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Wawan Setiawan
Universitas Pendidikan Indonesia
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Journal : Perfecting a Video Game with Game Metrics

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Parallel random projection using R high performance computing for planted motif search Lala Septem Riza; Tyas Farrah Dhiba; Wawan Setiawan; Topik Hidayat; Mahmoud Fahsi
TELKOMNIKA (Telecommunication Computing Electronics and Control) Vol 17, No 3: June 2019
Publisher : Universitas Ahmad Dahlan

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.12928/telkomnika.v17i3.11750

Abstract

Motif discovery in DNA sequences is one of the most important issues in bioinformatics. Thus, algorithms for dealing with the problem accurately and quickly have always been the goal of research in bioinformatics. Therefore, this study is intended to modify the random projection algorithm to be implemented on R high performance computing (i.e., the R package pbdMPI). Some steps are needed to achieve this objective, ie preprocessing data, splitting data according to number of batches, modifying and implementing random projection in the pbdMPI package, and then aggregating the results. To validate the proposed approach, some experiments have been conducted. Several benchmarking data were used in this study by sensitivity analysis on number of cores and batches. Experimental results show that computational cost can be reduced, which is that the computation cost of 6 cores is faster around 34 times compared with the standalone mode. Thus, the proposed approach can be used for motif discovery effectively and efficiently.
Co-Authors A. Suhandi Acep Aris Mubarok Achmad Samsudin Ade Gafar Abdullah, Ade Gafar Agi Firmansyah Agi Firmansyah Agus Setiawan Aim Abdulkarim Alivermana Wiguna Alvon Fadilah Andi Suhandi Andi Suhandi Anna Permanasari Any Fitriani Anzir Tanjung Ari Widodo Arifah Rahayu ariman ariman Asep Sigit Pranamulya Aulia Iskandarsyah Bahar Nugraha Praja Desmala Sari Diana Safitri Didik Priyandoko Effendy Effendy Eka Fitrajaya Rahman Eki Nugraha Elya Hartini Enjun Junaeti Erlangga, Erlangga Evi Novianti Fariati Fariati Fatimah Setiani Fitri Kurniati Fransisca Sudargo Tapilouw Hana Lestari Heni Safitri Herbert Siregar HERNANI - Herry Sofyan Ida Hamidah IDA HODIYAH Ida Kaniawati Ismail Ismail Juwairiah Juwairiah Kadek Dwi Hendratma Gunawan Kadek Dwi Hendratma Gunawan Kama Abdulhakam Ketut Gunawan KL Putri Kurniawan, Iwan Setia L Liliasari Lala Septem Riza Liliasari Liliasari , Liliasari Liliasari Mahmoud Fahsi Masrifah, Masrifah Nana Supriatna Nia Nurdiani Niken Vioreza Nirsetyo Wahdi Nuryani Rustaman Octavianus Lumban Tobing Oding Syafruddin Syafruddin P Sinaga Parlindungan Sinaga Parlindungan Sinaga Parlindungan Sinaga Parlindungan Sinaga Parsaoran Siaahan Parsaoran Siahaan Puspo Dewi Dirgantari Putut Sri Wijayanto Raden Ahmad Hadian Adhy Permana* Rahmat Rizal Restu Rinda Wijaya Ridwan Siskandar Rosmiati Rosmiati Rossy Rossy Agustriyanda Safitri, Koko Satriawan, Muhammad Siti Sriyati Sri Anggraeni Sugianto Sugianto TATI NURHAYATI Thoha Firdaus Topik Hidayat Tri Endro Pranowo Tyas Farrah Dhiba Ute Lies Khadijah Vioreza, Niken Wahyuni Handayani Wibisono, Yudi Wihardi, Yaya Willyanto Kartiko Kusumo Wiweka Wiweka Yudhitiya Dyah Sukmadewi, Yudhitiya Dyah Yulianti Yusal Yulianti Yusal Yulina, Indah Karina Yulison Herry Chrisnanto Yunina Surtiana Yunina Surtiana