Genetic data simulators and their applications: an overview

Abstract

Computer simulations have played an indispensable role in the development and applications of statistical models and methods for genetic studies across multiple disciplines. The need to simulate complex evolutionary scenarios and pseudo-datasets for various studies has fueled the development of dozens of computer programs with varying reliability, performance, and application areas. To help researchers compare and choose the most appropriate simulators for their studies, we have created the genetic simulation resources (GSR) website, which allows authors of simulation software to register their applications and describe them with more than 160 defined attributes. This article summarizes the properties of 93 simulators currently registered at GSR and provides an overview of the development and applications of genetic simulators. Unlike other review articles that address technical issues or compare simulators for particular application areas, we focus on software development, maintenance, and features of simulators, often from a historical perspective. Publications that cite these simulators are used to summarize both the applications of genetic simulations and the utilization of simulators.

Keywords: genetic simulation; genetic simulation resources; software.

Figure 1

Number of simulators that simulate different types of genetic sequences at each year. X-axis: initial release of simulator. Y-axis: number of simulators. A package that simulates multiple types of sequences will be displayed in multiple groups.

Figure 2

Number of newly developed simulators that use different simulation approaches at each year. X-axis: initial release of simulator. Y-axis: number of simulators. A simulator that uses multiple simulation methods will be displayed in multiple groups, as well as the “multiple methods” group.

Figure 3

Number of evolutionary features provided by simulators using different simulation methods. Y-axis: number of features provided. X-axis: number of packages.

Figure 4

Distribution of publications by Discipline. Number of publications that cite the catalogued simulators in GSR in different disciplines as categorized by Web of Science.

Figure 5

Distribution of simulation methods for publications that cite 93 catalogued simulators, from year 1990 to 2013. We group simulators by the simulation methods they use and count the number of publications that cite simulators in each group. Articles that cite more than one simulator or a simulator using multiple methods will be counted multiple times.