ArticleBMC systems biology2015
SEEK: a systems biology data and model management platform.
Article in BMC systems biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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Who cites it
50 citing papers in PubMed.
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- A Practical Guide to Reproducible Modeling for Biochemical Networks.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Integrative omics-analysis of lipid metabolism regulation by peroxisome proliferator-activated receptor a and b agonists in male Atlantic cod.Frontiers in physiology · 2023Article
- SODAR: managing multiomics study data and metadata.GigaScience · 2022Article
- The Leipzig Health Atlas-An Open Platform to Present, Archive, and Share Biomedical Data, Analyses, and Models Online.Methods of information in medicine · 2022Article
- FAIR data pipeline: provenance-driven data management for traceable scientific workflows.Philosophical transactions. Series A, Mathematical, physical, and engineering sciences · 2022Article
- ELIXIR biovalidator for semantic validation of life science metadata.Bioinformatics (Oxford, England) · 2022Article
- NExtSEEK: Extending SEEK for Active Management of Interoperable Metadata.Journal of biomolecular techniques : JBT · 2022Article
- Kinetic Modeling ofMetabolites · 2022Review
- Systems Biology in ELIXIR: modelling in the spotlight.F1000Research · 2022Article
- Approaches for the isolation and long-term expansion of pericytes from human and animal tissues.Frontiers in cardiovascular medicine · 2022Article
Corrections and comments
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Authors and funding
13 authors.
Funding
Abstract
backgroundSystems biology research typically involves the integration and analysis of heterogeneous data types in order to model and predict biological processes. Researchers therefore require tools and resources to facilitate the sharing and integration of data, and for linking of data to systems biology models. There are a large number of public repositories for storing biological data of a particular type, for example transcriptomics or proteomics, and there are several model repositories. However, this silo-type storage of data and models is not conducive to systems biology investigations. Interdependencies between multiple omics datasets and between datasets and models are essential. Researchers require an environment that will allow the management and sharing of heterogeneous data and models in the context of the experiments which created them.
resultsThe SEEK is a suite of tools to support the management, sharing and exploration of data and models in systems biology. The SEEK platform provides an access-controlled, web-based environment for scientists to share and exchange data and models for day-to-day collaboration and for public dissemination. A plug-in architecture allows the linking of experiments, their protocols, data, models and results in a configurable system that is available 'off the shelf'. Tools to run model simulations, plot experimental data and assist with data annotation and standardisation combine to produce a collection of resources that support analysis as well as sharing. Underlying semantic web resources additionally extract and serve SEEK metadata in RDF (Resource Description Format). SEEK RDF enables rich semantic queries, both within SEEK and between related resources in the web of Linked Open Data.
conclusionThe SEEK platform has been adopted by many systems biology consortia across Europe. It is a data management environment that has a low barrier of uptake and provides rich resources for collaboration. This paper provides an update on the functions and features of the SEEK software, and describes the use of the SEEK in the SysMO consortium (Systems biology for Micro-organisms), and the VLN (virtual Liver Network), two large systems biology initiatives with different research aims and different scientific communities.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.