The Systems Biology Institute
Non-profit research institute (est. 2000) focused on systems biology. Uses computational modelling, machine learning, multi-omics data analysis, standards development, interoperable software platforms, and laboratory automation to support hypothesis generation, simulation, pathway curation, toxicology, drug/therapy design, and translation to clinical and industrial contexts. Produces community tools, standards and publishes peer-reviewed research across modelling, omics, and computational methods.
Industries
Nr. of Employees
small (1-50)
The Systems Biology Institute
Saisei Ikedayama Bldg., 5-10-25 Higashi Gotanda, Shinagawa, Tokyo 141-0022, Japan
Products
Graphical model editor for biochemical and gene-regulatory networks
A graphical editor for constructing, annotating and exporting biochemical and regulatory network models with support for process-diagram notation and standardized model formats for simulation and exchange.
Multilevel physiological modelling environment
Platform for constructing hierarchical multilevel physiological models enabling hybrid models and integration of morphometric domains for PDE-based simulation.
Pathway exploration and curation portals
Mobile and web tools for browsing curated molecular pathway maps and pathway libraries, with capabilities for community curation and model annotation.
Web services for network pharmacology and cell-type enrichment analysis
Online services providing network pharmacology prediction, docking-informed analysis and cell-type enrichment identification from transcriptomic data.
Graphical model editor for biochemical and gene-regulatory networks
A graphical editor for constructing, annotating and exporting biochemical and regulatory network models with support for process-diagram notation and standardized model formats for simulation and exchange.
Multilevel physiological modelling environment
Platform for constructing hierarchical multilevel physiological models enabling hybrid models and integration of morphometric domains for PDE-based simulation.
Pathway exploration and curation portals
Mobile and web tools for browsing curated molecular pathway maps and pathway libraries, with capabilities for community curation and model annotation.
Web services for network pharmacology and cell-type enrichment analysis
Online services providing network pharmacology prediction, docking-informed analysis and cell-type enrichment identification from transcriptomic data.
Services
Integration services to connect biomedical applications, databases, and analysis tools via an open API framework for discovery and coordinated operation.
Hosting and maintenance of web portals and analysis services for specific domains such as infectious disease mapping, toxicology, pathway exploration and cell-type enrichment.
Provision and support for multi-omics analysis packages and deployment on scalable HPC/cloud infrastructure to support data-intensive analyses.
Integration services to connect biomedical applications, databases, and analysis tools via an open API framework for discovery and coordinated operation.
Hosting and maintenance of web portals and analysis services for specific domains such as infectious disease mapping, toxicology, pathway exploration and cell-type enrichment.
Provision and support for multi-omics analysis packages and deployment on scalable HPC/cloud infrastructure to support data-intensive analyses.
Expertise Areas
- AI for scientific discovery
- Computational platforms and interoperability
- Multilevel physiological modelling
- Network and pathway analysis and curation
Key Technologies
- Model representation standards (SBML)
- Graphical notation standards (SBGN, SBGN-ML)
- Physiological modelling languages and hybrid model formats (PHML/SBML hybrid)
- Multilevel systems simulation
News & Updates
Workshop on AI for autonomous scientific discovery, digital twins, automation, and translation into healthcare held in Tokyo to strengthen India–Japan collaborations.
Public launch and ongoing activities related to the Nobel Turing Challenge initiative focused on automating the scientific discovery process.
Public release of a COVID-19 literature-mining and data portal to accelerate research.
Report on use of robotic lab systems to scale experimental execution and enable crowd-sourced robotic biology workflows.
Study describing precise temporal proteomics profiling of signaling complexes using SWATH mass spectrometry.
Application of machine learning methods to identify key markers involved in brain development from single-cell transcriptomic data.
Workshop on AI for autonomous scientific discovery, digital twins, automation, and translation into healthcare held in Tokyo to strengthen India–Japan collaborations.
Public launch and ongoing activities related to the Nobel Turing Challenge initiative focused on automating the scientific discovery process.
Public release of a COVID-19 literature-mining and data portal to accelerate research.
Report on use of robotic lab systems to scale experimental execution and enable crowd-sourced robotic biology workflows.
Study describing precise temporal proteomics profiling of signaling complexes using SWATH mass spectrometry.
Application of machine learning methods to identify key markers involved in brain development from single-cell transcriptomic data.