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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 aggregate simulation results data. In addition, WholeCellSimDB enables users to share simulations with the broader research community. The database uses a hybrid relational/hierarchical data format architecture to efficiently store and retrieve both simulation setup metadata and results data. WholeCellSimDB provides a graphical Web-based interface to search, browse, plot and export simulations; a JavaScript Object Notation (JSON) Web service to retrieve data for web-based visualizations; a command-line interface to deposit simulations; and a Python API to retrieve data for advanced analysis. WholeCellSimDB will help researchers realize the full potential of whole-cell models for biological discovery, bioengineering and medicine.
MIRIAM / Minimal Information Required In the Annotation of Models
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 collection of free, open-source model organism databases designed specifically to enable comprehensive, dynamic simulations of entire cells and organisms. WholeCellKB provides comprehensive, quantitative descriptions of individual species including: cellular chemical composition, growth medium composition, gene locations, lengths, and directions, transcription unit organization and transcriptional regulation, macromolecule composition, reaction stoichiometry, kinetics, and catalysis, and extensive links and cross-links to all references used to construct each database. WholeCellKB currently contains a single database of Mycoplasma genitalium, an extremely small gram-positive bacterium and common human pathogen.
BioModels Database
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 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.
SSBD / Systems Science of Biological Dynamics
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.
KiMoSys / Kinetic Models of biological Systems
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.
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