Donal Stewart PhD

Donal Stewart


Research Interests

I am interested in computational modelling of molecular and membrane biological processes. My PhD project will involve comparative computational modelling of endocytosis mechanisms at the synaptic terminal to discover the potential reasons for conservation of multiple endocytosis mechanisms.

Publications:
2014
  FM-Sim: A Hybrid Protocol Simulator of Fluorescence Microscopy Neuroscience Assays with Integrated Bayesian Inference
Stewart, D, Cousin, M & Gilmore, S 2014, FM-Sim: A Hybrid Protocol Simulator of Fluorescence Microscopy Neuroscience Assays with Integrated Bayesian Inference. in Computational Methods in Systems Biology: 12th International Conference, CMSB 2014, Manchester, UK, November 17-19, 2014, Proceedings. Lecture Notes in Computer Science, vol. 8859, Springer International Publishing, pp. 248-251, Third International Workshop on Hybrid Systems Biology , Vienna, Austria, 23-24 July. DOI: 10.1007/978-3-319-27656-4_10
We present FM-Sim, a domain-specific simulator for defining and simulating fluorescence microscopy assays. Experimental protocols as performed in vitro may be defined in the simulator. The defined protocols then interact with a computational model of presynaptic behaviour in rodent central nervous system neurons, allowing simulation of fluorescent responses to varying stimuli. Rate parameters of the model may be obtained using Bayesian inference functions integrated into the simulator, given experimental fluorescence observations of the protocol performed in vitro as training data. These trained protocols allow for predictive in silico modelling of potential experimental outcomes prior to time-consuming and expensive in vitro studies.
General Information
Organisations: Laboratory for Foundations of Computer Science.
Authors: Stewart, Donal, Cousin, Michael & Gilmore, Stephen.
Number of pages: 4
Pages: 248-251
Publication Date: 2014
Publication Information
Category: Conference contribution
Original Language: English
DOIs: 10.1007/978-3-319-27656-4_10
  FM-Sim: Protocol Definition, Simulation and Rate Inference for Neuroscience Assays
Stewart, D, Gilmore, S & Cousin, MA 2014, FM-Sim: Protocol Definition, Simulation and Rate Inference for Neuroscience Assays. in Computational Methods in Systems Biology: 12th International Conference, CMSB 2014, Manchester, UK, November 17-19, 2014, Proceedings. vol. 8859, Lecture Notes in Computer Science, vol. 8859, Springer International Publishing, pp. 248-251. DOI: 10.1007/978-3-319-12982-2_19
Synaptic vesicle recycling at the presynaptic terminal of neurons is essential for the maintenance of neurotransmission at central synapses. Among the tools used to visualise the mechanics of this process is time-series fluorescence microscopy. Fluorescent dyes such as FM1-43, or engineered fluorescent versions of synaptic vesicle proteins such as pHluorins, have been employed to reveal different steps of this key process [3,7]. Predictive in silico modelling of potential experimental outcomes would be highly informative for these time consuming and expensive studies.
We present FM-Sim [9], user-friendly software for defining and simulating fluorescence microscopy experimental assays, with the following features: intuitive user definition of experimental protocols; automatic conversion of protocol definitions into time series rate value changes; domain-specific simulation model of a synaptic terminal; experimental data used for model parameter value inference; automatic Bayesian inference of parameter values [1,5] and reduction of inferred parameter set size for Bayesian inference.
General Information
Organisations: Centre for Integrative Physiology.
Authors: Stewart, Donal, Gilmore, Stephen & Cousin, Michael A..
Number of pages: 4
Pages: 248-251
Publication Date: 2014
Publication Information
Category: Conference contribution
Original Language: English
DOIs: 10.1007/978-3-319-12982-2_19

Projects:
Comparative computational modelling of endocytosis mechanisms at the pre-synaptic terminal (PhD)