a query is presented, to illustrate the complexity of the information spaces under consideration.
Visualisation techniques that have been applied to similar problems are discussed in the context of their applicability to the problem
of aiding the construction of complex queries over DigraBase, and the interpretation of their results.
 
Notes: 






Honours Dissertation




2004





 

Kieran  O'Neill    (2004)   Creation of an Extensible Environment for the Investigation of Genetic Algorithmic Solutions to 3D Cubic Lattice Protein Folding    [Honours Dissertation]    
Abstract: An environment for running and exploring a genetic algorithmic solution to the folding of HP lattice
proteins on the 3D cubic lattice was developed. The genetic algorithm created did not perform
competively with comparable algorithms cited in the literature. However, the environment proved
useful for exploring the functioning of genetic algorithms, as applied to this problem. The program
is also highly extensible, and can be used in the future as a basis for algorithm development and
testing.
 
Notes: 






Masters theses




2008





 

Kieran  O'Neill    (2008)   Relieving the Cognitive Load of Constructing Molecular Biological Ontology Based Queries by means of Visual Aids   University of KwaZulu-Natal    Pietermaritzburg:    
Abstract: The domain of molecular biology is complex and vast. Bio-ontologies and information visualisation have arisen in recent years as means to assist biologists in making sense of this information. Ontologies can enable the construction of conceptual queries, but existing systems to do this are too technical for most biologists. OntoDas, the software developed as part of this thesis work, demonstrates how the application of techniques from information visualisation and human computer interaction can result in software which enables biologists to construct conceptual queries.
 
Notes: 











 







     
     



















    


  Powered by publicationslist.org.