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.
Compiles whole-cell simulation setup and results data. WholeCellSimDB aims to furnish a unified platform enabling to browse and export both submitted data and metadata as well as to find out relevant simulations for a given analysis or to plot small subsets of simulation data. Searches can be made by full-text search or through a form to find simulations with specific parameter values, submodels or predicted phenotypes.
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 confidence that curated models are an accurate reflection of their associated reference descriptions, (ii) search collections of curated models with precision, (iii) quickly identify the biological phenomena that a given curated model or model constituent represents and (iv) facilitate model reuse and composition into large subcellular models. MIRIAM will enable the peer review process to become more efficient and its products more accessible.
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.
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.
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 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.
Consists of an open-access general repository of models distilled from protein networks. CellCircuits aggregates models derived from many separate studies into a single resource. The database enables experimentalists to access and cross-reference models across multiple publications. It also allows meta-analysis of the entire set of models to reveal inter-model relationships and to answer global questions. Users can access, query and export for further study hypothetical pathway models derived from large-scale protein networks.
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.
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 from Escherichia coli to Mus musculus. The data are provided in Biological Dynamics Markup Language (BDML) format and also through a REST API. In addition, SSBD provides 188 sets of time-lapse microscopy images from which the quantitative data were obtained and software tools for data visualization and analysis. SSBD supports, promotes, and contributes to advances in systems biology and various interdisciplinary research fields, and facilitate data-driven biology.
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 management, storage and sharing for a wider systems biology community. This community repository offers a web-based interface and upload facility to turn available data into publicly accessible, centralized and structured-format data files. Moreover, it compiles and integrates available kinetic models associated with the data. KiMoSys also integrates some tools to facilitate the kinetic model construction process of large-scale metabolic networks, especially when the systems biologists perform computational research.
Deals with cellular processes into Mycoplasma genitalium. WholeCellKB consists of a repository of whole-cell models which mainly focuses on assisting users in performs whole-cell simulations. Information is organized according to more than 10 sections including specifications about its subcellular organization, the binding sites and footprint of every DNA-binding protein and the organization and promoter of each transcription unit.
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 checked by specialists for their accuracy and then converted to 230 dynamic mathematical pathway models.
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