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 storage is important.
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 data management for signaling chemistry.
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 model is able to accurately reproduce the published results. As the CellML community grows, and more people add their models to the repository, model annotation will become increasingly important to facilitate data searches and information retrieval.
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 for storing and sharing systems biology research assets. It enables researchers to organize, share and publish data, models and protocols, interlink them in the context of the systems biology investigations that produced them, and to interrogate them via API interfaces. By using the FAIRDOMHub, researchers can achieve more effective exchange with geographically distributed collaborators during projects, ensure results are sustained and preserved and generate reproducible publications that adhere to the FAIR guiding principles of data stewardship.
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 helping to ensure that data entities are resolvable, thereby avoiding the creation of ‘dead ends’ in the network of linked data. The resolution of an Identifiers.org URL directs the user to an intermediate page listing all recorded physical locations where a record may be accessed, allowing the user to choose the most suitable one.
A repository of computational models of biological processes. BioModels Database hosts models described in peer-reviewed scientific literature and models generated automatically from pathway resources (Path2Models). A large number of models collected from literature are manually curated and semantically enriched with cross-references from external data resources (such as publications, databases of compounds and pathways, ontologies, etc.). The resource allows scientific community to store, search and retrieve mathematical models of their interest. In addition, features such as generation of sub-models, online simulation, conversion of models into different representational formats, and programmatic access via web services, are provided.
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