Riza, Lala, Nurfathiya, Muhammad, Kusnendar, Jajang, Abu Samah, Khyrina. (1400). DNA barcoding using particle swarm optimization on apache spark SQL case study: DNA of covid-19. هنرهای کاربردی, 12(Special Issue), 1561-1572. doi: 10.22075/ijnaa.2021.5812
Lala Septem Riza; Muhammad Ilham Nurfathiya; Jajang Kusnendar; Khyrina Airin Fariza Abu Samah. "DNA barcoding using particle swarm optimization on apache spark SQL case study: DNA of covid-19". هنرهای کاربردی, 12, Special Issue, 1400, 1561-1572. doi: 10.22075/ijnaa.2021.5812
Riza, Lala, Nurfathiya, Muhammad, Kusnendar, Jajang, Abu Samah, Khyrina. (1400). 'DNA barcoding using particle swarm optimization on apache spark SQL case study: DNA of covid-19', هنرهای کاربردی, 12(Special Issue), pp. 1561-1572. doi: 10.22075/ijnaa.2021.5812
Riza, Lala, Nurfathiya, Muhammad, Kusnendar, Jajang, Abu Samah, Khyrina. DNA barcoding using particle swarm optimization on apache spark SQL case study: DNA of covid-19. هنرهای کاربردی, 1400; 12(Special Issue): 1561-1572. doi: 10.22075/ijnaa.2021.5812

DNA barcoding using particle swarm optimization on apache spark SQL case study: DNA of covid-19

International Journal of Nonlinear Analysis and Applications
دوره 12، Special Issue، اسفند 2021، صفحه 1561-1572    اصل مقاله (611.8 K)
نوع مقاله: Research Paper
شناسه دیجیتال (DOI): 10.22075/ijnaa.2021.5812
نویسندگان
Lala Septem Riza* 1؛ Muhammad Ilham Nurfathiya1؛ Jajang Kusnendar1؛ Khyrina Airin Fariza Abu Samah2
1Department of Computer Science Education, Universitas Pendidikan Indonesia, Indonesia
2Faculty of Computer and Mathematical Sciences, University Teknologi MARA Cawangan Melaka Kampus Jasin, Melaka, Malaysia
چکیده
The objective of this research is to design and implement a computational model to determine DNA barcodes by utilizing the Particle Swarm Optimization (PSO) algorithms implemented on Big Data Platforms, namely Apache Hadoop and Apache Spark. The steps are as follows: (i) inputting DNA sequences to Hadoop Distributed File System (HDFS) in Apache Hadoop, (ii) pre-processing data, (iii) implementing PSO by utilizing the User Defined Function (UDF) in Apache Spark, (iv) collecting results and saving to HDFS. After obtaining the computational model, two following simulations have been done: the first scenario is using 4 cores and several worker nodes, meanwhile, the second one consists of a cluster with 2 worker nodes and several cores. In terms of computational time, the results show a significant acceleration between standalone and big data platforms with both experimental scenarios. This study proves that the computational model built on the big data platform shows the development of features and acceleration of previous research.
کلیدواژه‌ها
Big data؛ Algorithm؛ Particle swarm optimization؛ Similarity check؛ Motif discovery؛ DNA barcoding
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