{"created":"2025-01-18T22:50:57.699410+00:00","updated":"2025-01-22T22:56:59.955203+00:00","metadata":{"_oai":{"id":"oai:ipsj.ixsq.nii.ac.jp:00018153","sets":["934:1119:1120:1121"]},"path":["1121"],"owner":"1","recid":"18153","title":["FPGAを用いた高スループット確率モデル生化学シミュレータの設計と評価"],"pubdate":{"attribute_name":"公開日","attribute_value":"2008-12-22"},"_buckets":{"deposit":"cbeb3629-5258-4017-990a-8b70bc42318f"},"_deposit":{"id":"18153","pid":{"type":"depid","value":"18153","revision_id":0},"owners":[1],"status":"published","created_by":1},"item_title":"FPGAを用いた高スループット確率モデル生化学シミュレータの設計と評価","author_link":["0","0"],"item_titles":{"attribute_name":"タイトル","attribute_value_mlt":[{"subitem_title":"FPGAを用いた高スループット確率モデル生化学シミュレータの設計と評価"},{"subitem_title":"Design and Evaluation of an FPGA-based Stochastic Biochemical Simulator for High-throughput Execution","subitem_title_language":"en"}]},"item_keyword":{"attribute_name":"キーワード","attribute_value_mlt":[{"subitem_subject":"専用システム","subitem_subject_scheme":"Other"}]},"item_type_id":"3","publish_date":"2008-12-22","item_3_text_3":{"attribute_name":"著者所属","attribute_value_mlt":[{"subitem_text_value":"慶應義塾大学大学院理工学研究科"},{"subitem_text_value":"慶應義塾大学大学院理工学研究科"},{"subitem_text_value":"成蹊大学理工学部情報科学科"},{"subitem_text_value":"慶應義塾大学大学院理工学研究科"},{"subitem_text_value":"European Molecular Biology Laboratory  European Bioinformatics Institute  Wellcome Trust Genome Campus"},{"subitem_text_value":"長崎大学工学部情報システム工学科"},{"subitem_text_value":"長崎大学工学部情報システム工学科"},{"subitem_text_value":"科学技術振興機構北野共生システムプロジェクト"},{"subitem_text_value":"慶應義塾大学大学院理工学研究科"}]},"item_3_text_4":{"attribute_name":"著者所属(英)","attribute_value_mlt":[{"subitem_text_value":"Graduate School of Science and Technology, Keio University","subitem_text_language":"en"},{"subitem_text_value":"Graduate School of Science and Technology, Keio University","subitem_text_language":"en"},{"subitem_text_value":"Faculty of Science and Technology, Seikei University","subitem_text_language":"en"},{"subitem_text_value":"Graduate School of Science and Technology, Keio University","subitem_text_language":"en"},{"subitem_text_value":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus","subitem_text_language":"en"},{"subitem_text_value":"Department of Computer and Information Sciences, Nagasaki University","subitem_text_language":"en"},{"subitem_text_value":"Department of Computer and Information Sciences, Nagasaki University","subitem_text_language":"en"},{"subitem_text_value":"Kitano Symbiotic Systems Project, ERATO-SORST, Japan Science and Technology Agency","subitem_text_language":"en"},{"subitem_text_value":"Graduate School of Science and Technology, Keio University","subitem_text_language":"en"}]},"item_language":{"attribute_name":"言語","attribute_value_mlt":[{"subitem_language":"jpn"}]},"item_publisher":{"attribute_name":"出版者","attribute_value_mlt":[{"subitem_publisher":"情報処理学会","subitem_publisher_language":"ja"}]},"publish_status":"0","weko_shared_id":-1,"item_file_price":{"attribute_name":"Billing file","attribute_type":"file","attribute_value_mlt":[{"url":{"url":"https://ipsj.ixsq.nii.ac.jp/record/18153/files/IPSJ-TACS0103011.pdf"},"date":[{"dateType":"Available","dateValue":"2010-12-22"}],"format":"application/pdf","billing":["billing_file"],"filename":"IPSJ-TACS0103011.pdf","filesize":[{"value":"2.3 MB"}],"mimetype":"application/pdf","priceinfo":[{"tax":["include_tax"],"price":"660","billingrole":"5"},{"tax":["include_tax"],"price":"330","billingrole":"6"},{"tax":["include_tax"],"price":"0","billingrole":"16"},{"tax":["include_tax"],"price":"0","billingrole":"11"},{"tax":["include_tax"],"price":"0","billingrole":"14"},{"tax":["include_tax"],"price":"0","billingrole":"15"},{"tax":["include_tax"],"price":"0","billingrole":"44"}],"accessrole":"open_date","version_id":"34eab4b9-c396-4d87-90f6-16b0635c2c9c","displaytype":"detail","licensetype":"license_note","license_note":"Copyright (c) 2008 by the Information Processing Society of Japan"}]},"item_3_creator_5":{"attribute_name":"著者名","attribute_type":"creator","attribute_value_mlt":[{"creatorNames":[{"creatorName":"吉見, 真聡"},{"creatorName":"西川, 由理"},{"creatorName":"長名, 保範"},{"creatorName":"舟橋, 啓"},{"creatorName":"広井, 賀子"},{"creatorName":"柴田, 裕一郎"},{"creatorName":"山田, 英樹"},{"creatorName":"北野, 宏明"},{"creatorName":"天野, 英晴"}],"nameIdentifiers":[{}]}]},"item_3_creator_6":{"attribute_name":"著者名(英)","attribute_type":"creator","attribute_value_mlt":[{"creatorNames":[{"creatorName":"Masato, Yoshimi","creatorNameLang":"en"},{"creatorName":"Yuri, Nishikawa","creatorNameLang":"en"},{"creatorName":"Yasunori, Osana","creatorNameLang":"en"},{"creatorName":"Akira, Funahashi","creatorNameLang":"en"},{"creatorName":"Noriko, Hiroi","creatorNameLang":"en"},{"creatorName":"Yuichiro, Shibata","creatorNameLang":"en"},{"creatorName":"Hideki, Yamada","creatorNameLang":"en"},{"creatorName":"Hiroaki, Kitano","creatorNameLang":"en"},{"creatorName":"Hideharu, Amano","creatorNameLang":"en"}],"nameIdentifiers":[{}]}]},"item_3_source_id_9":{"attribute_name":"書誌レコードID","attribute_value_mlt":[{"subitem_source_identifier":"AA11833852","subitem_source_identifier_type":"NCID"}]},"item_resource_type":{"attribute_name":"資源タイプ","attribute_value_mlt":[{"resourceuri":"http://purl.org/coar/resource_type/c_6501","resourcetype":"journal article"}]},"item_3_source_id_11":{"attribute_name":"ISSN","attribute_value_mlt":[{"subitem_source_identifier":"1882-7829","subitem_source_identifier_type":"ISSN"}]},"item_3_description_7":{"attribute_name":"論文抄録","attribute_value_mlt":[{"subitem_description":"確率モデル生化学シミュレーションアルゴリズム（SSA）は，生化学モデルの確率的挙動を厳密に計算できる手法として知られている．しかしその一方で，SSAを用いてモデルを評価するためには，膨大な回数の演算が繰り返されるので，高スループットな実行環境が求められている．本論文では，FPGAを用いて計算効率の良いSSAであるNext Reaction Method（NRM）を高スループットに実行するハードウェアの構造について述べ，性能評価を行う．このハードウェアは，シミュレーションスレッドの状態を保持するスレッドモジュールが，データ転送網を介して算術演算器やデータメモリを共有する構造を持ち，マルチスレッド実行を行う．また，モジュール間の接続を変更することで，特定のFPGAに限定されない構成の変更が可能である．ミドルレンジのFPGA上に構成することを想定して16スレッドの並列実行を行うハードウェアを実装し，評価用によく利用されるHSRモデルによるRTLシミュレーションを通してスループットを計測した結果，Core 2 Quad Q6600 2.40 GHzのシングルスレッド実行と比べて約4.2倍，HSRを並べて作成した反応数の多い仮想のモデルでは約5.4倍のスループットの向上が可能であることを確認した．","subitem_description_type":"Other"}]},"item_3_description_8":{"attribute_name":"論文抄録(英)","attribute_value_mlt":[{"subitem_description":"Stochastic biochemical simulation algorithms (SSAs) are generally known as exact methods to trace stochastic behaviors of target biochemical models. Due to vast amount of computation attributed to the nature of Monte Carlo Method, which SSAs are originated from, there is a strong urge for high-throughput execution environment. This paper proposes an FPGA implementation of a stochastic simulation system based on a computationally-efficient SSA called the Next Reaction Method, and studies the evaluation results of area and throughput in detail. The system conducts high-throughput multi-thread execution, using multiple thread modules accessing shared arithmetic and data modules. The network between modules are configurable, and supports flexible network structure according to target FPGAs. In order to evaluate the proposed design, the stochastic simulation system, which is capable of running 16 threads in parallel, was implemented on a middle-range FPGA. As the result of comparing the throughput in RTL simulation with software simulation run on Core 2 Quad Q6600, the system marked 4.2 times higher throughput using a real biochemical model called HSR. When several versions of virtually largescale models were tested on the same simulation environment, maximum of 5.4 times higher throughput was confirmed.","subitem_description_type":"Other"}]},"item_3_biblio_info_10":{"attribute_name":"書誌情報","attribute_value_mlt":[{"bibliographicPageEnd":"135","bibliographic_titles":[{"bibliographic_title":"情報処理学会論文誌コンピューティングシステム（ACS）"}],"bibliographicPageStart":"120","bibliographicIssueDates":{"bibliographicIssueDate":"2008-12-22","bibliographicIssueDateType":"Issued"},"bibliographicIssueNumber":"3","bibliographicVolumeNumber":"1"}]},"relation_version_is_last":true,"weko_creator_id":"1"},"id":18153,"links":{}}