FM-Sim: Protocol Definition, Simulation and Rate Inference for Neuroscience Assays
- 1.1k Downloads
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 , 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.
Unable to display preview. Download preview PDF.
- 2.Barrio, M., Burrage, K., Leier, A., Tian, T.: Oscillatory regulation of Hes1: discrete stochastic delay modelling and simulation. PLoS Computational Biology 2(9), e117 (2006)Google Scholar
- 3.Cousin, M.: Use of FM1-43 and Other Derivatives to Investigate Neuronal Function. In: Current Protocols in Neuroscience, pp. 2–6 (2008)Google Scholar
- 9.Stewart, D., Gilmore, S., Cousin, M.A.: FM-Sim : A hybrid protocol simulator of fluorescence microscopy neuroscience assays with integrated Bayesian inference. To be published in Proceedings Third International Workshop on Hybrid Systems Biology, Vienna, Austria (July 2014)Google Scholar