FY2021 Annual Report

Integrated Open Systems Unit
Professor Hiroaki Kitano



In the Integrated Open Systems Unit, we conduct research and development focusing on the microbiome as the first initiative under our research theme of "AI for Scientific Discovery." We aim to build a new research experimentation and analysis platform that accelerates scientific discovery by fusing robotics and AI technology in the field of microbiome research. In 2021, while continuing feasibility studies of introducing experimental robots and prototyping control systems from the previous fiscal year, we proceeded with concept design and fundraising in preparation for this research and development project.


1. Staff

  • Kenichiro ARAKAKI, Research Unit Technician
  • Sachie YUKAWA, Ph.D. Student
  • Tomoko YOSHINO, Research Unit Administrator


2. Collaborations

2.1 COVID-19 Immunology Project (with Prof. Ishikawa)

  • Description: Investigation of the immune reaction to COVID-19 vaccination using a system biology approach based on multi-omics analyses.
  • Type of collaboration: Collaborative research within OIST units


3. Activities and Findings

3.1 Designing the Laboratory Automation System

Continuing from the previous year, we carried out the test environment construction at C522 of the automated laboratory and the conceptual design of the control system. A custom-made end effector (robot hand) was implemented on the industrial robot arm (EPSON C8-901, Pic 1). The newly introduced open-source version of collaborative robot No. 2 aims to build its control system utilizing ROS (or ROS 2). We created a prototype cluster (Pic 2) for an automation system from Raspberry Pi(s) and Apache Kafka distributed event streaming platform. We designed a robot connection diagram in the test environment (Fig 1) and a conceptual design of the control architecture of the automated laboratory (Fig 2), including the high-throughput liquid handling system (TECAN). We plan to build our automated laboratory at a new location in the Lab5 building from the next fiscal year onwards.

Pic 1: Seiko EPSON C8-901S with a Custom-made Hand End-Effector

Pic 2: Prototype of the Protocol Dispatcher on Raspberry Pi Cluster (RPI 3 B+ and RPI Zero x 3)

Fig 1: Robot System Connection Diagram (Testing Environment) - Updated


Fig 2: Control Architecture for Automation System - Conceptual Design


3.2 COVID-19 Immunology Project (with Prof. Ishikawa)

In collaboration with Prof. Ishikawa, we have investigated immune reaction for COVID-19 vaccination. About 100 participants are recruited locally, and blood and fecal samples are collected for identify antibody, T-cell reactivity and other COVID-19 related immunological status. In the preliminary analysis, we found some participants who had low-level of reactions (i.e. low antibody level and low T-cell reactivity even after vaccination) may have characteristic fecal microbiome composition.
Furthermore T-cell cross reactivities against four common cold corona virus as well as three corona virus not introduced to human community were investigated.
One of challenges are to see if we can develop computational predictor of vaccine reactions for each individual, but this need to be generalized as most individuals have already vaccinated and predictions are not useful anymore. However, we have found Gut-microbiome may have certain influence on the host reaction to vaccination, it provided useful insights on design of further work.


4. Publications

4.1 Journals

  • Hiroaki Kitano, Nobel Turing Challenge: creating the engine for scientific discovery, npj Syst Biol Appl 7, 29 (2021), June 18, 2021,  https://doi.org/10.1038/s41540-021-00189-3 

  • Viridiana Avila-Magaña, Bishoy Kamel, Michael DeSalvo, Kelly Gómez-Campo, Susana Enríquez, Hiroaki Kitano, Rori V. Rohlfs, Roberto Iglesias-Prieto & Mónica Medina, Elucidating gene expression adaptation of phylogenetically divergent coral holobionts under heat stress, Nature Communications, 12, Article number: 5731 (2021), https://doi.org/10.1038/s41467-021-25950-4

  • Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, Orta-Resendiz A, Singh V, Aghamiri SS, Acencio ML, Glaab E, Ruepp A, Fobo G, Montrone C, Brauner B, Frishman G, Monraz Gómez LC, Somers J, Hoch M, Kumar Gupta S, Scheel J, Borlinghaus H, Czauderna T, Schreiber F, Montagud A, Ponce de Leon M, Funahashi A, Hiki Y, Hiroi N, Yamada TG, Dräger A, Renz A, Naveez M, Bocskei Z, Messina F, Börnigen D, Fergusson L, Conti M, Rameil M, Nakonecnij V, Vanhoefer J, Schmiester L, Wang M, Ackerman EE, Shoemaker JE, Zucker J, Oxford K, Teuton J, Kocakaya E, Summak GY, Hanspers K, Kutmon M, Coort S, Eijssen L, Ehrhart F, Rex DAB, Slenter D, Martens M, Pham N, Haw R, Jassal B, Matthews L, Orlic-Milacic M, Senff Ribeiro A, Rothfels K, Shamovsky V, Stephan R, Sevilla C, Varusai T, Ravel JM, Fraser R, Ortseifen V, Marchesi S, Gawron P, Smula E, Heirendt L, Satagopam V, Wu G, Riutta A, Golebiewski M, Owen S, Goble C, Hu X, Overall RW, Maier D, Bauch A, Gyori BM, Bachman JA, Vega C, Grouès V, Vazquez M, Porras P, Licata L, Iannuccelli M, Sacco F, Nesterova A, Yuryev A, de Waard A, Turei D, Luna A, Babur O, Soliman S, Valdeolivas A, Esteban-Medina M, Peña-Chilet M, Rian K, Helikar T, Puniya BL, Modos D, Treveil A, Olbei M, De Meulder B, Ballereau S, Dugourd A, Naldi A, Noël V, Calzone L, Sander C, Demir E, Korcsmaros T, Freeman TC, Augé F, Beckmann JS, Hasenauer J, Wolkenhauer O, Wilighagen EL, Pico AR, Evelo CT, Gillespie ME, Stein LD, Hermjakob H, D'Eustachio P, Saez-Rodriguez J, Dopazo J, Valencia A, Kitano H, Barillot E, Auffray C, Balling R, Schneider R; COVID-19 Disease Map Community. COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Molecular System Biology. 2021 Oct;17(10):e10387. doi: 10.15252/msb.202110387. PMID: 34664389

  • Galindo-Martínez CT, Weber M, Avila-Magaña V, Enríquez S, Kitano H, Medina M, Iglesias-Prieto R. The role of the endolithic alga Ostreobium spp. during coral bleaching recovery. Sci Rep. 2022 Feb 22;12(1):2977. doi: 10.1038/s41598-022-07017-6. PMID: 35194106; PMCID: PMC8863988.,

4.2 Books and other one-time publications

Nothing to report

4.3 Oral and Poster Presentations

  • Hiroaki Kitano / 北野宏明, The details of the COVID-19 AI simulation project of the Cabinet Secretariat / 内閣官房新型コロナAIシミュレーションプロジェクトの経緯,  Section Ⅱ Subcommittee on Large-Scale Infectious Disease Prevention and Control System (The 25th period ・ The 7th periodical meeting) / 第二部大規模感染症予防・制圧体制検討分科会(第25期・第7回), Tokyo(online) / 東京(ビデオ会議), May 18, 2021

  • Hiroaki Kitano / 北野宏明, Current status of the COVID-19 epidemic in the Tokyo Area and future epidemic forecasts / 首都圏等での新型コロナ流行の現状と今後の流行予測,  Section Ⅱ Subcommittee on Large-Scale Infectious Disease Prevention and Control System (The 25th period ・ The 8th periodical meeting) / 第二部大規模感染症予防・制圧体制検討分科会(第25期・第8回), Tokyo(online) / 東京(ビデオ会議), Jun 15, 2021

  • Hiroaki Kitano / 北野宏明, Nobel Turing Challenge, 14th SINGULARITY NIGHT「シンギュラリティナイト」第14回, Digital Hollywood University / デジタルハリウッド大学, Tokyo(Webinar) / 東京(Zoomウェビナー), July 13, 2021(invited)

  • Hiroaki Kitano / 北野宏明, AI Simulation Project To Prevent The Next Wave /「AIシミュレーションプロジェクト 次の波を防ぐために」, Section Ⅱ Subcommittee on Large-Scale Infectious Disease Prevention and Control System (The 25th period ・ The 9th periodical meeting) / 第二部大規模感染症予防・制圧体制検討分科会(第25期・第9回), Science Council of Japan / 日本学術会議(ビデオ会議), Tokyo(online) /東京, July 16, 2021(invited)

  • Hiroaki, Kitano, Nobel Turing Challenge – Creating the Engine of Scientific Discovery, SUPERCOMPUTING FRONTIERS EUROPE 2021, ICM, Warsaw(virtual), July 21, 2021(invited)

  • Hiroaki Kitano / 北野宏明, Research for the Future of Humanity/ 人類の未来のための研究, TMC TALK, Tokyo Media Center, Tokyo(online) / 東京(オンライン), Aug 1, 2021(invited)

  • Hiroak Kitano, “Nobel Turing Challenge: Creating the engine for scientific discovery”, the 34th International Workshop on Qualitative Reasoning, IJCAI, Montreal(virtual), Aug 19, 2021(invited)

  • Hiroaki Kitano / 北野宏明, Current status of the new corona epidemic and future epidemic forecast /「新型コロナ流行の現状と今後の流行予測」, Section Ⅱ Subcommittee on Large-Scale Infectious Disease Prevention and Control System (The 25th period ・ The 10th periodical meeting)第二部大規模感染症予防・制圧体制検討分科会(第25期・第10回), Science Council of Japan / 日本学術会議(ビデオ会議), Tokyo(online) / 東京, Aug 23, 2021(invited)

  • 北野宏明, 「システムバイオロジーと漢方」, 第 40 回産婦人科漢方研究会学術集会, ツムラ株式会社, 岐阜(オンライン), Sep 5, 2021(invited)

  • Hiroaki Kitano, Defining the future of our reality - How the pandemic could reshape our world, Maker Faire Rome 2021, Rome (Virtual), Oct 7, 2021(invited)

  • Hiroaki Kitano, 北野宏明, Future measures against COVID-19 infection /「COVID-19 感染に対する今後の対策について」, Section Ⅱ Subcommittee on Large-Scale Infectious Disease Prevention and Control System (The 25th period ・ The 12th periodical meeting) / 第二部大規模感染症予防・制圧体制検討分科会(第 25 期・第 12 回), Science Council of Japan / 日本学術会議(ビデオ会議), Tokyo (Online)/ 東京(オンライン), Oct 19, 2021(invited)

  • Hiroaki Kitano / 北野宏明, Nobel Turing Challenge: Creating the Engine for Scientific Discovery / ノーベル・チューリング・チャレンジ:科学的発見のエンジンを作る, Accelerating Life Sciences by Robotic Biology” Kick-off Symposium /「ロボティックバイオロジーによる生命科学の加速」キックオフシンポジウム, JST MIRAI Program /JST 未来社会創造事業, Zoom Webinar / Zoomウェビナー, Oct 20, 2021(invited)

  • Hiroaki Kitano / 北野宏明, From Systems Biology toward Nobel Turing Challenge / システムバイオロジーからノーベルチューリングチャレンジへ,  15th Young Investigator Symposium on Clinical Pharmaceutical Science, 第15回次世代を担う若手医療薬科学シンポジウム, The Academy of Pharmaceutical Science and Technology Japan / 公益社団法人日本薬剤学会, Tokyo(Online) / 東京(オンライン), Oct 23, 2021(invited)

  • Hiroaki Kitano, Augmenting human imagination and creativity with AI , Deep Tech in 2050 Singapore Innovation and Technology Week (SWITCH), SGInnovate, Singapore (Online), Nov 8, 2021(invited)

  • Hiroaki Kitano / 北野宏明,In Search of the Future We Want to Create / 作りたい未来の姿を求めて, Plustic 2021 / Plustic講演会 2021, Aichi Institute of Technology / 愛知工業大学, Nagoya(Online) / 名古屋(オンライン), Nov 8, 2021(invited)

  • Kitano Hiroaki / 北野宏明, Update on AI simulation project regarding to COVID-19 /AIシミュレーションプロジェクトの現状,  COVID-19 Medical Advisor and iCDC Epidemiology Public Health Team Joint Study Group / 新型コロナ感染症医療アドバイザー・iCDC疫学公衆衛生チーム合同勉強会, Bureau of Social Welfare and Public Health / 東京都福祉保健局, Tokyo(Online) / 東京(オンライン), Nov 15, 2021(invited)

  • Hiroaki Kitano / 北野宏明, Keidanren's Opinion on AI Utilization  / AI利活用に関する経団連の意見, 12th Japan-EU ICT Strategy Workshop / 第12回 日EU ICT戦略ワークショップ, MIC / 総務省, Tokyo(Online) / 東京(オンライン), Nov 17, 2021(invited)

  • Hiroaki Kitano / 北野宏明, Global Agenda and Future of Japan, ICU Short program / ICU授業, ICU Univ / 国際基督教大学, Tokyo(Online) / 東京(オンライン), Nov 25, 2021(invited)

  • Hiroaki Kitano / 北野宏明, Nobel Turing Challenge: Creating the Engine for Scientific Discovery / ノーベル・チューリング・チャレンジ:科学的発見のエンジンを作る, AIAMEC Symposium 2021 / AISMECシンポジウム2021, Yamaguchi University Graduate School of Medicine / 山口大学大学院医学系研究科, Yamaguchi(Online) / 山口(オンライン), Nov 27, 2021(invited)

  • Hiroaki Kitano/ 北野宏明, Future measures against COVID-19 infection / COVID-19感染に対する今後の対策について, Section Ⅱ Subcommittee on Large-Scale Infectious Disease Prevention and Control System (The 25th period ・ The 14th periodical meeting) 第二部大規模感染症予防・制圧体制検討分科会(第25期・第14回), Tokyo(Online) / 東京(オンライン), Feb 18, 2022(invited)

  • Hiroaki Kitano / 北野宏明, About the new AI strategy at Headquarters for the Economic Growth Strategy / 自民党経済成長戦略本部における新AI戦略について, Headquarters for the Economic Growth Strategy / 経済成長戦略本部, Tokyo(The Liberal Democratic Party of Japan) / 東京(自由民主党本部), Feb 28, 2022(invited)

  • Hiroaki Kitano, OIST “Japan’s and the United States’ Quest to Achieve a Carbon-Free Power Sector: Necessary Breakthroughs in Policy, Science and Technology, and Business Models”, USJC, Virtual event, Mar 1, 2022(invited)

  • Hiroaki Kitano / 北野宏明, Inspirational Talk, Keio Colloquium 2022 / 慶應コロキアム2022, Keio Univ / 慶応大学, Tokyo(Online) /, Mar 6, 2022(invited)

  • Hiroaki Kitano / 北野宏明, How far can AI accelerate drug discovery? / AIによって創薬はどこまで加速できるか? , Kobe Port Island Drug Discovery Forum / 神戸ポートアイラインド創薬フォーラム, Kobe / 神戸(Online), Mar 11, 2022

  • Hiroaki Kitano / 北野宏明, Creating the Engine for Scientific Discovery : development of AI systems to win the Nobel Prize  / AIによる科学的発見(ノーベル賞を獲るAI)の挑戦, Fukui University of Technology AI&IoT Center Symposium / 福井工業大学AI & IoTセンターシンポジウム, FUT AI & IoT Center / 福井工業大学AI & IoTセンター, Fukui (Online) / 福井(Online), Mar 14, 2022(invited)

  • Hiroaki Kitano / 北野宏明, PLANETARY AGENDA AND FUTURE OF JAPAN, Tokyo Institute of technology InfoSyEnergy Consortium The3rd Public Symposium / 東工大InfoSyEnergy研究/教育コンソーシアム第3回公開シンポジウム, Tokyo Institute of technology / 東工大, Tokyo(Online) / 東京(Online), Mar 22, 2022(invited)

  • Hiroaki Kitano / 北野宏明, Creating the engine for scientific discovery / 人工知能による科学的発見, Kobe University Graduate School of Medicine / 神戸大学医学研究科, Kobe(Online) / 神戸(Online), Mar 30,2022 (invited)


5. Intellectual Property Rights and Other Specific Achievements

Nothing to report

6. Meetings and Events

Nothing to report

7. Other

Nothing to report.