Thomas Hunniford | Search PubMed

PubMed2005

Reverse-engineering gene-regulatory networks using evolutionary algorithms and grid computing.

OBJECTIVE: Living organisms regulate the expression of genes using complex interactions of transcription factors, messenger RNA and active protein products. Due to their complexity, gene-regulatory networks are not fully understood.However, by building computational models it is possible to gain insight into their function and operation. METHODS: Evolutionary algorithms are used to create computational models of gene-regulatory networks based on observed microarray data. These algorithms can be computationally intensive. They will be implemented within an existing grid computing infrastructure, that has been developed for data mining purposes, and which is able to deliver the required compute power. RESULTS: We discuss how models can built achieved using distributed and grid computing technology. In particular we investigate how Condor and JavaSpaces technology is suited to the requirements of our modeling approach. CONCLUSIONS: Determining network models of gene-regulatory networks using evolutionary algorithms not only requires considerable computational power, but also a modeling formalism that can explain the underlying dynamics.

Algorithms↗

PubMed2004

Assessment of disease severity (in terms of function) using the internet.

OBJECTIVE: To determine whether visual analog scales (VAS) can be used over the Internet to assess the patient with ankylosing spondylitis (AS) accurately or if the use of this different medium will affect the results. METHODS: Patients with AS (n = 50) attending a physiotherapy/educational course completed both an Internet based and a paper based version of the Bath Ankylosing Spondylitis Functional Index (BASFI) that uses VAS. The Internet version was completed twice to assess intrarespondent variation reliability and compared with the paper version to assess interrespondent variation reliability. Patients were also asked to assess ease of use and to suggest changes to the Internet version. RESULTS: The interclass coefficient of intra- and interrespondent reliability were 0.989 (p < 0.001) and 0.976 (p < 0.001), respectively. There was a 3% difference in assessments carried out over the Internet compared to those on paper and a 2% difference in repeatability of Internet assessed questionnaires. Bland and Altman plots showed a mean difference between paper compared to the Internet version was 0.0156 with 95% limits of agreement at -1.07 to 1.03. More than half the participants reported that the Internet version was easier to complete than the paper version (96% rated usability as 1 on a scale of 1-10, with 1 being extremely easy and 10 being impossible). CONCLUSION: Assessment of disease severity by VAS may be accurately carried out over the Internet. This means that the evaluation of disease status and the longterm followup of people in different countries and perhaps in different languages may now be possible, using the Internet.

Adult↗