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Model repositories | Synthetic biology

Systems Biology requires a tight integration of experimental data and detailed computer models to obtain a quantitative understanding of the system under study. To facilitate this integration a standardization of data and model representation and…
WholeCellSimDB
Dataset

WholeCellSimDB

A database for organizing whole-cell simulations. WholeCellSimDB was designed…

A database for organizing whole-cell simulations. WholeCellSimDB was designed to enable researchers to search simulation metadata to identify simulations for further analysis, and quickly slice and…

BioModels…
Dataset

BioModels Database

A repository of computational models of biological processes. BioModels…

A repository of computational models of biological processes. BioModels Database hosts models described in peer-reviewed scientific literature and models generated automatically from pathway…

Identifiers.org
Dataset

Identifiers.org

Provides directly resolvable identifiers, based on the information stored in…

Provides directly resolvable identifiers, based on the information stored in the Minimum Information Required in the Annotation of Models (MIRIAM) Registry. Identifiers.org is a resolving system…

FAIRDOMHub
Dataset

FAIRDOMHub

A repository for publishing FAIR (Findable, Accessible, Interoperable and…

A repository for publishing FAIR (Findable, Accessible, Interoperable and Reusable) Data, Operating procedures and Models for the Systems Biology community. FAIRDOMHub is a web-accessible repository…

WholeCellKB
Dataset

WholeCellKB

A collection of free, open-source model organism databases designed…

A collection of free, open-source model organism databases designed specifically to enable comprehensive, dynamic simulations of entire cells and organisms. WholeCellKB provides comprehensive,…

MIRIAM
Dataset

MIRIAM Minimal Information Required In the Annotation of Models

Provides unique, perennial and location-independent identifiers for data used…

Provides unique, perennial and location-independent identifiers for data used in the biomedical domain. MIRIAM provides both an identifier scheme and resolution system. It enables users to (i) have…

SSBD
Dataset

SSBD Systems Science of Biological Dynamics

Stores and shares quantitative biological dynamics data. SSBD currently…

Stores and shares quantitative biological dynamics data. SSBD currently provides 311 sets of quantitative data for single molecules, nuclei, and whole organisms in a wide variety of model organisms…

CellCircuits
Dataset

CellCircuits

An open-access database of molecular network models, designed to bridge the gap…

An open-access database of molecular network models, designed to bridge the gap between databases of individual pairwise molecular interactions and databases of validated pathways. CellCircuits…

CellML Model…
Dataset

CellML Model Repository

Provides free access to biological models. The vast majority of these models…

Provides free access to biological models. The vast majority of these models are derived from published, peer-reviewed papers. Model curation is an important and ongoing process to ensure the CellML…

JWS Online
Web

JWS Online

Allows biological systems modelling. JWS Online (Java Web Simulation) is a web…

Allows biological systems modelling. JWS Online (Java Web Simulation) is a web server which permits to construct, modify and simulate kinetic models and also to store curated models. User can build…

DOQCS
Dataset

DOQCS Database Of Quantitative Cellular Signaling

A repository of models of signaling pathways. DOQCS is intended both to serve…

A repository of models of signaling pathways. DOQCS is intended both to serve the growing field of chemical-reaction level simulation of signaling networks, and to anticipate issues in large-scale…

KiMoSys
Dataset

KiMoSys Kinetic Models of biological Systems

A user-friendly platform that includes a public data repository of published…

A user-friendly platform that includes a public data repository of published experimental data, containing concentration data of metabolites and enzymes and flux data. It was designed to ensure data…

MACPAK
Dataset

MACPAK Macrophage Pathway Knowledgebase

A computational system that allows biomedical researchers to query and study…

A computational system that allows biomedical researchers to query and study the dynamic behaviors of macrophage molecular pathways. MACPAK integrates the knowledge of 230 reviews that were carefully…

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