The Systems Biology Institute

What The Systems Biology Institute does

The Systems Biology Institute (SBI; 特定非営利活動法人 システム・バイオロジー研究機構) is a non-profit private research institution founded in 2000 in Tokyo, Japan and formally registered as an NPO in April 2001. It conducts fundamental and applied research in systems biology, with the stated mission of using AI to overcome cognitive limitations in biomedical science — culminating in the Nobel Turing Challenge initiative to develop AI capable of Nobel-level scientific discovery. SBI is small (11–50 employees) and led by Dr. Hiroaki Kitano, who concurrently serves as President & CEO of Sony Computer Science Laboratories and Principal Investigator at OIST.

The institute's core technology stack consists of two categories. First, foundational open standards: SBML (Systems Biology Markup Language) and SBGN (Systems Biology Graphical Notation), both initiated by SBI researchers and now widely adopted as community standards for representing biochemical and gene-regulatory network models. Second, an open-source software portfolio: CellDesigner (SBML/SBGN-compliant diagram editor), Garuda Platform (an integration framework and language-independent API that connects biomedical software, databases, and services as "gadgets"), PhysioDesigner (multilevel physiological modeling in PHML/CellML/SBML), and iPathways (mobile pathway viewer with 200+ pathways). On top of these, SBI has built the Gandhara AI framework and supplementary AI tools (DTox, systemsDock, MelAnalyze, ProtoCode, IQCELL, CTen) for hypothesis generation, text mining, toxicogenomics prediction, and pathway curation.

SBI does not sell products. Instead, it funds operations through Japanese government grants (JST, MEXT, MHLW, AMED, NEDO), private foundation grants (Canon Foundation), international research funding (Luxembourg LCSB on Parkinson's), and industrial/regulatory contracts — including a multi-year collaboration with the US FDA and a multi-omics partnership with Shimadzu Corporation. Its software is distributed free under open-source licenses, and its research footprint is extended through MoUs with universities and institutes across the US, UK, Australia, Luxembourg, Poland, India, China, Singapore, France, Germany, and others, with SBI Australia jointly housed at Monash University since 2012. Distribution channels are academic: peer-reviewed publications in Nature-family journals, international workshops (ICSB, Nobel Turing Challenge, India-Japan meetings), and the npj Systems Biology and Applications open-access journal co-launched with Nature Publishing Group in 2014.

Name

The Systems Biology Institute

Legal name

The Systems Biology Institute

Website

https://sbi.jp

Company type

Private

Founded year

2000

Operating status

Operating

Headcount range

11–50 employees

Short description

The Systems Biology Institute is a Tokyo-based non-profit research organization (founded 2000) that develops open-source computational platforms, biological standards (SBML, SBGN), and AI tools — including the Nobel Turing Challenge — to advance systems biology and AI-driven scientific discovery for academic, pharmaceutical, and regulatory partners worldwide.

Ownership category

akta.pro rank

Product category

Computational Biology Software

NAICS

Scientific Research and Development Services (5417), Research and Development in Biotechnology (except Nanobiotechnology) (541714), Computer Systems Design and Related Services (54151)

SIC

Laboratory Analytical Instruments (3826)

akta.pro primary industry

Bioinformatics & Multi-omics Analysis Software (HLAGAJAD)

akta.pro secondary industry

AI/ML Platforms for Drug Discovery & Experiment Optimization (HLAGAJAO)

Keywords

• Systems biology research
• Computational biology tools
• Biomedical AI platforms
• Open-source research software
• Biological pathway modeling

Headquarters

HQ city

Higashi-shinagawa

HQ country

Japan

HQ region

Asia

Offices2 records

Markets served

GTM type

B2B

Offering type

Software

Cost components

Personnel, Technology or R&D, Operations, Marketing or Sales, Infrastructure

Revenue model

1. Government Research Grants: SBI receives substantial funding from Japanese government agencies including Japan Science and Technology Agency (JST), Ministry of Education, Culture, Sports, Science and Technology (MEXT), Ministry of Agriculture, Ministry of Health, Labour and Welfare (MHLW), and New Energy Development Organization (NEDO). Funding supports various research programs including ERATO projects.
2. Private Foundation Grants: Funding from private foundations including Canon Foundation for specific research projects such as Coral Reef Systems Biology (2010-2013).
3. International Funding: International research funding from sources including Luxembourg for projects such as Luxembourg Centre for Systems Biology collaboration on Parkinson's disease (2011-2015).
4. Private Industrial Contracts: Extensive private contracts with corporations for industrial applications of systems biology research in drug discovery and other areas, including collaboration with US FDA.

Go-to-market motion2 records

Distribution channels3 records

Marketing channels5 records

Core offering

The Systems Biology Institute develops and distributes open-source computational platforms, standards, and AI frameworks for systems biology research. Core offerings include the Garuda Platform (integration framework for biomedical applications), CellDesigner and PhysioDesigner (modeling tools supporting SBML/SBGN standards), the Gandhara AI framework for AI-driven scientific discovery, and disease-specific tools such as the COVID-19 Taxila Portal and Influenza Pathway Map.

Product overview

The Systems Biology Institute (SBI) is a non-profit private research institution that has developed a comprehensive suite of computational platforms and standards for systems biology research. The core product portfolio includes the Garuda Platform (an open, community-driven integration platform for biomedical research), CellDesigner (a structured diagram editor for gene-regulatory and biochemical networks supporting SBML/SBGN standards), PhysioDesigner (for multilevel physiological system modeling), and iPathways (mobile pathway exploration). SBI has also developed the Gandhara AI framework as infrastructure for AI-driven scientific discovery as part of the Nobel Turing Challenge initiative. The organization contributes major open standards including SBML and SBGN, and maintains specialized tools like COVID-19 Taxila Portal, CTen for cell type enrichment, and the Influenza Pathway Map. The portfolio spans from standards-based modeling tools to AI-powered platforms for automated hypothesis generation and knowledge synthesis.

Differentiator

Problem solved

Functional benefit

Brands

• Garuda Platform: An open, community-driven platform providing framework to interface, discover, and navigate through different applications, databases and services in biomedical research.
• CellDesigner
• PhysioDesigner
• COVID-19 Taxila Portal
• Nobel Turing Challenge

Products and services

• Garuda Platform An open, community-driven common platform providing a framework to interface, discover, and navigate through different applications, databases, and services in biomedical research. It offers a language-independent API to connect software as gadgets, explore them through a gateway, and operate them through a dashboard. Targeted at the biomedical research community.
• CellDesigner A structured diagram editor for drawing gene-regulatory and biochemical networks based on the Systems Biology Graphical Notation (SBGN) process diagram, with networks stored using Systems Biology Markup Language (SBML) standard. Designed for systems biologists and bioinformaticians.
• PhysioDesigner An open platform for supporting multilevel modeling of physiological systems in life-science and systems biology including physiology and neuroscience. Models are stored in PHML (Physiological Hierarchy Markup Language) format with support for CellML and SBML-PHML hybrid models. Targeted at physiological and neuroscience researchers.
• iPathways An iPad/iPhone application for exploring biological pathways with an extended library of over 200 pathways covering Cancer, Signaling, Panther pathways, and KEGG metabolic pathways. Targeted at students, educators, and researchers needing mobile access to pathway information.
• COVID-19 Taxila Portal A web portal providing access to the COVID-19 Disease Map, a computational repository of SARS-CoV-2 virus-host interaction mechanisms and related scientific literature for accelerating COVID-19 research. Targeted at infectious disease researchers globally.
• Gandhara AI Framework An AI framework developed as basic infrastructure for the Nobel Turing Challenge, designed to assist scientific activities and evolve to generate hypotheses, verify them, and reorganize knowledge for automated scientific discovery. Targeted at researchers pursuing AI-driven scientific research.
• CTen (Cell Type Enrichment) A web-based enrichment algorithm to identify changes in cell-type demographics of in vivo tissue samples from gene lists, designed for immunology studies to connect gene expression to immune cell migration. Targeted at immunology and tissue biology researchers.
• Influenza Pathway Map A comprehensive map of the influenza A virus replication cycle and host response pathways for influenza research. Targeted at virologists and infectious disease researchers.

Quantifiable outcome

• SBML paper exceeded 500 citations in ISI Web of Knowledge by 2010
• +1 more outcomes

Named customers4 records

Segments4 records

Ideal customer profiles3 records

Technology focussed Yes

API detail

Has API

No

API docs

API detail

Core technology

AI maturity

App detail

AI capability11 records

Feature8 records

Partnerships

15 partnerships are on record, tiered core.

• ICM (Interdisciplinary Centre for Mathematical and Computational Modelling), Warsaw UniversitycoreStrategic or Co-development Partner · 1 January 2020Partnership starting December 2020 for developing integrated platform for GARUDA-based biomedical, omics analysis, and machine learning research in Central Europe.
• Shimadzu CorporationcoreStrategic or Co-development Partner · 1 January 2017Collaboration on open platform multi-omics data analysis package. Started in June 2017 for providing analysis tools through an open platform approach with Osaka University.
• Monash IVFcoreStrategic or Co-development Partner · 1 January 2013Collaboration on systems biology of reproductive medicine to improve clinical success. Joint research with Australian Regenerative Medicine Institute (ARMI) and SBI Australia.
• US Food and Drug Administration (FDA)coreStrategic or Co-development Partner · 1 January 2012Collaboration on drug safety and systems biology research. SBI works with US FDA on joint research to apply systems biology approaches to drug safety assessment and regulatory science.
• EMBL AustraliacoreStrategic or Co-development Partner · 1 January 2012Joint research collaboration with EMBL Australia signed March 2012 to support Australian life science research through workshops, training and expertise sharing.
• SBI Australia at Monash UniversitycoreStrategic or Co-development Partner · 1 January 2012SBI Australia established at Monash University in collaboration with Australian Regenerative Medicine Institute (ARMI) to advance systems biology research in Australia.
• Luxembourg Centre for Systems Biomedicine (LCSB)coreStrategic or Co-development Partner · 1 January 2011Joint research on Parkinson's disease since 2011. LCSB and SBI working together on deeper understanding of complex systems of Parkinson's disease.
• Key Laboratory of Systems Biology, Shanghai Institute of Biological Sciences (SIBS)coreStrategic or Co-development Partner · 1 January 2010Comprehensive joint research, education, and promotion of systems biology signed March 2010 including series of workshops and joint research programs.
• Council of Scientific and Industrial Research (CSIR), IndiacoreStrategic or Co-development Partner · 1 January 2009MoU signed to seek collaborative initiatives to promote systems biology and its medical and environmental applications in India and Japan.
• University of EdinburghcoreStrategic or Co-development Partner · 1 January 2006MoU signed with University of Edinburgh's College of Science and Engineering in Scotland for collaboration in systems biology field.
• Sony Computer Science LaboratoriescoreStrategic or Co-development PartnerDr. Hiroaki Kitano serves as President & CEO of Sony Computer Science Laboratories while leading SBI. Close institutional relationship through shared leadership.
• Okinawa Institute of Science and Technology (OIST)coreStrategic or Co-development PartnerDr. Kitano serves as Principal Investigator of the Open Biology Unit at OIST. Joint workshops and collaborative research including Nobel Turing Challenge workshops.
• Keio UniversitycoreStrategic or Co-development PartnerCollaboration on COVID-19 Disease Map project building computational repository of SARS-CoV-2 virus-host interaction mechanisms.
• RikencoreStrategic or Co-development PartnerCollaboration on various research projects including influenza research and systems biology modeling. Co-organizer of workshops including Second Workshop on Nobel Turing Challenge.
• Nature Publishing GroupcoreStrategic or Co-development PartnerPartnership to launch npj Systems Biology and Applications, an online open access journal dedicated to publishing high quality systems biology research.

Scale indicators3 records

Recent moves7 records

Expansion highlights6 records

Direct peers

• Sage Bionetworks: Non-profit biomedical research organization that builds open computational platforms (Synapse) for collaborative analysis of biological data. Highly comparable to SBI as a non-profit building standards and software infrastructure for systems biology and biomedical research communities.
• Allen Institute for AI (AI2): Non-profit AI research institute that pursues AI for science (including biomedicine) and builds open models and tools for the research community. Comparable to SBI as a non-profit advancing AI infrastructure for scientific discovery and open releases to the research community.
• Arc Institute: Non-profit research organization combining experimental biology and AI/machine learning to advance biomedical discovery, with flagship faculty model similar in spirit to SBI's researcher-led structure. Highly comparable as a non-profit combining systems biology with AI-driven autonomous discovery.

Emerging players

• Recursion Pharmaceuticals: Clinical-stage biotech using AI, high-throughput experimental biology, and automated labs to discover novel therapeutics. Comparable to SBI's autonomous experiment optimization (Maholo LabDroids, Bayesian optimization for iPS cell differentiation) but as a commercial pharma player.
• Chan Zuckerberg Biohub (CZ Biohub): Non-profit biomedical research organization backed by the Chan Zuckerberg Initiative that develops new technologies and tools (including AI/ML infrastructure such as cz-biotools and cell atlas projects) for biomedical research. Comparable in mission and non-profit funding model to SBI.
• Exscientia: AI-driven precision medicine and drug design company applying machine learning to small molecule design. Comparable to SBI's drug discovery applications (systemsDock, DTox, multi-target drug design) but operating commercially with pharma partnerships and pipeline assets.
• Insitro: Commercial AI-driven drug discovery company combining high-throughput biology with machine learning to predict drug behavior. Comparable to SBI's Gandhara/DTox/systemsDock capabilities but operating as a venture-backed commercial entity rather than a non-profit standards steward.

Broad incumbents

• Broad Institute: Major non-profit biomedical and genomic research organization affiliated with MIT and Harvard that builds computational tools and datasets (GATK, CellProfiler, DepMap) for the research community. Comparable to SBI as a non-profit standards-and-tooling provider for systems-level biology, but at substantially larger scale.
• Allen Institute: Non-profit bioscience research organization running large-scale research programs in brain science, cell science, and immunology. Comparable to SBI as a large-scale non-profit biomedical research institution, though focused on experimental rather than computational biology.
• EMBL-EBI (European Bioinformatics Institute): Major intergovernmental bioinformatics research organization that develops widely adopted open data standards and tools (UniProt, Ensembl, BioModels) for life sciences. Comparable to SBI as a public-good bioinformatics standards and infrastructure provider, though broader in scope and larger in scale.

Market position

Strengths5 records

Weaknesses5 records

Competitive moat5 records

Key risks6 records

Key highlights7 records

Customer concentration

• YouTubeyoutube.com/@nobelturingchallenge5259

Revenue estimate

Valuation estimate

Number of profiles

Profiles2 records

Subsidiaries2 records

Funding overview

Funding rounds

Investors

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M&A

Investments

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Frequently asked questions about The Systems Biology Institute