Predicting the effects of parameters changes in stochastic models through parallel synthetic experiments and multivariate analysis

Michele Forlin, Tommaso Mazza, Davide Prandi

Research output: Chapter in Book/Report/Conference proceedingConference contribution

3 Citations (Scopus)

Abstract

Usually researchers require many experiments to verify how biological systems respond to stimuli. However, the high cost of reagents and facilities as well as the time required to carry out experiments are sometimes the main cause of failure. In this regards, Information Technology offers a valuable help: modeling and simulation are mathematical tools to execute virtual experiments on computing devices. Through synthetic experimentation, researchers can sample the parameters space of a biological system and obtain hundreds of potential results, ready to be reused to design and conduct more targeted wet-lab experiments. A non negligible achievement of this is the enormous saving of resources and time. In this paper, we present a plug-in-based software prototype that combines high performance computing and statistics. Our framework relies on parallel computing to run large numbers of synthetic experiments. Multivariate analysis is then used to interpret and validate results. The software is tested on two well-known oscillatory models: Predator-Prey (Lotka-Volterra) and Repressilator.

Original languageEnglish
Title of host publicationProceedings of the 9th Int. Workshop on Parallel and Distributed Methods in Verification, PDMC 2010 - Joint with the 2nd Int. Workshop on High Performance Computational Systems Biology, HiBi 2010
Pages105-115
Number of pages11
DOIs
Publication statusPublished - 2010
Event9th International Workshop on Parallel and Distributed Methods in Verification, PDMC 2010 - Joint with the 2nd International Workshop on High-Performance Computational Systems Biology, HiBi 2010 - Enschede, Netherlands
Duration: Sep 30 2010Oct 1 2010

Other

Other9th International Workshop on Parallel and Distributed Methods in Verification, PDMC 2010 - Joint with the 2nd International Workshop on High-Performance Computational Systems Biology, HiBi 2010
CountryNetherlands
CityEnschede
Period9/30/1010/1/10

Fingerprint

Stochastic models
Software
Multivariate Analysis
Computing Methodologies
Research Personnel
Biological systems
Experiments
Technology
Costs and Cost Analysis
Equipment and Supplies
Parallel processing systems
Information technology
Statistics
Costs

ASJC Scopus subject areas

  • Computational Theory and Mathematics
  • Biochemistry, Genetics and Molecular Biology (miscellaneous)

Cite this

Forlin, M., Mazza, T., & Prandi, D. (2010). Predicting the effects of parameters changes in stochastic models through parallel synthetic experiments and multivariate analysis. In Proceedings of the 9th Int. Workshop on Parallel and Distributed Methods in Verification, PDMC 2010 - Joint with the 2nd Int. Workshop on High Performance Computational Systems Biology, HiBi 2010 (pp. 105-115). [5698476] https://doi.org/10.1109/PDMC-HiBi.2010.22

Predicting the effects of parameters changes in stochastic models through parallel synthetic experiments and multivariate analysis. / Forlin, Michele; Mazza, Tommaso; Prandi, Davide.

Proceedings of the 9th Int. Workshop on Parallel and Distributed Methods in Verification, PDMC 2010 - Joint with the 2nd Int. Workshop on High Performance Computational Systems Biology, HiBi 2010. 2010. p. 105-115 5698476.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Forlin, M, Mazza, T & Prandi, D 2010, Predicting the effects of parameters changes in stochastic models through parallel synthetic experiments and multivariate analysis. in Proceedings of the 9th Int. Workshop on Parallel and Distributed Methods in Verification, PDMC 2010 - Joint with the 2nd Int. Workshop on High Performance Computational Systems Biology, HiBi 2010., 5698476, pp. 105-115, 9th International Workshop on Parallel and Distributed Methods in Verification, PDMC 2010 - Joint with the 2nd International Workshop on High-Performance Computational Systems Biology, HiBi 2010, Enschede, Netherlands, 9/30/10. https://doi.org/10.1109/PDMC-HiBi.2010.22
Forlin M, Mazza T, Prandi D. Predicting the effects of parameters changes in stochastic models through parallel synthetic experiments and multivariate analysis. In Proceedings of the 9th Int. Workshop on Parallel and Distributed Methods in Verification, PDMC 2010 - Joint with the 2nd Int. Workshop on High Performance Computational Systems Biology, HiBi 2010. 2010. p. 105-115. 5698476 https://doi.org/10.1109/PDMC-HiBi.2010.22
Forlin, Michele ; Mazza, Tommaso ; Prandi, Davide. / Predicting the effects of parameters changes in stochastic models through parallel synthetic experiments and multivariate analysis. Proceedings of the 9th Int. Workshop on Parallel and Distributed Methods in Verification, PDMC 2010 - Joint with the 2nd Int. Workshop on High Performance Computational Systems Biology, HiBi 2010. 2010. pp. 105-115
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