Omid Abbaszadeh, Ali Reza Khanteymoori* and Ali Azarpeyvand Pages 603 - 614 ( 12 )
System biology problems such as whole-genome network construction from large-scale gene expression data are sophisticated and time-consuming. Therefore, using sequential algorithms are not feasible to obtain a solution in an acceptable amount of time. Today, by using massively parallel computing, it is possible to infer large-scale gene regulatory networks. Recently, establishing gene regulatory networks from large-scale datasets have drawn the noticeable attention of researchers in the field of parallel computing and system biology. In this paper, we attempt to provide a more detailed overview of the recent parallel algorithms for constructing gene regulatory networks. Firstly, fundamentals of gene regulatory networks inference and large-scale datasets challenges are given. Secondly, a detailed description of the four parallel frameworks and libraries including CUDA, OpenMP, MPI, and Hadoop is discussed. Thirdly, parallel algorithms are reviewed. Finally, some conclusions and guidelines for parallel reverse engineering are described.
Gene regulatory network, Parallel algorithms, Parallel processing, Reverse engineering, CUDA, OpenMP, MPI, Hadoop.
Department of Electrical and Computer Engineering, University of Zanjan, Zanjan, Department of Electrical and Computer Engineering, University of Zanjan, Zanjan, Department of Electrical and Computer Engineering, University of Zanjan, Zanjan