Browsing by Author "Gordon, Paul M. K."
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- ItemOpen AccessBluejay 1.0: genome browsing and comparison with rich customization provision and dynamic resource linking(BioMed Central, 2008) Soh, Jung; Gordon, Paul M. K.; Taschuk, Morgan L.; Dong, Anguo; Ah-Seng, Andrew C.; Turinsky, Andrei L; Sensen, Christoph W.
- ItemOpen AccessEvaluation of Dynamic Time Warp Barycenter Averaging (DBA) for its Potential in Generating a Consensus Nanopore Signal for Genetic and Epigenetic Sequences(IEEE, 2018-07) Chan, Rachel; Gordon, Paul M. K.; Smith, Michael RichardEpigenetics is a chemical modification to DNA without changes in the base sequence. While it is known that epigenetic modifications have far reaching implications on how genes are expressed, it is difficult to identify what the modification is or where it can be found. A next-generation method of sequencing called nanopore sequencing may be the solution. Nanopore sequencing runs a voltage bias across the DNA sequence and outputs a unique electric response to each genetic unit. Epigenetic modifications may then be identified by their distinct electric response. In this paper we provide preliminary results of applying dynamic time warp Barycenter Averaging (DBA) to multiple noisy nanopore streams to generate a consensus signal that can be used to identify genetic sequences and their modifications. DBA convergence rates, time complexity, together with qualitative and quantitative metrics to compare the consensus signal with gold standards are evaluated.
- ItemOpen AccessA Pilot Study into the Usability of a Scientific Workflow Construction Tool(2007-07-24) Gordon, Paul M. K.; Sensen, Christoph W.We describe a recent pilot study into the usability of the scientific workflow creation and enactment tool called Taverna. Both programmers and non-programmers were used as subjects for a defined programming task. We used a combination of user observation and questionnaires to determine programming efficiency roadblocks in the tool. More generally, differences between the roadblocks encountered by programmers and nonprogrammers suggest that pilot studies are crucial to inform the proper evaluation of novice programming tools. The study also suggests that there is a high demand for reusable Life Sciences workflows, due to both their ability to facilitate human-human communication about data analysis, and their ability to simplify repetitive operations used by bench scientists. Most roadblocks to Taverna programming are interface related, but a more fundamental issue is related to data input and type enforcement. Despite UI issues, we discovered users willingness to re-use and modify workflows, which leads us to suggest that programs first be created in simpler tools as a stepping stone in end-user development for the Life Sciences.
- ItemOpen AccessSpatiotemporal integration of molecular and anatomical data in virtual reality using semantic mapping(Dove Medical Press, 2009-04-01) Soh, Jung; Turinsky, Andrei L.; Trinh, Quang M.; Chang, Jasmine; Sabhaney, Ajay; Dong, Xiaoli; Gordon, Paul M. K.; Janzen, Ryan P. W.; Hau, David; Xia, Jianguo; Wishart, David S.; Sensen, Christoph W.