Clotho: addressing the scalability of forward time population genetic simulation

BMC Bioinformatics

Ge Zhang²  Philip A. Wilsey¹  Patrick P. Putnam¹ 

[1]Department of Electrical Engineering and Computing Systems, University of Cincinnati, PO Box 210030, Cincinnati 45221–0030, OH, USA

[2]Human Genetics, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Ave, Cincinnati 45229–3026, OH, USA

关键词: Scalability;    Sequence representation;    Data structures;    Population genetic simulation;   

Others  :  1232177
DOI  :  10.1186/s12859-015-0631-z

 received in 2014-12-31, accepted in 2015-05-29,  发布年份 2015

【 摘 要 】

Background

Forward Time Population Genetic Simulations offer a flexible framework for modeling the various evolutionary processes occurring in nature. Often this model expressibility is countered by an increased memory usage or computational overhead. With the complexity of simulation scenarios continuing to increase, addressing the scalability of the underlying simulation framework is a growing consideration.

Results

We propose a general method for representing in silico genetic sequences using implicit data structures. We provide a generalized implementation as a C++ template library called Clotho. We compare the performance and scalability of our approach with those taken in other simulation frameworks, namely: FWDPP and simuPOP.

Conclusions

We show that this technique offers a 4x reduction in memory utilization. Additionally, with larger scale simulation scenarios we are able to offer a speedup of 6x - 46x.

【 授权许可】

   
2015 Putnam et al.; licensee BioMed Central.

【 图 表 】

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