FM-Sim: A Hybrid Protocol Simulator of Fluorescence Microscopy Neuroscience Assays with Integrated Bayesian Inference

Donal Stewart; Michael Cousin; Stephen Gilmore

doi:10.1007/978-3-319-27656-4_10

FM-Sim: A Hybrid Protocol Simulator of Fluorescence Microscopy Neuroscience Assays with Integrated Bayesian Inference

Donal Stewart, Michael Cousin, Stephen Gilmore

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Abstract

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.

Original language	English
Title of host publication	Computational Methods in Systems Biology
Subtitle of host publication	12th International Conference, CMSB 2014, Manchester, UK, November 17-19, 2014, Proceedings
Publisher	Springer
Pages	248-251
Number of pages	4
ISBN (Electronic)	978-3-319-12982-2
ISBN (Print)	978-3-319-12981-5
DOIs	https://doi.org/10.1007/978-3-319-27656-4_10
Publication status	Published - 2014
Event	Third International Workshop on Hybrid Systems Biology - Vienna, Austria Duration: 23 Jul 2014 → 24 Jul 2014

Publication series

Name	Lecture Notes in Computer Science
Volume	8859
ISSN (Print)	0302-9743

Workshop

Workshop	Third International Workshop on Hybrid Systems Biology
Country/Territory	Austria
City	Vienna
Period	23/07/14 → 24/07/14

Access to Document

10.1007/978-3-319-27656-4_10

FM-Sim-LNCSAccepted author manuscript, 530 KB

http://link.springer.com/chapter/10.1007%2F978-3-319-12982-2_19

Systems Training in Maths, Informatics and Computational Biology (SySMIC)
Gilmore, S. (Principal Investigator)
BBSRC
1/01/12 → 31/12/16
Project: Research

Cite this

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 (pp. 248-251). (Lecture Notes in Computer Science; Vol. 8859). Springer. https://doi.org/10.1007/978-3-319-27656-4_10

Stewart, Donal ; Cousin, Michael ; Gilmore, Stephen. / FM-Sim: A Hybrid Protocol Simulator of Fluorescence Microscopy Neuroscience Assays with Integrated Bayesian Inference. Computational Methods in Systems Biology: 12th International Conference, CMSB 2014, Manchester, UK, November 17-19, 2014, Proceedings. Springer, 2014. pp. 248-251 (Lecture Notes in Computer Science).

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title = "FM-Sim: A Hybrid Protocol Simulator of Fluorescence Microscopy Neuroscience Assays with Integrated Bayesian Inference",

abstract = "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.",

author = "Donal Stewart and Michael Cousin and Stephen Gilmore",

year = "2014",

doi = "10.1007/978-3-319-27656-4_10",

language = "English",

isbn = "978-3-319-12981-5",

series = "Lecture Notes in Computer Science",

publisher = "Springer",

pages = "248--251",

booktitle = "Computational Methods in Systems Biology",

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note = "Third International Workshop on Hybrid Systems Biology ; Conference date: 23-07-2014 Through 24-07-2014",

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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, pp. 248-251, Third International Workshop on Hybrid Systems Biology , Vienna, Austria, 23/07/14. https://doi.org/10.1007/978-3-319-27656-4_10

FM-Sim: A Hybrid Protocol Simulator of Fluorescence Microscopy Neuroscience Assays with Integrated Bayesian Inference. / Stewart, Donal; Cousin, Michael ; Gilmore, Stephen.
Computational Methods in Systems Biology: 12th International Conference, CMSB 2014, Manchester, UK, November 17-19, 2014, Proceedings. Springer, 2014. p. 248-251 (Lecture Notes in Computer Science; Vol. 8859).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

TY - GEN

T1 - FM-Sim: A Hybrid Protocol Simulator of Fluorescence Microscopy Neuroscience Assays with Integrated Bayesian Inference

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N2 - 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.

AB - 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.

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SN - 978-3-319-12981-5

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BT - Computational Methods in Systems Biology

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Stewart D, Cousin M , Gilmore S. 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. Springer. 2014. p. 248-251. (Lecture Notes in Computer Science). doi: 10.1007/978-3-319-27656-4_10

FM-Sim: A Hybrid Protocol Simulator of Fluorescence Microscopy Neuroscience Assays with Integrated Bayesian Inference

Abstract

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Systems Training in Maths, Informatics and Computational Biology (SySMIC)

Cite this