Linked Life Data

20056731

Source:http://linkedlifedata.com/resource/pubmed/id/20056731

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
3
pubmed:dateCreated
2010-5-18
pubmed:abstractText
Dynamic simulation modelling of complex biological processes forms the backbone of systems biology. Discrete stochastic models are particularly appropriate for describing sub-cellular molecular interactions, especially when critical molecular species are thought to be present at low copy-numbers. For example, these stochastic effects play an important role in models of human ageing, where ageing results from the long-term accumulation of random damage at various biological scales. Unfortunately, realistic stochastic simulation of discrete biological processes is highly computationally intensive, requiring specialist hardware, and can benefit greatly from parallel and distributed approaches to computation and analysis. For these reasons, we have developed the BASIS system for the simulation and storage of stochastic SBML models together with associated simulation results. This system is exposed as a set of web services to allow users to incorporate its simulation tools into their workflows. Parameter inference for stochastic models is also difficult and computationally expensive. The CaliBayes system provides a set of web services (together with an R package for consuming these and formatting data) which addresses this problem for SBML models. It uses a sequential Bayesian MCMC method, which is powerful and flexible, providing very rich information. However this approach is exceptionally computationally intensive and requires the use of a carefully designed architecture. Again, these tools are exposed as web services to allow users to take advantage of this system. In this article, we describe these two systems and demonstrate their integrated use with an example workflow to estimate the parameters of a simple model of Saccharomyces cerevisiae growth on agar plates.
pubmed:grant
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:status
MEDLINE
pubmed:month
May
pubmed:issn
1477-4054
pubmed:author
pubmed:issnType
Electronic
pubmed:volume
11
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
278-89
pubmed:meshHeading
pubmed:year
2010
pubmed:articleTitle
CaliBayes and BASIS: integrated tools for the calibration, simulation and storage of biological simulation models.
pubmed:affiliation
Institute for Ageing and Health, Centre for Integrated Systems Biology of Ageing and Nutrition at Newcastle, UK.
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't