Database List
Databases developed and released by RIKEN.
1 Life Sciences / Biological Resources
1.1 Genetics & Genomics
| Domain | Database Name (Abbreviation) | Description | Release Date | Center/Headquarters |
|---|---|---|---|---|
| Life Science/Sustainability Science Domain | BioResouce MetaDatabase (BRMD) | The BioResource MetaDatabase (BRMD) is a data repository that stores metadata for bioresources provided by the RIKEN BioResource Research Center (BRC). These bioresources include experimental mice, experimental plants, cell lines, gene materials, and microbial strains. The BRMD integrates essential information about bioresources, ontology terms like phenotypes and diseases, and orthologous (homologous) gene information. It publishes data based on the Semantic Web and Resource Description Framework (RDF), which are recognized as global standard technologies for metadata. Users can retrieve and download all data using SPARQL, a query language. This database also links with the online catalogs for each resource at BRC. | 2019/12/24 | RIKEN BioResource Research CenterIntegrated Bioresource Information Division |
| Life Science Domain | Mouse Phenotype Publish Database (Pheno-pub) | The Mouse Phenomics Division conducts the Japan Mouse Clinic, a comprehensive analysis of phenotypes mainly in genetically modified mice, with the aim of understanding the pathophysiology of human diseases and elucidating gene functions. Pheno-pub publishes the data analyzed in the Japan Mouse Clinic with the client's approval, contributing to the maintenance of mouse resources and intellectual infrastructure. | 2009/5/13 | RIKEN BioResource Research CenterMouse Phenomics Division |
| Life Science Domain | MoG+, Mouse Genome Database with High Added Value (MoG+) | MoG+ is a genomic variation database for diverse laboratory mouse strains provided by RIKEN BRC, with a focus on wild-derived and disease model strains. It supports visualization and comparison of SNPs, indels, and structural variants across multiple reference genome versions. Publicly available variation data are also incorporated where appropriate. This comprehensive platform enables researchers to perform high-precision analyses of gene and regulatory regions while accounting for genome variants. MoG+ serves as a valuable resource for disease research and functional genomics. | 2020/3/27 | RIKEN BioResource Research CenterIntegrated Bioresource Information Division |
| Life Science/Sustainability Science Domain | RIKEN BRC BioResouce Xsearch (RBBX) | The RIKEN BioResource Xsearch (RBRX) system, accessible on the RIKEN BioResource Research Center (BRC) website (https://web.brc.riken.jp/), is a search platform that enables comprehensive, cross-database searching of data for experimental mice, experimental plants, cell lines, gene materials, and microbial strains. Users can efficiently search for relevant bioresources by using keywords such as bioresource names, gene names, or ontology terms related to diseases and phenotypes. The system also offers an advanced search function for more detailed queries. This system operates with the BioResource MetaDatabase (BRMD), serving as its backend database. | 2019/7/1 | RIKEN BioResource Research CenterIntegrated Bioresource Information Division |
| Life Science/Sustainability Science Domain | RIKEN BRC DNA Resource Catalog | The Gene Engineering Division of the RIKEN BRC, also known as RIKEN DNA Bank, collects important and valuable genetic materials including cDNA clones from human, animal, microbe and virus. We distribute them to scientists after rigorous quality control. Users can access detailed information of the genetic materials including their full-length sequences and related publications. （54 words） | 2011/8/18 | RIKEN BioResource Research CenterGene Engineering Division |
| Life Science/Sustainability Science Domain | RIKEN BRC Exp-Plant Catalog | The Experimental Plant Division of the RIKEN BioResource Research Center collects, preserves, maintains, distributes a wide range of biological resources, including natural accessions, mutants, and transgenic lines of Arabidopsis thaliana; plant cultured cells; and plant gene clones and plasmids. Users can explore these bioresources via an interactive search platform, accessing detailed lineage information and trait data to support advanced plant research. (61 words) | 2017/10/31 | RIKEN BioResource Research CenterExperimental Animal Division |
| Life Science/Sustainability Science Domain | RIKEN BRC plant cell line documentation | The Experimental Plant Division of the RIKEN BioResource Research Center offers comprehensive handling protocols for plant cultured cells, covering medium preparation, subculturing techniques, and a range of related methodologies. These include advanced protocols for genotyping, genetic transformation, and cryopreservation. Users can access detailed quality information, including genotyping results and maintenance history, to support reliable and reproducible research. (57 words) | 2018/6/19 | RIKEN BioResource Research CenterExperimental Plant Division |
| Life Science Domain | NHP_NNP Personality & Genotype (NHPNNPPG) | A database on personality and genetic information of primate animals, analysed in conjunction with the brain MRI database mentioned above, can help investigate the relationship between personality, genes and functional brain structures. | 2020/8/2 | RIKEN Center for Biosystems Dynamics ResearchLaboratory for Brain Connectomics Imaging |
| Life Science Domain | fanta.bio (fanta.bio) | fanta.bio (Functional genome ANnotations with Transcriptional Activities) is a database that collects functional annotations of genomes for studying gene regulation, with a primary focus on cis-regulatory elements (CREs) such as promoters and enhancers. Identification of CREs in fanta.bio is based on transcription signatures. Both promoters and enhancers produce specific sets of RNAs, including mRNA, lncRNA, uaRNA (upstream antisense RNA), and eRNA (enhancer RNA). These transcription signatures are effectively used in the course of the identification. The pioneering work of transcriptome-based CRE identification was carried out in the FANTOM5 project, and we here applied an advanced approach to an expanded dataset. We additionally collect relevant resources, such as genome binding sites of transcription factors (“trans” factors) and genome variations across individuals. | 2023/3/28 | RIKEN Center for Integrative Medical SciencesLaboratory for Large-Scale Biomedical Data Technology |
| Life Science Domain | FANTOM5 Web Resource (FANTOM5) | The FANTOM5 dataset consists of approximately 3,000 files that measure the activity of transcription start sites (TSSs) for genes in various human and mouse samples, including primary cultured cells, cell lines, tissues, and time-course samples during development, differentiation, or stimulation. It includes not only gene-level data but also information on the activity of promoters and enhancers, as well as the expression of miRNAs and lncRNAs. | RIKEN Center for Integrative Medical SciencesLaboratory for Large-Scale Biomedical Data Technology | |
| Life Science Domain | FANTOM6 Web Resource (FANTOM6) | In FANTOM6, with the aim of elucidating the functions of non-coding RNAs, gene expression profiling and analysis were conducted after knockdown of non-coding RNAs across several cell types and their stimulation conditions. Additionally, data on RNA–genome interactions were acquired and analyzed. These datasets and the corresponding analysis results have been made publicly available and can be accessed through this web resource. | RIKEN Center for Integrative Medical SciencesLaboratory for Large-Scale Biomedical Data Technology | |
| Life Science Domain | Gene Expression Commons | Each gene has a different dynamic-range of its expression. Gene Expression Commons provides dynamic-range of each gene by meta analysis of thousands of microarray data. By mapping your data onto it, you can profile absolute expression of any gene on the microarray. Goodbye, profiling relative difference of gene expression in pari-wise comparison. | 2016 | RIKEN Center for Integrative Medical SciencesLaboratory for Integrative Genomics |
| Life Science Domain | Japanese ENcyclopedia of GEnetic associations libraRy (JENGER) | This database provides summary statistics of genome-wide association study (GWAS), quantitative trait loci (QTL), and expression quantitative trait loci (eQTL) using the BioBank Japan (mainly Japanese subjects). In addition, it includes allele frequency and structural variation (SV) information derived from whole-genome sequencing data, making it a comprehensive resource for genome-related analyses in the Japanese population. | 2017/10/17 | RIKEN Center for Integrative Medical SciencesLaboratory for Statistical and Translational Genetics |
| Life Science/Sustainability Science Domain | JCM On-line Catalogue of Strains | The Microbe Division in RIKEN-BRC, also widely known as Japan Collection of Microorganisms (JCM) is committed to collecting, preserving, and distributing cultured microbial strains in order to contribute to scientific communities by maintaining and serving high-quality microbial resources useful for general microbial studies and various research fields particularly in environmental and health science. The JCM online catalogue provides academic information of scientific name, taxonomy, and related publications, as well as cultural properties of these microorganisms. | 1996~1997 | RIKEN BioResource Research CenterMicrobe Division |
| Life Science Domain | Marmoset Gene Atlas (MGA) | Our goal is to establish a genome-wide, high-resolution atlas of the gene expression throughout the common marmoset (Callithrix jacchus) brain. We employ in situ hybridization (ISH) analysis to systematically analyze changes in gene expression over the course of postnatal brain development to adult stage. We anticipate that these data will provide sufficient information to develop tools that allow us to reveal primate specific brain structure, function and connectivity. | 2017/10/27 | RIKEN Center for Brain ScienceLaboratory for Molecular Mechanisms of Brain Development |
| Sustainability Science/Life Science Domain | RARGE : RIKEN Arabidopsis Genome Encyclopedia (Ver.2) (RARGE 2) | RIKEN Arabidopsis Genome Encyclopedia, commonly known as RARGE, is a Web database that provides basic information about the Arabidopsis genome, such as information related to cDNA sequences and transposon insertion mutants. | 2013/11/6 | RIKEN Center for Sustainable Resource ScienceMetabolome Informatics Research Team |
| Life Science Domain | refTSS (refTSS) | The refTSS is an annotated reference dataset for transcriptional start sites (TSS) in human and mouse. The dataset is generated by collecting, reprocessing and assembling various public resources. The database interface provides a search for TSSs, a browse of TSS annotations, and enrichment analysis of LD regions within a set of TSSs. | 2016/12/22 | RIKEN Center for Integrative Medical SciencesLaboratory for Large-Scale Biomedical Data Technology |
| Sustainability Science/Life Science Domain | rsoy:RIKEN Soybean Full-Length cDNA Database (rsoy) | This database provides access to all data of soybean full-length cDNAs. RIKEN has analyzed soybean full-length cDNAs on a large scale for the first time in the world and has made all data of about 23,000 cDNAs publicly available. In this study, after isolating about 40,000 full-length cDNAs of “Norin No.2” which is the root of the representative soybean cultivar in Japan, partial nucleotide sequence information (EST) of about 23,000 cDNAs excluding duplicates was determined, and full-length cDNA sequences of about 4,700 species were determined from them. | 2014/4/2 | RIKEN Center for Sustainable Resource ScienceMetabolome Informatics Research Team |
| Life Science Domain | scPortalen2 (scPortalen2) | scPortalen2 is a comprehensive database designed to reuse and visualize single-cell RNA sequencing (scRNA-seq) data from human and mouse samples. It compiles publicly available datasets, reanalyzes them through a standardized pipeline, and provides gene expression profiles across various cell types. The platform supports interactive exploration, allowing users to search for genes or cell populations of interest and to compare expression patterns. By ensuring consistency in data processing, scPortalen2 facilitates reliable cross-study comparisons and aids in uncovering cellular heterogeneity in biological systems. | 2016 | RIKEN Center for Integrative Medical SciencesLaboratory for Large-Scale Biomedical Data Technology |
| Life Science Domain | wPGSA online (wPGSA) | wPGSA (Weighted Parametric Gene Set Analysis) is a computational method designed to estimate the relative activity of transcription factors based on transcriptome data. Users can upload their own gene expression datasets and obtain analysis results, including heatmaps and tables that visualize transcription factor activity, using only a web browser interface. The tool primarily targets researchers in bioinformatics and aims to support the exploration of biological regulatory mechanisms and hypothesis generation. | 2004/02/16 | RIKEN Center for Integrative Medical SciencesMedical Data Mathematical Reasoning Special Team |
1.2 Phenotypes
| Domain | Database Name (Abbreviation) | Description | Release Date | Center/Headquarters |
|---|---|---|---|---|
| Life Science/Sustainability Science Domain | BioResouce MetaDatabase (BRMD) | The BioResource MetaDatabase (BRMD) is a data repository that stores metadata for bioresources provided by the RIKEN BioResource Research Center (BRC). These bioresources include experimental mice, experimental plants, cell lines, gene materials, and microbial strains. The BRMD integrates essential information about bioresources, ontology terms like phenotypes and diseases, and orthologous (homologous) gene information. It publishes data based on the Semantic Web and Resource Description Framework (RDF), which are recognized as global standard technologies for metadata. Users can retrieve and download all data using SPARQL, a query language. This database also links with the online catalogs for each resource at BRC. | 2019/12/24 | RIKEN BioResource Research CenterIntegrated Bioresource Information Division |
| Life Science Domain | Mouse Phenotype Publish Database (Pheno-pub) | The Mouse Phenomics Division conducts the Japan Mouse Clinic, a comprehensive analysis of phenotypes mainly in genetically modified mice, with the aim of understanding the pathophysiology of human diseases and elucidating gene functions. Pheno-pub publishes the data analyzed in the Japan Mouse Clinic with the client's approval, contributing to the maintenance of mouse resources and intellectual infrastructure. | 2009/5/13 | RIKEN BioResource Research CenterMouse Phenomics Division |
| Life Science/Sustainability Science Domain | RIKEN BRC BioResouce Xsearch (RBBX) | The RIKEN BioResource Xsearch (RBRX) system, accessible on the RIKEN BioResource Research Center (BRC) website (https://web.brc.riken.jp/), is a search platform that enables comprehensive, cross-database searching of data for experimental mice, experimental plants, cell lines, gene materials, and microbial strains. Users can efficiently search for relevant bioresources by using keywords such as bioresource names, gene names, or ontology terms related to diseases and phenotypes. The system also offers an advanced search function for more detailed queries. This system operates with the BioResource MetaDatabase (BRMD), serving as its backend database. | 2019/7/1 | RIKEN BioResource Research CenterIntegrated Bioresource Information Division |
| Life Science Domain | RIKEN BRC Mouse Strain Data Databese | The Experimental Animal Division of the RIKEN BioResource Research Center (BRC) provides public access to information on mouse strains that the division collects, preserves, quality-controls, and distributes. Users can search for mouse strains and access detailed information including strain characteristics, health reports, donor DNA for genetic modifications, preservation status, documents for distribution, and publications by user scientists. | RIKEN BioResource Research CenterExperimental Animal Division | |
| Life Science Domain | RIKEN BRC CELL SEARCH SYSTEM | This is data on cell resources held by the RIKEN Cell Bank. It includes details such as the type of resource, the cell name, the cell ID, a description, the provider, photos and related papers. | 2017 | RIKEN BioResource Research CenterCell Engineering Division |
| Life Science/Sustainability Science Domain | RIKEN BRC Exp-Plant Catalog | The Experimental Plant Division of the RIKEN BioResource Research Center collects, preserves, maintains, distributes a wide range of biological resources, including natural accessions, mutants, and transgenic lines of Arabidopsis thaliana; plant cultured cells; and plant gene clones and plasmids. Users can explore these bioresources via an interactive search platform, accessing detailed lineage information and trait data to support advanced plant research. (61 words) | 2017/10/31 | RIKEN BioResource Research CenterExperimental Animal Division |
| Life Science/Sustainability Science Domain | JCM On-line Catalogue of Strains | The Microbe Division in RIKEN-BRC, also widely known as Japan Collection of Microorganisms (JCM) is committed to collecting, preserving, and distributing cultured microbial strains in order to contribute to scientific communities by maintaining and serving high-quality microbial resources useful for general microbial studies and various research fields particularly in environmental and health science. The JCM online catalogue provides academic information of scientific name, taxonomy, and related publications, as well as cultural properties of these microorganisms. | 1996~1997 | RIKEN BioResource Research CenterMicrobe Division |
| Sustainability Science/Life Science Domain | Proteomic profiling for classification of compounds (ChemProteoBase) | ChemProteoBase is a database that includes the proteomic changes of HeLa cells treated with compounds with well-known action. The data were obtained using 2D-DIGE, a proteome analysis method based on two-dimensional electrophoresis. In addition, a spot map showing the identification of major protein spots is also included. This information is expected to be important for the analysis of bioactive compounds. | Before 2016 | RIKEN Center for Sustainable Resource ScienceChemical Resource Development Research Unit |
| Life Science Domain | WDDD2 (WDDD2) | The WDDD2 database provides a comprehensive collection of quantitative data on nuclear division dynamics during early embryogenesis in Caenorhabditis elegans. Using 4D differential interference contrast (DIC) microscopy and bioimage informatics techniques, the study collected data from 33 wild-type embryos and 1142 embryos in which 263 essential embryonic genes were individually silenced by RNA interference (RNAi). For 189 genes, five or more datasets were obtained. Statistical analysis identified 8660 reproducible RNAi-induced phenotypes across 421 phenotypic characters, and clustering analysis suggested 24 functional processes essential for early development. WDDD2 offers a valuable resource for exploring gene function and understanding the mechanisms of animal development. | 2020/2/7 | RIKEN Center for Biosystems Dynamics ResearchLaboratory for Developmental Dynamics |
| Life Science Domain | Worm Developmental Dynamics Database (WDDD) | Our project aims to obtain a collection of quantitative information about cell division dynamics in early Caenorhabditis elegans embryos when each of all essential embryonic genes is silenced individually by RNA interference (RNAi). The information is obtained by combining four-dimensional differential contrast interference (DIC) microscopy and computer image processing (Hamahashi et al. 2007). The information collection provides novel opportunities for developing quantitative and computational approaches towards understanding animal development. | 2012/5/18 | RIKEN Center for Biosystems Dynamics ResearchLaboratory for Developmental Dynamics |
| Life Science Domain | Comprehensive Brain Science Network Platform (CBSN-PF) | The Comprehensive Brain Science platform (CBSN-PF) comprises following the databases. 1) The CBSN database primarily contains information on researchers who provide support to other researchers in the CBSN. 2) The Neuroscientist-SNS is a social networking service to promote the exchange of information and communication among scientists in the field of brain sciences. 3) The Mouse Phenotype Database contains the raw data of behavioral tests derived from various genetically engineered mice. The development of this site has been completed in FY2016, and archived since FY2019 with the end of the INCF Japan Node activities. | 2010 | RIKEN Center for Brain ScienceNeuroinformatics Unit |
1.3 Biomolecules & Metabolites
| Domain | Database Name (Abbreviation) | Description | Release Date | Center/Headquarters |
|---|---|---|---|---|
| Sustainability Science/Life Science Domain | Alga-PrAS (Algal Protein Annotation Suite) (Alga-PrAS) | Recently, algae are one of the most focused species in environmental, food study, etc., since there are potential abilities as high production rate of biomass, reduction of carbon dioxide, creation of food and nutritional supplement, etc. In addition, vast quantities of genome sequence data in algae have been produced with whole genome-sequences analysis in recent times. However, general information of algae proteomes are still very poor. Therefore, we developed analytical proteome database site to understand tendency of general algae proteomes. This database allows easily comparative analysis of proteomes each species, biological class, habitat environment, and functional class, etc. | 2017/7/1 | RIKEN Center for Sustainable Resource ScienceMetabolome Informatics Research Team |
| Life Science Domain | Computational mass spectrometry (CompMS) | Software developed by the administrators for lipidomics analysis can be downloaded from this database. MS and MS/MS spectra, CCS values, and other related information obtained using these tools are also publicly available. | 2018 | RIKEN Center for Integrative Medical SciencesLaboratory for Metabolomics |
| Sustainability Science/Life Science Domain | DROP Met (DROPMet) | DROP Met is a repository and distribution site of the dataset obtained from our multiple MS-based metabolome analyses. Various kinds of datasets, ranging from raw fundamental data on analytical conditions to metabolic profiles of biological samples, are available to the public. We release some datasets in the raw, hoping that users in bioinformatics and metabolomics fields will develop novel algorithms and methodologies of metabolomics using our datasets. | 2006/8/16 | RIKEN Center for Sustainable Resource ScienceMetabolome Informatics Research Team |
| Sustainability Science/Life Science Domain | Natural Products Encyclopedia (NPEdia) | NPEdia (Natural Products Encyclopedia) is a database compiled by the Chemical Biology Research Group at RIKEN that collects information on natural compounds such as secondary metabolites isolated from actinomycetes, fungi, plants, and other organisms.Some compounds registered in the Natural Compounds Bank (RIKEN NPdepo) are also included and available for public access. The database includes information such as compound names, CAS numbers, molecular weights, structures, and InChI information, and allows searching by compound names, InChIKey, or substructures. | Before 2006 | RIKEN Center for Sustainable Resource ScienceChemical Resource Development Research Unit |
| Sustainability Science/Life Science Domain | PlanMAXdb: Plant Metabolite Alliance eXplorer database (PlanMAXdb) | It leverages a comprehensive metabolome dataset spanning diverse plant species and their chemical landscapes to unveil undiscovered compounds, including medicinal phytochemicals. Through a molecular network relationships approach utilizing MS/MS datasets, PlanMAXdb constructs molecular networks from 434 plant samples, encompassing 157 species across 108 genera and 25 plant orders. | 2024/1/10 | RIKEN Center for Sustainable Resource ScienceMetabolome Informatics Research Team |
| Sustainability Science/Life Science Domain | Proteomic profiling for classification of compounds (ChemProteoBase) | ChemProteoBase is a database that includes the proteomic changes of HeLa cells treated with compounds with well-known action. The data were obtained using 2D-DIGE, a proteome analysis method based on two-dimensional electrophoresis. In addition, a spot map showing the identification of major protein spots is also included. This information is expected to be important for the analysis of bioactive compounds. | Before 2016 | RIKEN Center for Sustainable Resource ScienceChemical Resource Development Research Unit |
| Life Science/Sustainability Science Domain | RIKEN LIPIDOMICS | This database provides access to the results of non-targeted lipidomics analyses conducted on major mouse organs, human plasma, commonly used cell lines, as well as plants and algae. It also allows users to browse data based on molecular weight, CCS values, and other criteria, and to search for lipid structures using MS/MS spectra. | 2020/11/25 | RIKEN Center for Integrative Medical Sciences/RIKEN Center for Sustainable Resource ScienceLaboratory for Metabolomics/Metabolome Informatics Research Team |
1.4 Cells, Tissues & Bioresources
| Domain | Database Name (Abbreviation) | Description | Release Date | Center/Headquarters |
|---|---|---|---|---|
| Life Science/Sustainability Science Domain | BioResouce MetaDatabase (BRMD) | The BioResource MetaDatabase (BRMD) is a data repository that stores metadata for bioresources provided by the RIKEN BioResource Research Center (BRC). These bioresources include experimental mice, experimental plants, cell lines, gene materials, and microbial strains. The BRMD integrates essential information about bioresources, ontology terms like phenotypes and diseases, and orthologous (homologous) gene information. It publishes data based on the Semantic Web and Resource Description Framework (RDF), which are recognized as global standard technologies for metadata. Users can retrieve and download all data using SPARQL, a query language. This database also links with the online catalogs for each resource at BRC. | 2019/12/24 | RIKEN BioResource Research CenterIntegrated Bioresource Information Division |
| Life Science Domain | Homeostasis Imbalance Process Ontology (HOIP) | The Homeostasis Imbalance Process Ontology (HOIP) formalizes the course of biological processes that arise when systemic or cellular homeostasis is disrupted. Focusing on two prototypical courses—SARS-CoV-2 infection and cellular senescence—it delivers logically coherent classes and relations that span molecular triggers, signaling cascades, tissue dysfunction, and clinical outcomes. HOIP thus serves as a computable reference for annotating experimental evidence, comparing pathogenic pathways, and enabling automated reasoning across diverse homeostasis-imbalance courses. | 2020/8/22 | RIKEN BioResource Research CenterIntegrated Bioresource Information Division |
| Life Science Domain | Mouse Phenotype Publish Database (Pheno-pub) | The Mouse Phenomics Division conducts the Japan Mouse Clinic, a comprehensive analysis of phenotypes mainly in genetically modified mice, with the aim of understanding the pathophysiology of human diseases and elucidating gene functions. Pheno-pub publishes the data analyzed in the Japan Mouse Clinic with the client's approval, contributing to the maintenance of mouse resources and intellectual infrastructure. | 2009/5/13 | RIKEN BioResource Research CenterMouse Phenomics Division |
| Life Science Domain | MoG+, Mouse Genome Database with High Added Value (MoG+) | MoG+ is a genomic variation database for diverse laboratory mouse strains provided by RIKEN BRC, with a focus on wild-derived and disease model strains. It supports visualization and comparison of SNPs, indels, and structural variants across multiple reference genome versions. Publicly available variation data are also incorporated where appropriate. This comprehensive platform enables researchers to perform high-precision analyses of gene and regulatory regions while accounting for genome variants. MoG+ serves as a valuable resource for disease research and functional genomics. | 2020/3/27 | RIKEN BioResource Research CenterIntegrated Bioresource Information Division |
| Life Science Domain | Brain Atlas of Neurogenic Tagging Mouse Lines (NeuroGT database) | The NeuroGT database (Brain Atlas of Neurogenic Tagging Mouse Lines) is a comprehensive resource that provides image data of neurons tagged at specific embryonic stages across the mouse brain. By administering tamoxifen on a single embryonic day (E9.5–E18.5), neurons generated at that stage are selectively labeled. These neurons are visualized either by nuclear staining with nls-βGAL or by labeling the entire cell morphology using membrane-bound GFP (mGFP). This atlas allows researchers to explore spatial and temporal patterns of neurogenesis and to identify driver lines suitable for tagging neurons born at defined developmental time points. | 2020/11/21 | RIKEN Center for Biosystems Dynamics ResearchLaboratory for Developmental Dynamics |
| Life Science Domain | Brain/MINDS Marmoset Connectivity Resource (BMCR) | The BMCR is a resource that provides access to anterograde and retrograde neuronal tracer data, currently restricted to injections into the prefrontal cortex of a marmoset brain. We are currently extending the resources with ISH gene expression image data from the Marmoset Gene Atlas (https://gene-atlas.brainminds.jp/), and integrating data from anterograde tracer injections covering the entire marmoset cortex. It comprises post-processed data and tools for exploring and reviewing the data, and for integration with other marmoset brain image databases and cross-species comparisons. We visualize data of different individuals in a common reference space at an unprecedented high resolution. | 2024/9/17 | RIKEN Center for Brain ScienceBrain Image Analysis Unit |
| Life Science Domain | CBS Data Sharing Platform (CBS Repository) | We aim to achieve an analysis platform for the open neuroscience data to expand the research field for each individual in RIKEN CBS. CBS Data Sharing Platform (CBS-DSP) provides comprehensive data collection, which allows CBS scientists to generate and stimulate data-driven cross-modal neuroscience. We also plan to expand the platform for all RIKEN, which we expect for CBS researchers to broaden their research field beyond neuroscience. | 2022/6/1 | RIKEN Center for Brain ScienceNeuroinformatics Unit |
| Life Science Domain | CelLoc3D | CelLoc-3D is a database of the 3D arrangement of neocortical cells (gultamatargic/excitatory, GABAergic/inhibitory and/or astrocytes) identified in vivo in layer 2/3 of the primary visual cortex of the mouse by two-photon imaging. Users can construct and download their own dataset by choosing the parameters of 1) the age of the mice, 2) the size of the imaging volume, and 3) the number of each type of cells included in the volume. This database is developed by the Laboratory for Cortical Circuit Plasticity, RIKEN Brain Science Institute with the support of the BSI Neuroinformatics (BSI-NI) project. This site has been archived since FY2019. | 2014/12/26 | RIKEN Center for Brain ScienceNeuroinformatics Unit |
| Life Science/Sustainability Science Domain | RIKEN BRC BioResouce Xsearch (RBBX) | The RIKEN BioResource Xsearch (RBRX) system, accessible on the RIKEN BioResource Research Center (BRC) website (https://web.brc.riken.jp/), is a search platform that enables comprehensive, cross-database searching of data for experimental mice, experimental plants, cell lines, gene materials, and microbial strains. Users can efficiently search for relevant bioresources by using keywords such as bioresource names, gene names, or ontology terms related to diseases and phenotypes. The system also offers an advanced search function for more detailed queries. This system operates with the BioResource MetaDatabase (BRMD), serving as its backend database. | 2019/7/1 | RIKEN BioResource Research CenterIntegrated Bioresource Information Division |
| Life Science Domain | RIKEN BRC Mouse Strain Data Databese | The Experimental Animal Division of the RIKEN BioResource Research Center (BRC) provides public access to information on mouse strains that the division collects, preserves, quality-controls, and distributes. Users can search for mouse strains and access detailed information including strain characteristics, health reports, donor DNA for genetic modifications, preservation status, documents for distribution, and publications by user scientists. | RIKEN BioResource Research CenterExperimental Animal Division | |
| Life Science Domain | RIKEN BRC CELL SEARCH SYSTEM | This is data on cell resources held by the RIKEN Cell Bank. It includes details such as the type of resource, the cell name, the cell ID, a description, the provider, photos and related papers. | 2017 | RIKEN BioResource Research CenterCell Engineering Division |
| Life Science/Sustainability Science Domain | RIKEN BRC DNA Resource Catalog | The Gene Engineering Division of the RIKEN BRC, also known as RIKEN DNA Bank, collects important and valuable genetic materials including cDNA clones from human, animal, microbe and virus. We distribute them to scientists after rigorous quality control. Users can access detailed information of the genetic materials including their full-length sequences and related publications. （54 words） | 2011/8/18 | RIKEN BioResource Research CenterGene Engineering Division |
| Life Science/Sustainability Science Domain | RIKEN BRC Exp-Plant Catalog | The Experimental Plant Division of the RIKEN BioResource Research Center collects, preserves, maintains, distributes a wide range of biological resources, including natural accessions, mutants, and transgenic lines of Arabidopsis thaliana; plant cultured cells; and plant gene clones and plasmids. Users can explore these bioresources via an interactive search platform, accessing detailed lineage information and trait data to support advanced plant research. (61 words) | 2017/10/31 | RIKEN BioResource Research CenterExperimental Animal Division |
| Life Science/Sustainability Science Domain | RIKEN BRC plant cell line documentation | The Experimental Plant Division of the RIKEN BioResource Research Center offers comprehensive handling protocols for plant cultured cells, covering medium preparation, subculturing techniques, and a range of related methodologies. These include advanced protocols for genotyping, genetic transformation, and cryopreservation. Users can access detailed quality information, including genotyping results and maintenance history, to support reliable and reproducible research. (57 words) | 2018/6/19 | RIKEN BioResource Research CenterExperimental Plant Division |
| Life Science Domain | FANTOM5 Web Resource (FANTOM5) | The FANTOM5 dataset consists of approximately 3,000 files that measure the activity of transcription start sites (TSSs) for genes in various human and mouse samples, including primary cultured cells, cell lines, tissues, and time-course samples during development, differentiation, or stimulation. It includes not only gene-level data but also information on the activity of promoters and enhancers, as well as the expression of miRNAs and lncRNAs. | RIKEN Center for Integrative Medical SciencesLaboratory for Large-Scale Biomedical Data Technology | |
| Life Science Domain | FANTOM6 Web Resource (FANTOM6) | In FANTOM6, with the aim of elucidating the functions of non-coding RNAs, gene expression profiling and analysis were conducted after knockdown of non-coding RNAs across several cell types and their stimulation conditions. Additionally, data on RNA–genome interactions were acquired and analyzed. These datasets and the corresponding analysis results have been made publicly available and can be accessed through this web resource. | RIKEN Center for Integrative Medical SciencesLaboratory for Large-Scale Biomedical Data Technology | |
| Life Science/Sustainability Science Domain | JCM On-line Catalogue of Strains | The Microbe Division in RIKEN-BRC, also widely known as Japan Collection of Microorganisms (JCM) is committed to collecting, preserving, and distributing cultured microbial strains in order to contribute to scientific communities by maintaining and serving high-quality microbial resources useful for general microbial studies and various research fields particularly in environmental and health science. The JCM online catalogue provides academic information of scientific name, taxonomy, and related publications, as well as cultural properties of these microorganisms. | 1996~1997 | RIKEN BioResource Research CenterMicrobe Division |
| Life Science Domain | LEAVES (LEAVES) | Leaves is a mechanism-interpretation support system built on the Homeostasis Imbalance Process Ontology (HOIP). It annotates literature-based evidence for disruptions such as cellular senescence, COVID-19 infection, and chemical toxicity, enabling researchers to trace causal chains—from molecular events through organ damage to clinical outcomes—within an interactive graph. Leaves advances mechanism interpretation, hypothesis generation, and multi-layer ontology reasoning in life-science research. | 2024/1/25 | RIKEN BioResource Research CenterIntegrated Bioresource Information Division |
| Sustainability Science/Life Science Domain | Proteomic profiling for classification of compounds (ChemProteoBase) | ChemProteoBase is a database that includes the proteomic changes of HeLa cells treated with compounds with well-known action. The data were obtained using 2D-DIGE, a proteome analysis method based on two-dimensional electrophoresis. In addition, a spot map showing the identification of major protein spots is also included. This information is expected to be important for the analysis of bioactive compounds. | Before 2016 | RIKEN Center for Sustainable Resource ScienceChemical Resource Development Research Unit |
| Life Science/Sustainability Science Domain | RIKEN LIPIDOMICS | This database provides access to the results of non-targeted lipidomics analyses conducted on major mouse organs, human plasma, commonly used cell lines, as well as plants and algae. It also allows users to browse data based on molecular weight, CCS values, and other criteria, and to search for lipid structures using MS/MS spectra. | 2020/11/25 | RIKEN Center for Integrative Medical Sciences/RIKEN Center for Sustainable Resource ScienceLaboratory for Metabolomics/Metabolome Informatics Research Team |
| Life Science Domain | scPortalen2 (scPortalen2) | scPortalen2 is a comprehensive database designed to reuse and visualize single-cell RNA sequencing (scRNA-seq) data from human and mouse samples. It compiles publicly available datasets, reanalyzes them through a standardized pipeline, and provides gene expression profiles across various cell types. The platform supports interactive exploration, allowing users to search for genes or cell populations of interest and to compare expression patterns. By ensuring consistency in data processing, scPortalen2 facilitates reliable cross-study comparisons and aids in uncovering cellular heterogeneity in biological systems. | 2016 | RIKEN Center for Integrative Medical SciencesLaboratory for Large-Scale Biomedical Data Technology |
| Life Science Domain | WDDD2 (WDDD2) | The WDDD2 database provides a comprehensive collection of quantitative data on nuclear division dynamics during early embryogenesis in Caenorhabditis elegans. Using 4D differential interference contrast (DIC) microscopy and bioimage informatics techniques, the study collected data from 33 wild-type embryos and 1142 embryos in which 263 essential embryonic genes were individually silenced by RNA interference (RNAi). For 189 genes, five or more datasets were obtained. Statistical analysis identified 8660 reproducible RNAi-induced phenotypes across 421 phenotypic characters, and clustering analysis suggested 24 functional processes essential for early development. WDDD2 offers a valuable resource for exploring gene function and understanding the mechanisms of animal development. | 2020/2/7 | RIKEN Center for Biosystems Dynamics ResearchLaboratory for Developmental Dynamics |
| Life Science Domain | Worm Developmental Dynamics Database (WDDD) | Our project aims to obtain a collection of quantitative information about cell division dynamics in early Caenorhabditis elegans embryos when each of all essential embryonic genes is silenced individually by RNA interference (RNAi). The information is obtained by combining four-dimensional differential contrast interference (DIC) microscopy and computer image processing (Hamahashi et al. 2007). The information collection provides novel opportunities for developing quantitative and computational approaches towards understanding animal development. | 2012/5/18 | RIKEN Center for Biosystems Dynamics ResearchLaboratory for Developmental Dynamics |
1.5 Imaging
| Domain | Database Name (Abbreviation) | Description | Release Date | Center/Headquarters |
|---|---|---|---|---|
| Life Science Domain | Adult Zebrafish Brain Gene Expression Database (AZEBEX) | Zebrafish are useful model organisms in neuroscience. This database allows users to view and download in situ hybridization data of gene expression in the adult brain. Methods: Three to five fish were sampled for each gene. The sampled brains were fixed with PFA, embedded in paraffin, and sectioned into whole-brain serial sections.The entire zebrafish brain can be mounted on a single slide glass. After mapping gene expression via in situ hybridization, the slides were scanned using a NanoZoomer HT slide scanner (Hamamatsu Photonics). This data serves as a valuable resource for neuroscience research utilizing zebrafish. | 2023/3/27 | RIKEN Center for Brain Science/RIKEN Center for Biosystems Dynamics ResearchLaboratory for Systems Molecular Ethology/Laboratory for Developmental Dynamics |
| Life Science Domain | NeuroImaging Platform (NIMG-PF) | NeuroImaging Platform (NIMG-PF) has been accumulating information relating to neuroimaging research field. It provides not only information of published papers, experimental data, measurement and analysis methods, but also tutorial course introducing brain research particularly for novice researchers. As well, unique reference function of papers based on brain activity region is equipped for advanced researchers. This site was archived starting in 2019 with the end of the INCF Japan Node activities. | 2006 | RIKEN Center for Brain ScienceNeuroinformatics Unit |
| Life Science Domain | Mouse Phenotype Publish Database (Pheno-pub) | The Mouse Phenomics Division conducts the Japan Mouse Clinic, a comprehensive analysis of phenotypes mainly in genetically modified mice, with the aim of understanding the pathophysiology of human diseases and elucidating gene functions. Pheno-pub publishes the data analyzed in the Japan Mouse Clinic with the client's approval, contributing to the maintenance of mouse resources and intellectual infrastructure. | 2009/5/13 | RIKEN BioResource Research CenterMouse Phenomics Division |
| Life Science Domain | Brain Atlas of Neurogenic Tagging Mouse Lines (NeuroGT database) | The NeuroGT database (Brain Atlas of Neurogenic Tagging Mouse Lines) is a comprehensive resource that provides image data of neurons tagged at specific embryonic stages across the mouse brain. By administering tamoxifen on a single embryonic day (E9.5–E18.5), neurons generated at that stage are selectively labeled. These neurons are visualized either by nuclear staining with nls-βGAL or by labeling the entire cell morphology using membrane-bound GFP (mGFP). This atlas allows researchers to explore spatial and temporal patterns of neurogenesis and to identify driver lines suitable for tagging neurons born at defined developmental time points. | 2020/11/21 | RIKEN Center for Biosystems Dynamics ResearchLaboratory for Developmental Dynamics |
| Life Science Domain | Brain/MINDS Marmoset Connectivity Resource (BMCR) | The BMCR is a resource that provides access to anterograde and retrograde neuronal tracer data, currently restricted to injections into the prefrontal cortex of a marmoset brain. We are currently extending the resources with ISH gene expression image data from the Marmoset Gene Atlas (https://gene-atlas.brainminds.jp/), and integrating data from anterograde tracer injections covering the entire marmoset cortex. It comprises post-processed data and tools for exploring and reviewing the data, and for integration with other marmoset brain image databases and cross-species comparisons. We visualize data of different individuals in a common reference space at an unprecedented high resolution. | 2024/9/17 | RIKEN Center for Brain ScienceBrain Image Analysis Unit |
| Life Science Domain | CBS Data Sharing Platform (CBS Repository) | We aim to achieve an analysis platform for the open neuroscience data to expand the research field for each individual in RIKEN CBS. CBS Data Sharing Platform (CBS-DSP) provides comprehensive data collection, which allows CBS scientists to generate and stimulate data-driven cross-modal neuroscience. We also plan to expand the platform for all RIKEN, which we expect for CBS researchers to broaden their research field beyond neuroscience. | 2022/6/1 | RIKEN Center for Brain ScienceNeuroinformatics Unit |
| Life Science Domain | CelLoc3D | CelLoc-3D is a database of the 3D arrangement of neocortical cells (gultamatargic/excitatory, GABAergic/inhibitory and/or astrocytes) identified in vivo in layer 2/3 of the primary visual cortex of the mouse by two-photon imaging. Users can construct and download their own dataset by choosing the parameters of 1) the age of the mice, 2) the size of the imaging volume, and 3) the number of each type of cells included in the volume. This database is developed by the Laboratory for Cortical Circuit Plasticity, RIKEN Brain Science Institute with the support of the BSI Neuroinformatics (BSI-NI) project. This site has been archived since FY2019. | 2014/12/26 | RIKEN Center for Brain ScienceNeuroinformatics Unit |
| Life Science Domain | Invertebrate Brain Platform (IVB-PF) | The Invertebrate Brain Platform offers you direct access to a growing database of information on nervous systems and behaviour of various species of invertebrates and a large body of ancillary material to promote the use of invertebrate systems in research and edcuation and facilitate information transfer to engineers that are looking for mechanisms that may be useful to solve a wide range of technological problems . The database is linked to explanations of the contents to allow users to familiarise themselves with the data and the context in which they were obtained. This site was archived starting in 2019 with the end of the INCF Japan Node activities. | 2006 | RIKEN Center for Brain ScienceNeuroinformatics Unit |
| Life Science Domain | RIKEN BRC Mouse Strain Data Databese | The Experimental Animal Division of the RIKEN BioResource Research Center (BRC) provides public access to information on mouse strains that the division collects, preserves, quality-controls, and distributes. Users can search for mouse strains and access detailed information including strain characteristics, health reports, donor DNA for genetic modifications, preservation status, documents for distribution, and publications by user scientists. | RIKEN BioResource Research CenterExperimental Animal Division | |
| Life Science Domain | RIKEN BRC CELL SEARCH SYSTEM | This is data on cell resources held by the RIKEN Cell Bank. It includes details such as the type of resource, the cell name, the cell ID, a description, the provider, photos and related papers. | 2017 | RIKEN BioResource Research CenterCell Engineering Division |
| Life Science/Sustainability Science Domain | RIKEN BRC Exp-Plant Catalog | The Experimental Plant Division of the RIKEN BioResource Research Center collects, preserves, maintains, distributes a wide range of biological resources, including natural accessions, mutants, and transgenic lines of Arabidopsis thaliana; plant cultured cells; and plant gene clones and plasmids. Users can explore these bioresources via an interactive search platform, accessing detailed lineage information and trait data to support advanced plant research. (61 words) | 2017/10/31 | RIKEN BioResource Research CenterExperimental Animal Division |
| Sustainability Science/Life Science Domain | Electron Microscope Atlas (EM ATLAS) | Advancements in light microscopy have enabled visualization of cellular and molecular dynamics, but understanding the ultrastructural details of organelles still requires electron microscopy. We developed an automated wide-area TEM imaging system that captures and stitches tens of thousands of TEM images from plant tissues or cultured cells, generating gigapixel-scale datasets. Today, wide-area imaging is standard in modern TEMs, and large resin sections on slides can also be observed with SEM for broader and higher-resolution imaging. Our “EM Atlas” allows users to intuitively explore these detailed electron micrographs—zooming, panning, and navigating freely—much like using Google Maps, providing a powerful tool for understanding the ultrastructure of cells and tissues. | 2014/4/1 | RIKEN Center for Sustainable Resource ScienceMass Spectrometry and Microscopy Unit |
| Life Science Domain | NHP-NNP database (NHPNNP) | Brain structural, functional and diffusion MRI data of non-human primates (macaque, marmoset and jacaque monkeys). By releasing pre- and post-analysis data in various formats (NIFTI, CIFTI, GIFTI) and individual information, as well as standard brain template atlas data created from a large number of cases, many researchers can collate data on the same standard brain atlas template and accumulate information on brain function, structure, molecules, cells and expression. This information is important for accumulating information on brain function, structure, molecules and cellular expression. ※This database is scheduled to be made publicly available in 2026. | RIKEN Center for Biosystems Dynamics ResearchLaboratory for Brain Connectomics Imaging | |
| Life Science Domain | Brain/MINDS Data Portal | The Brain/MINDS Data Portal is a marmoset brain database that facilitates the unrestricted sharing of original data generated by the Brain/MINDS project to encourage collaboration. Created to make structural and gene expression data accessible to researchers worldwide, the Brain/MINDS Data Portal is the largest neuroimaging database of the common marmoset. All data on the online portal are mapped to a standard marmoset brain atlas, making the cross-referencing of data belonging to different modalities effortless. The database provides control data to detect abnormalities in disease model marmosets and allows integration with other database for cross-species comparisons. | 2017/3/21 | RIKEN Center for Brain ScienceNeuroinformatics Unit |
| Life Science/Sustainability Science Domain | JCM On-line Catalogue of Strains | The Microbe Division in RIKEN-BRC, also widely known as Japan Collection of Microorganisms (JCM) is committed to collecting, preserving, and distributing cultured microbial strains in order to contribute to scientific communities by maintaining and serving high-quality microbial resources useful for general microbial studies and various research fields particularly in environmental and health science. The JCM online catalogue provides academic information of scientific name, taxonomy, and related publications, as well as cultural properties of these microorganisms. | 1996~1997 | RIKEN BioResource Research CenterMicrobe Division |
| Life Science Domain | Marmoset Gene Atlas (MGA) | Our goal is to establish a genome-wide, high-resolution atlas of the gene expression throughout the common marmoset (Callithrix jacchus) brain. We employ in situ hybridization (ISH) analysis to systematically analyze changes in gene expression over the course of postnatal brain development to adult stage. We anticipate that these data will provide sufficient information to develop tools that allow us to reveal primate specific brain structure, function and connectivity. | 2017/10/27 | RIKEN Center for Brain ScienceLaboratory for Molecular Mechanisms of Brain Development |
| Life Science Domain | SSBD (SSBD) | SSBD is a platform designed to promote the sharing and reuse of bioimaging data. SSBD:repository is a data repository that collects and shares biological image data published in original research articles, as well as quantitative data on biological dynamics obtained through image analysis and computational simulations. In contrast, SSBD:database is an added-value database for biological dynamics, which systematically compiles and provides access to high-quality microscopy images acquired using cutting-edge techniques, the corresponding quantitative data derived through image analysis and simulations, and various tools used for data analysis. | 2013/9/2 | RIKEN Center for Biosystems Dynamics ResearchLaboratory for Developmental Dynamics |
| Life Science Domain | Visiome Platform (VP) | Visiome Platform (VP) is a web-based database system with a variety of digital research resources in Vision Science. This platform provides several types of contents, such as Experimental data, Mathematical model, Illusion stimulus, Analytical tools. This site was archived starting in 2019 with the end of the INCF Japan Node activities. | 2002 | RIKEN Center for Brain ScienceNeuroinformatics Unit |
| Life Science Domain | WDDD2 (WDDD2) | The WDDD2 database provides a comprehensive collection of quantitative data on nuclear division dynamics during early embryogenesis in Caenorhabditis elegans. Using 4D differential interference contrast (DIC) microscopy and bioimage informatics techniques, the study collected data from 33 wild-type embryos and 1142 embryos in which 263 essential embryonic genes were individually silenced by RNA interference (RNAi). For 189 genes, five or more datasets were obtained. Statistical analysis identified 8660 reproducible RNAi-induced phenotypes across 421 phenotypic characters, and clustering analysis suggested 24 functional processes essential for early development. WDDD2 offers a valuable resource for exploring gene function and understanding the mechanisms of animal development. | 2020/2/7 | RIKEN Center for Biosystems Dynamics ResearchLaboratory for Developmental Dynamics |
| Life Science Domain | Worm Developmental Dynamics Database (WDDD) | Our project aims to obtain a collection of quantitative information about cell division dynamics in early Caenorhabditis elegans embryos when each of all essential embryonic genes is silenced individually by RNA interference (RNAi). The information is obtained by combining four-dimensional differential contrast interference (DIC) microscopy and computer image processing (Hamahashi et al. 2007). The information collection provides novel opportunities for developing quantitative and computational approaches towards understanding animal development. | 2012/5/18 | RIKEN Center for Biosystems Dynamics ResearchLaboratory for Developmental Dynamics |
1.6 Others (Publications, Terminology, Tools, Models, etc.)
| Domain | Database Name (Abbreviation) | Description | Release Date | Center/Headquarters |
|---|---|---|---|---|
| Life Science Domain | OpenNeuro Repository | The OpenNeuro Repository is started the service early summer in 2018. This site provides a reliable opportunity for researchers in the field of experimental and computational neuroscience to share supplemental materials to their peer-reviewed publications in academic journals and conference proceedings that are available in the public domain. It aims at playing a core role for promoting and accelerating neuroscience. Toward this end, we encourage databasing of complete sets of experimental image and/or time-series data, audiovisual materials, computational models, which have been described and/or analyzed in the publications. This site was archived starting in 2019 with the end of the INCF Japan Node activities. | 2018/8/8 | RIKEN Center for Brain ScienceNeuroinformatics Unit |
| Life Science Domain | DynamicBrain Platform (DB-PF) | This site promotes studies on the dynamic principles of brain functions through unifying experimental and computational approaches in cellular, local circuit, global network and behavioral levels. Our goal is to capture the autonomy and the creativity in living organisms which enlightens the complexity of nature and society. This site was archived starting in 2019 with the end of the INCF Japan Node activities. | 2009 | RIKEN Center for Brain ScienceNeuroinformatics Unit |
| Life Science Domain | NeuroImaging Platform (NIMG-PF) | NeuroImaging Platform (NIMG-PF) has been accumulating information relating to neuroimaging research field. It provides not only information of published papers, experimental data, measurement and analysis methods, but also tutorial course introducing brain research particularly for novice researchers. As well, unique reference function of papers based on brain activity region is equipped for advanced researchers. This site was archived starting in 2019 with the end of the INCF Japan Node activities. | 2006 | RIKEN Center for Brain ScienceNeuroinformatics Unit |
| Life Science/Sustainability Science Domain | BioResouce MetaDatabase (BRMD) | The BioResource MetaDatabase (BRMD) is a data repository that stores metadata for bioresources provided by the RIKEN BioResource Research Center (BRC). These bioresources include experimental mice, experimental plants, cell lines, gene materials, and microbial strains. The BRMD integrates essential information about bioresources, ontology terms like phenotypes and diseases, and orthologous (homologous) gene information. It publishes data based on the Semantic Web and Resource Description Framework (RDF), which are recognized as global standard technologies for metadata. Users can retrieve and download all data using SPARQL, a query language. This database also links with the online catalogs for each resource at BRC. | 2019/12/24 | RIKEN BioResource Research CenterIntegrated Bioresource Information Division |
| Life Science Domain | Homeostasis Imbalance Process Ontology (HOIP) | The Homeostasis Imbalance Process Ontology (HOIP) formalizes the course of biological processes that arise when systemic or cellular homeostasis is disrupted. Focusing on two prototypical courses—SARS-CoV-2 infection and cellular senescence—it delivers logically coherent classes and relations that span molecular triggers, signaling cascades, tissue dysfunction, and clinical outcomes. HOIP thus serves as a computable reference for annotating experimental evidence, comparing pathogenic pathways, and enabling automated reasoning across diverse homeostasis-imbalance courses. | 2020/8/22 | RIKEN BioResource Research CenterIntegrated Bioresource Information Division |
| Life Science Domain | BMI Platform (BMI-PF) | Brain Machine Interface Platform (BMI-PF) accumulates BMI(Brain Machine Interface)-related data that are useful for education and experiment. The platform consists of the following five databases. 1) Database of BMI (Brain Machine Interfaces)-related papers, 2) Database of original contents 3) Database of BMI-related research sites, 4) Database of BMI-related materials and 5) BMI-related column in Japanese. The development of this site has been completed in FY2016, and archived since FY2019 with the end of the INCF Japan Node activities. | 2005 | RIKEN Center for Brain ScienceNeuroinformatics Unit |
| Life Science Domain | Brain Atlas | This site provides three databases developed by the Laboratory for Symbolic Cognitive Development, RIKEN Brain Science Institute with the support of the BSI Neuroinformatics (BSI-NI) project: Degu 3D brain atlas, Marmoset 3D brain atlas, and Marmoset MRI Standard brain, along with a visualization tool. This site has been archived since FY2019. | 2012 | RIKEN Center for Brain ScienceNeuroinformatics Unit |
| Life Science Domain | Brain/MINDS Marmoset Connectivity Resource (BMCR) | The BMCR is a resource that provides access to anterograde and retrograde neuronal tracer data, currently restricted to injections into the prefrontal cortex of a marmoset brain. We are currently extending the resources with ISH gene expression image data from the Marmoset Gene Atlas (https://gene-atlas.brainminds.jp/), and integrating data from anterograde tracer injections covering the entire marmoset cortex. It comprises post-processed data and tools for exploring and reviewing the data, and for integration with other marmoset brain image databases and cross-species comparisons. We visualize data of different individuals in a common reference space at an unprecedented high resolution. | 2024/9/17 | RIKEN Center for Brain ScienceBrain Image Analysis Unit |
| Life Science Domain | BSI Neuroinformatics (BSI-NI) | BSI Neuroinformatics (BSI-NI) project was launched in 2007 as an original database obtained by laboratories of RIKEN Brain Science Institute (BSI). Databases and tools created by RIKEN BSI laboratories in BSI-NI Project(FY2007-FY2017) are available from this website. We hope this site helps to promote further development of brain research. This site has been archived since FY2019. | 2011/9/5 | RIKEN Center for Brain ScienceNeuroinformatics Unit |
| Life Science Domain | CBS Data Sharing Platform (CBS Repository) | We aim to achieve an analysis platform for the open neuroscience data to expand the research field for each individual in RIKEN CBS. CBS Data Sharing Platform (CBS-DSP) provides comprehensive data collection, which allows CBS scientists to generate and stimulate data-driven cross-modal neuroscience. We also plan to expand the platform for all RIKEN, which we expect for CBS researchers to broaden their research field beyond neuroscience. | 2022/6/1 | RIKEN Center for Brain ScienceNeuroinformatics Unit |
| Life Science Domain | Invertebrate Brain Platform (IVB-PF) | The Invertebrate Brain Platform offers you direct access to a growing database of information on nervous systems and behaviour of various species of invertebrates and a large body of ancillary material to promote the use of invertebrate systems in research and edcuation and facilitate information transfer to engineers that are looking for mechanisms that may be useful to solve a wide range of technological problems . The database is linked to explanations of the contents to allow users to familiarise themselves with the data and the context in which they were obtained. This site was archived starting in 2019 with the end of the INCF Japan Node activities. | 2006 | RIKEN Center for Brain ScienceNeuroinformatics Unit |
| Life Science Domain | RIKEN BRC Mouse Strain Data Databese | The Experimental Animal Division of the RIKEN BioResource Research Center (BRC) provides public access to information on mouse strains that the division collects, preserves, quality-controls, and distributes. Users can search for mouse strains and access detailed information including strain characteristics, health reports, donor DNA for genetic modifications, preservation status, documents for distribution, and publications by user scientists. | RIKEN BioResource Research CenterExperimental Animal Division | |
| Life Science Domain | RIKEN BRC CELL SEARCH SYSTEM | This is data on cell resources held by the RIKEN Cell Bank. It includes details such as the type of resource, the cell name, the cell ID, a description, the provider, photos and related papers. | 2017 | RIKEN BioResource Research CenterCell Engineering Division |
| Life Science/Sustainability Science Domain | RIKEN BRC DNA Resource Catalog | The Gene Engineering Division of the RIKEN BRC, also known as RIKEN DNA Bank, collects important and valuable genetic materials including cDNA clones from human, animal, microbe and virus. We distribute them to scientists after rigorous quality control. Users can access detailed information of the genetic materials including their full-length sequences and related publications. （54 words） | 2011/8/18 | RIKEN BioResource Research CenterGene Engineering Division |
| Life Science/Sustainability Science Domain | RIKEN BRC Exp-Plant Catalog | The Experimental Plant Division of the RIKEN BioResource Research Center collects, preserves, maintains, distributes a wide range of biological resources, including natural accessions, mutants, and transgenic lines of Arabidopsis thaliana; plant cultured cells; and plant gene clones and plasmids. Users can explore these bioresources via an interactive search platform, accessing detailed lineage information and trait data to support advanced plant research. (61 words) | 2017/10/31 | RIKEN BioResource Research CenterExperimental Animal Division |
| Life Science/Sustainability Science Domain | RIKEN BRC plant cell line documentation | The Experimental Plant Division of the RIKEN BioResource Research Center offers comprehensive handling protocols for plant cultured cells, covering medium preparation, subculturing techniques, and a range of related methodologies. These include advanced protocols for genotyping, genetic transformation, and cryopreservation. Users can access detailed quality information, including genotyping results and maintenance history, to support reliable and reproducible research. (57 words) | 2018/6/19 | RIKEN BioResource Research CenterExperimental Plant Division |
| Life Science Domain | Brain Science Dictionary (BSD) | Brain Science Dictionary is an online dictionary for students and researchers in neuroscience field. It is in a Wikipedia style but written only by invited authors with peer reviewing process. Articles are explained in Japanese, which can be accessed by anybody without any fee. The dictionary is managed by the Editorial Committee chaired by Dr. Yasunori Hayashi (in Kyoto University Graduate School of Medicine) as an official activity of the The Japan Neuroscience Society with support of RIKEN Center for Brain Science. Our effort is totally non-profit, researcher-initiated, public awareness activity. | 2011/6/7 | RIKEN Center for Brain ScienceNeuroinformatics Unit |
| Life Science/Sustainability Science Domain | JCM On-line Catalogue of Strains | The Microbe Division in RIKEN-BRC, also widely known as Japan Collection of Microorganisms (JCM) is committed to collecting, preserving, and distributing cultured microbial strains in order to contribute to scientific communities by maintaining and serving high-quality microbial resources useful for general microbial studies and various research fields particularly in environmental and health science. The JCM online catalogue provides academic information of scientific name, taxonomy, and related publications, as well as cultural properties of these microorganisms. | 1996~1997 | RIKEN BioResource Research CenterMicrobe Division |
| Life Science Domain | LEAVES (LEAVES) | Leaves is a mechanism-interpretation support system built on the Homeostasis Imbalance Process Ontology (HOIP). It annotates literature-based evidence for disruptions such as cellular senescence, COVID-19 infection, and chemical toxicity, enabling researchers to trace causal chains—from molecular events through organ damage to clinical outcomes—within an interactive graph. Leaves advances mechanism interpretation, hypothesis generation, and multi-layer ontology reasoning in life-science research. | 2024/1/25 | RIKEN BioResource Research CenterIntegrated Bioresource Information Division |
| Life Science Domain | Pupil Platform | The Pupil Platform has been developed by Laboratory for Neuroinfomatics, RIKEN Brain Science Institute in 2007. Which is the one of the practical applications of XooNIps base platform system. The Pupil Platform collects and publishes the following four datasets to facilitate research on pupils. 1) Literature information, 2) Mthematical models, 3) Experimental data, and 4) Conference information. This site has been archived since FY2019. | 2007 | RIKEN Center for Brain ScienceNeuroinformatics Unit |
| Life Science Domain | SSBD (SSBD) | SSBD is a platform designed to promote the sharing and reuse of bioimaging data. SSBD:repository is a data repository that collects and shares biological image data published in original research articles, as well as quantitative data on biological dynamics obtained through image analysis and computational simulations. In contrast, SSBD:database is an added-value database for biological dynamics, which systematically compiles and provides access to high-quality microscopy images acquired using cutting-edge techniques, the corresponding quantitative data derived through image analysis and simulations, and various tools used for data analysis. | 2013/9/2 | RIKEN Center for Biosystems Dynamics ResearchLaboratory for Developmental Dynamics |
| Life Science Domain | SSBD Ontology (SSBD Ontology) | The SSBD ontology, aligned with FAIR principles, provides a comprehensive metadata schema for bioimaging data. Bibliographic records, authors, imaging techniques, instruments, and biological samples are modeled in OWL-DL. Biological terms reuse OBO Foundry ontologies (ChEBI, CL, CLO, UBERON, GO, FBbi, OBI, IAO) to maximize interoperability and enable rich cross-layer annotations. Each dataset is published as an RDF instance and linked to large-scale image data through OME-NGFF/Zarr. This architecture accelerates data sharing and reuse of the global bio-imaging ecosystem. | 2025/5/8 | RIKEN Center for Biosystems Dynamics ResearchLaboratory for Developmental Dynamics |
| Life Science Domain | Visiome Platform (VP) | Visiome Platform (VP) is a web-based database system with a variety of digital research resources in Vision Science. This platform provides several types of contents, such as Experimental data, Mathematical model, Illusion stimulus, Analytical tools. This site was archived starting in 2019 with the end of the INCF Japan Node activities. | 2002 | RIKEN Center for Brain ScienceNeuroinformatics Unit |
| Life Science Domain | Comprehensive Brain Science Network Platform (CBSN-PF) | The Comprehensive Brain Science platform (CBSN-PF) comprises following the databases. 1) The CBSN database primarily contains information on researchers who provide support to other researchers in the CBSN. 2) The Neuroscientist-SNS is a social networking service to promote the exchange of information and communication among scientists in the field of brain sciences. 3) The Mouse Phenotype Database contains the raw data of behavioral tests derived from various genetically engineered mice. The development of this site has been completed in FY2016, and archived since FY2019 with the end of the INCF Japan Node activities. | 2010 | RIKEN Center for Brain ScienceNeuroinformatics Unit |
| Life Science Domain | Cerebellar Platform (Cerebellar-PF) | Cerebellar Platform is an integrated database for cerebellar research. This database contains mini-reviews of contemporary cerebellar research, list of papers and mathematical models for cerebellar operation. It allows users to browse by an index tree or data types (model, paper, picture, etc.). This site was archived starting in 2019 with the end of the INCF Japan Node activities. | 2006 | RIKEN Center for Brain ScienceNeuroinformatics Unit |
1.7 Portals
| Domain | Database Name (Abbreviation) | Description | Release Date | Center/Headquarters |
|---|---|---|---|---|
| Life Science Domain | DynamicBrain Platform (DB-PF) | This site promotes studies on the dynamic principles of brain functions through unifying experimental and computational approaches in cellular, local circuit, global network and behavioral levels. Our goal is to capture the autonomy and the creativity in living organisms which enlightens the complexity of nature and society. This site was archived starting in 2019 with the end of the INCF Japan Node activities. | 2009 | RIKEN Center for Brain ScienceNeuroinformatics Unit |
| Life Science Domain | NeuroImaging Platform (NIMG-PF) | NeuroImaging Platform (NIMG-PF) has been accumulating information relating to neuroimaging research field. It provides not only information of published papers, experimental data, measurement and analysis methods, but also tutorial course introducing brain research particularly for novice researchers. As well, unique reference function of papers based on brain activity region is equipped for advanced researchers. This site was archived starting in 2019 with the end of the INCF Japan Node activities. | 2006 | RIKEN Center for Brain ScienceNeuroinformatics Unit |
| Life Science Domain | BMI Platform (BMI-PF) | Brain Machine Interface Platform (BMI-PF) accumulates BMI(Brain Machine Interface)-related data that are useful for education and experiment. The platform consists of the following five databases. 1) Database of BMI (Brain Machine Interfaces)-related papers, 2) Database of original contents 3) Database of BMI-related research sites, 4) Database of BMI-related materials and 5) BMI-related column in Japanese. The development of this site has been completed in FY2016, and archived since FY2019 with the end of the INCF Japan Node activities. | 2005 | RIKEN Center for Brain ScienceNeuroinformatics Unit |
| Life Science Domain | BSI Neuroinformatics (BSI-NI) | BSI Neuroinformatics (BSI-NI) project was launched in 2007 as an original database obtained by laboratories of RIKEN Brain Science Institute (BSI). Databases and tools created by RIKEN BSI laboratories in BSI-NI Project(FY2007-FY2017) are available from this website. We hope this site helps to promote further development of brain research. This site has been archived since FY2019. | 2011/9/5 | RIKEN Center for Brain ScienceNeuroinformatics Unit |
| Life Science Domain | CBS Data Sharing Platform (CBS Repository) | We aim to achieve an analysis platform for the open neuroscience data to expand the research field for each individual in RIKEN CBS. CBS Data Sharing Platform (CBS-DSP) provides comprehensive data collection, which allows CBS scientists to generate and stimulate data-driven cross-modal neuroscience. We also plan to expand the platform for all RIKEN, which we expect for CBS researchers to broaden their research field beyond neuroscience. | 2022/6/1 | RIKEN Center for Brain ScienceNeuroinformatics Unit |
| Life Science Domain | Invertebrate Brain Platform (IVB-PF) | The Invertebrate Brain Platform offers you direct access to a growing database of information on nervous systems and behaviour of various species of invertebrates and a large body of ancillary material to promote the use of invertebrate systems in research and edcuation and facilitate information transfer to engineers that are looking for mechanisms that may be useful to solve a wide range of technological problems . The database is linked to explanations of the contents to allow users to familiarise themselves with the data and the context in which they were obtained. This site was archived starting in 2019 with the end of the INCF Japan Node activities. | 2006 | RIKEN Center for Brain ScienceNeuroinformatics Unit |
| Life Science Domain | RIKEN Open Science Portal | RIKEN is the most comprehensive research institute for natural sciences in Japan that researches a wide range of fields in the natural sciences. To disseminate research results into society, we work towards open science realization which includes but is not limited to: cooperation with universities and companies, transferring technology, property, and intellectual rights to industry. Under the ICT approach, we maximize the utilization of research data with our management infrastructure that promotes data-driven research projects and strategic disclosure of research data. Activities and related information will be sent from this portal site. | 2021/3/26 | RIKEN Information R&D and Strategy HeadquartersData Knowledge Organization Unit |
| Life Science Domain | RIKEN Open Life Science Platform | This page provides an overview of RIKEN's primary databases, along with links to the data, which serve as platforms for life science field. RIKEN Open Life Science Platform aims to develop analytical foundation (platform) for the open big data era. It aggregates and integrates multi-modal data spanning multiple levels from molecules to organisms and derived from diverse measurement methods, enabling data-driven, precise prediction and manipulation of cellular and organismal states. | 2025/10/3 | RIKEN Information R&D and Strategy HeadquartersLife Science Data Sharing Unit |
| Life Science Domain | RIKEN MetaDatabase | This database portal site is used to provide information on RIKEN's various life science databases to order to help researchers around the world make full use of RIKEN's research results. The database provides life-science data in the bases of standardized metadata techniques including semantic web and Resource Description Framework (RDF). | 2015/4/1 | RIKEN Information R&D and Strategy HeadquartersData Knowledge Organization Unit |
| Life Science Domain | Brain/MINDS Data Portal | The Brain/MINDS Data Portal is a marmoset brain database that facilitates the unrestricted sharing of original data generated by the Brain/MINDS project to encourage collaboration. Created to make structural and gene expression data accessible to researchers worldwide, the Brain/MINDS Data Portal is the largest neuroimaging database of the common marmoset. All data on the online portal are mapped to a standard marmoset brain atlas, making the cross-referencing of data belonging to different modalities effortless. The database provides control data to detect abnormalities in disease model marmosets and allows integration with other database for cross-species comparisons. | 2017/3/21 | RIKEN Center for Brain ScienceNeuroinformatics Unit |
| Life Science Domain | INCF Japan Node Portal | The INCF Japan Node was established in 2005, with its secretariat located at the Neuroinformatics Japan Center within the RIKEN Brain Science Institute (BSI). Its major activities are 1)Shaping domestic neuroinformatics research and directions. 2)Advising on intellectual property rights and protecting experimental subjects. 3)Developing and publishing brain science databases. 4)Coordinating database management. 5)Disseminating neuroinformatics information via the web portal. 6) Developing the infrastructure for brain science information and neuroinformatics. 7)Supporting the development and spreading of neuroinformatics technology. These activities concluded in March 2019, and this portal site has since been archived and remains publicly accessible. | 2005 | RIKEN Center for Brain ScienceNeuroinformatics Unit |
| Life Science Domain | SSBD (SSBD) | SSBD is a platform designed to promote the sharing and reuse of bioimaging data. SSBD:repository is a data repository that collects and shares biological image data published in original research articles, as well as quantitative data on biological dynamics obtained through image analysis and computational simulations. In contrast, SSBD:database is an added-value database for biological dynamics, which systematically compiles and provides access to high-quality microscopy images acquired using cutting-edge techniques, the corresponding quantitative data derived through image analysis and simulations, and various tools used for data analysis. | 2013/9/2 | RIKEN Center for Biosystems Dynamics ResearchLaboratory for Developmental Dynamics |
| Life Science Domain | Visiome Platform (VP) | Visiome Platform (VP) is a web-based database system with a variety of digital research resources in Vision Science. This platform provides several types of contents, such as Experimental data, Mathematical model, Illusion stimulus, Analytical tools. This site was archived starting in 2019 with the end of the INCF Japan Node activities. | 2002 | RIKEN Center for Brain ScienceNeuroinformatics Unit |
| Life Science Domain | Comprehensive Brain Science Network Platform (CBSN-PF) | The Comprehensive Brain Science platform (CBSN-PF) comprises following the databases. 1) The CBSN database primarily contains information on researchers who provide support to other researchers in the CBSN. 2) The Neuroscientist-SNS is a social networking service to promote the exchange of information and communication among scientists in the field of brain sciences. 3) The Mouse Phenotype Database contains the raw data of behavioral tests derived from various genetically engineered mice. The development of this site has been completed in FY2016, and archived since FY2019 with the end of the INCF Japan Node activities. | 2010 | RIKEN Center for Brain ScienceNeuroinformatics Unit |
| Life Science Domain | Cerebellar Platform (Cerebellar-PF) | Cerebellar Platform is an integrated database for cerebellar research. This database contains mini-reviews of contemporary cerebellar research, list of papers and mathematical models for cerebellar operation. It allows users to browse by an index tree or data types (model, paper, picture, etc.). This site was archived starting in 2019 with the end of the INCF Japan Node activities. | 2006 | RIKEN Center for Brain ScienceNeuroinformatics Unit |
2 Physical Sciences
| Domain | Database Name (Abbreviation) | Description | Release Date | Center/Headquarters |
|---|---|---|---|---|
| Physical Science Domain | Muon Nuclear Data (µND) | Muon Nuclear Data collects experimental and theoretical muon nuclear reactions and releases them as evaluated nuclear data. This database includes the muonic X-ray energies, lifetimes of muonic atoms, production branching ratios of residual nuclei by muon capture, and energy distributions of evaporation particles. It contributes to research and development in various fields such as semiconductor device soft error countermeasures, radiation safety, RI production for medical use, and non-destructive elemental analysis. | Under development with the goal of releasing it within FY2025 | RIKEN Nishina Center for Accelerator-Based ScienceNuclear Transmutation Data Group |
| Physical Science Domain | Database of RI beams produced at BigRIPS | This database provides information on radioactive isotope (RI) beams produced using the BigRIPS separator at the RI Beam Factory (RIBF), operated by the RIKEN Nishina Center for Accelerator-Based Science. BigRIPS is a powerful device for producing RI beams far from the line of beta stability. The database offers essential data on RI production yields to support researchers in planning nuclear physics experiments at RIBF. | 2019/6/6 | RIKEN Nishina Center for Accelerator-Based ScienceBigRIPS Team |
| Pioneering Science/Physical Science Domain | All-sky X-ray Image public data (MAXI) | This is a database of X-ray variable sources across the entire sky, measured by the Monitor of All-sky X-ray Image (MAXI) installed on the International Space Station (ISS). MAXI has been monitoring of the whole sky in the X-ray (2-20 keV) band since 2009. This database contains alerts for transient objects, and intensity variations of about 500 X-ray sources. It serves basic information for the multi-wavelength astronomy, ranging from radio to gamma-ray, as well as for the multi-messenger astronomy with gravitational waves and neutrino astronomy. MAXI data are publicly available from RIKEN, and also from NASA's HEASARC database, and the JAXA's DART database. | 2009/8/15 | RIKEN Pioneering Research Institute/RIKEN Nishina Center for Accelerator-Based Science |
3 Mathematical, Computational, and Information Sciences
| Domain | Database Name (Abbreviation) | Description | Release Date | Center/Headquarters |
|---|---|---|---|---|
| Mathematical, Computational and Information Science Domain | Program Code | This page contains the program codes developed by the RIKEN AIP teams in their algorithm papers. The source codes are listed by team to help you build on their work. | 2022/2/8 | RIKEN Center for Advanced Intelligence ProjectRIKEN Center for Advanced Intelligence Project |
| Mathematical, Computational and Information Science Domain | RIKEN nowcast | Programs for our precipitation nowcasting system (RIKEN nowcast). We use a kinematic approach based on an advection equation and a data-driven approach based on motion of precipitation pattern. To improve the system further, we are investigating a deep-learning-based algorithm. | 2018/6/7 | RIKEN Center for Interdisciplinary Theoretical and Mathematical SciencesPrediction Science Research Team |
| Mathematical, Computational and Information Science Domain | Open-set Scene Graph dataset (OSG dataset) | Based on the Visual Genome scene graph dataset, this code expand the dataset to the open-set scene graph setting (processing script for the expansion). | 2022/4/21 | RIKEN Information R&D and Strategy HeadquartersMultimodal Data Recognition Research Team |
| Mathematical, Computational and Information Science Domain | Replica Semantic Scene Graph dataset (ReplicaSSG) | A dataset to which Visual Genome dataset-compatible scene graph annotations have been added to the replica dataset. | 2025/8/1 | RIKEN Information R&D and Strategy HeadquartersMultimodal Data Recognition Research Team |
| Mathematical, Computational and Information Science Domain | RIKEN facial expression database (RIKEN Facial Database) | A new facial database that includes multiple theoretical views of emotions and expressers’ individualized events with multi-angle and depth information. | 2023/12/8 | RIKEN Information R&D and Strategy HeadquartersPsychological Process Research Team |
| Mathematical, Computational and Information Science Domain | sbPOM-LETKF (sbPOM-LETKF) | LETKF implementation for a regional ocean model sbPOM. | 2022/6/27 | RIKEN Center for Interdisciplinary Theoretical and Mathematical SciencesPrediction Science Research Team |
| Mathematical, Computational and Information Science Domain | SCALE-LETKF (SCALE-LETKF) | LETKF implementation for a regional atmospheric model SCALE-RM. | 2024/4/5 | RIKEN Center for Interdisciplinary Theoretical and Mathematical SciencesPrediction Science Research Team |
| Mathematical, Computational and Information Science Domain | Scene-Specific Anomalous Relationship Detection indoor dataset (SARD indoor dataset) | A dataset consisting of a group of indoor images defining normal conditions for each scene and images containing abnormal conditions of the scene that differ from normal conditions. | 2025/6/19 | RIKEN Information R&D and Strategy HeadquartersMultimodal Data Recognition Research Team |
| Mathematical, Computational and Information Science Domain | SEIB-PF (SEIB-PF) | SEIB-PF can assimilate Leaf Area Index with SEIB-DGVM (Spatially Explicit Individual Based Dynamic Global Vegetation Model) using Particle Filter. | 2019/10/24 | RIKEN Center for Interdisciplinary Theoretical and Mathematical SciencesPrediction Science Research Team |
| Mathematical, Computational and Information Science Domain | Control simulation experiments (CSE) | Program code for control simulation experiments. https://doi.org/10.5194/npg-29-133-2022 https://doi.org/10.5194/npg-30-117-2023 | 2022/8/31 2023/7/17 | RIKEN Center for Interdisciplinary Theoretical and Mathematical SciencesPrediction Science Research Team |
| Mathematical, Computational and Information Science Domain | Local Ensemble Transform Kalman Filter (LETKF) | Generic Fortran modules for LETKF and its implementations for specific models (e.g. Lorenz-96, Speedy, WRF...). | RIKEN Center for Interdisciplinary Theoretical and Mathematical SciencesPrediction Science Research Team |