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Physiome.jp (http://physiome.jp) is a portal site inaugurated in 2007 to support model-based research in physiome and systems biology. At Physiome.jp, several tools and databases are available to support construction of physiological, multi-hierarchical, large-scale models. There are three databases in Physiome.jp, housing mathematical models, morphological data, and time-series data. In late 2013, the site was fully renovated, and in May 2015, new functions were implemented to provide information infrastructure to support collaborative activities for developing models and performing simulations within the database framework. This article describes updates to the databases implemented since 2013, including cooperation among the three databases, interactive model browsing, user management, version management of models, management of parameter sets, and interoperability with applications.
Pubmed ID: 26441671
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A note taking software that synchronizes information such as notes, web clips, audio files, photos and video collected across multiple devices. It allows for easy sharing and collaboration on projects.
View all literature mentionsA resource for sharing and collaboratively developing computational models of neural systems. While models can be submitted and developed in any format, the use of open standards such as NeuroML and PyNN is encouraged, to ensure transparency, modularity, accessibility and cross simulator portability. OSB will provide advanced facilities to analyze, visualize and transform models in these formats, and to connect researchers interested in models of specific neurons, brain regions and disease states. Research themes include: Basal ganglia modelling, Cerebellar Granule cell modelling, Cerebellar modelling, Hippocampal modelling, Neocortical modelling, Whole brain models. Additional themes are welcome.
View all literature mentionsRepository of mathematical models of biological and biomedical systems. Hosts selection of existing literature based physiologically and pharmaceutically relevant mechanistic models in standard formats. Features programmatic access via Web Services. Each model is curated to verify that it corresponds to reference publication and gives proper numerical results. Curators also annotate components of models with terms from controlled vocabularies and links to other relevant data resources allowing users to search accurately for models they need. Models can be retrieved in SBML format and import/export facilities are being developed to extend spectrum of formats supported by resource.
View all literature mentionsCurated database of published models so that they can be openly accessed, downloaded, and tested to support computational neuroscience. Provides accessible location for storing and efficiently retrieving computational neuroscience models.Coupled with NeuronDB. Models can be coded in any language for any environment. Model code can be viewed before downloading and browsers can be set to auto-launch the models. The model source code has to be available from publicly accessible online repository or WWW site. Original source code is used to generate simulation results from which authors derived their published insights and conclusions.
View all literature mentionsPhysiome.jp has been established to provide building blocks useful to develop in silico human. The blocks will include mathematical models and experimental data representing physiological functions. Physiome.jp is a part of the Worldwide Integrative Biomedical Research Cooperation to promote Physiome and Systems Biology. The building blocks (modules, models, biological data) representing biological functions and structure are databased and served as elements in the catalogue of human knowledge. They can be reused for deeper understanding of human physiology, eventually contributing to establishment of in silico medicine and predictive medicine. The databases (insilicoDB) at www.physiome.jp currently include a Model Database and a Morphology Database. The Model Database stores a number of modules representing biological/physiological functions. Those models are formulated by mathematical equations to describe dynamic changes of states, i.e., specific biological functions. All models in the database are written in an XML format called insilicoML. The Morphology Database provides datasets representing morphometric models of biological organs. The morphometric data are provided in several data-types including surface data such as STL and VRML and volume/voxel data. The database contents are in the public domain and aim to provide valuable models to the scientific community for model sharing/reuse, simulation, model validation, visualization of biological structure, and morphology-based dynamic simulation of biological functions. These can be accomplished by combining insilicoML models with appropriate morphology datasets. Models and related data in the insilicoDB may be freely downloaded and reused for non-profit scientific purposes. When using the models in the Model Database, we ask the users to respect the effort spent in arranging/serving the mathematical models as well as the original model construction. For any reuse of the morphology data, we also ask the users to respect the intellectual property of those who provided the original data. This should be done by acknowledging [email protected] for model reuse and by including appropriate attribution information for any reuse of the morphology data. The insilicoDB owners will not be held responsible for misuse of the Morphology Database and/or Model Database, or damage caused by use of the data and models contained therein.
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