title: SimBA: simulation algorithm to fit extant-population distributions.
abstract: BACKGROUND
  Simulation of populations with specified characteristics such as allele frequencies, linkage disequilibrium etc., is an integral component of many studies, including in-silico breeding optimization. Since the accuracy and sensitivity of population simulation is critical to the quality of the output of the applications that use them, accurate algorithms are required to provide a strong foundation to the methods in these studies.
  
  
  RESULTS
  In this paper we present SimBA (Simulation using Best-fit Algorithm) a non-generative approach, based on a combination of stochastic techniques and discrete methods. We optimize a hill climbing algorithm and extend the framework to include multiple subpopulation structures. Additionally, we show that SimBA is very sensitive to the input specifications, i.e., very similar but distinct input characteristics result in distinct outputs with high fidelity to the specified distributions. This property of the simulation is not explicitly modeled or studied by previous methods.
  
  
  CONCLUSIONS
  We show that SimBA outperforms the existing population simulation methods, both in terms of accuracy as well as time-efficiency. Not only does it construct populations that meet the input specifications more stringently than other published methods, SimBA is also easy to use. It does not require explicit parameter adaptations or calibrations. Also, it can work with input specified as distributions, without an exemplar matrix or population as required by some methods. SimBA is available at http://researcher.ibm.com/project/5669 .
authors.affiliation: Computational Biology Center, IBM T. J. Watson Research, Yorktown Heights, NY, USA. parida@us.ibm.com.
authors.forename: Laxmi
authors.initials: L
authors.lastname: Parida
authors.affiliation: Computational Biology Center, IBM T. J. Watson Research, Yorktown Heights, NY, USA. nshaimin@us.ibm.com.
authors.forename: Niina
authors.initials: N
authors.lastname: Haiminen
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D003247:Conservation of Natural Resources; D005787:Gene Frequency; D005828:Genetics, Population; D006801:Humans; D015810:Linkage Disequilibrium; D008962:Models, Theoretical; D011157:Population Dynamics