Whole-Cell Knowledge Base
Names
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Whole-Cell Knowledge Base
metasource: Fairsharing.org
version: FAIRsharing.org: WholeCellKB; Whole-Cell Knowledge Base; DOI: https://doi.org/10.25504/FAIRsharing.4dfs3p; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
WholeCellKB
metasource: Fairsharing.org
version: FAIRsharing.org: WholeCellKB; Whole-Cell Knowledge Base; DOI: https://doi.org/10.25504/FAIRsharing.4dfs3p; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Names
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Whole-Cell Knowledge Base
metasource: Fairsharing.orgversion: FAIRsharing.org: WholeCellKB; Whole-Cell Knowledge Base; DOI: https://doi.org/10.25504/FAIRsharing.4dfs3p; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
WholeCellKB
metasource: Fairsharing.orgversion: FAIRsharing.org: WholeCellKB; Whole-Cell Knowledge Base; DOI: https://doi.org/10.25504/FAIRsharing.4dfs3p; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Names
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Whole-Cell Knowledge Base
metasource: Fairsharing.orgversion: FAIRsharing.org: WholeCellKB; Whole-Cell Knowledge Base; DOI: https://doi.org/10.25504/FAIRsharing.4dfs3p; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
WholeCellKB
metasource: Fairsharing.orgversion: FAIRsharing.org: WholeCellKB; Whole-Cell Knowledge Base; DOI: https://doi.org/10.25504/FAIRsharing.4dfs3p; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
WholeCellKB is a collection of open-access model organism databases specifically designed to enable whole-cell models. Currently, WholeCellKB contains a database of Mycoplasma genitalium, a Gram-positive bacterium and common human pathogen. The M. genitalium database is the most comprehensive description of any single organism to date, and was used to develop the first whole-cell computational model. The M. genitalium database was curated from over 900 primary research articles, reviews, books, and databases. The M. genitalium database is extensively cross-referenced to external resources including BioCyc, KEGG, and UniProt. WholeCellKB is also an open-source web-based software program for constructing model organism databases. The WholeCellKB software provides an extensive and fully customizable data model that fully describes individual species including the structure and function of each gene, protein, reaction, and pathway. WholeCellKB is freely accessible via a web-based user interface as well as via a RESTful web service.
Description
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WholeCellKB is a collection of open-access model organism databases specifically designed to enable whole-cell models. Currently, WholeCellKB contains a database of Mycoplasma genitalium, a Gram-positive bacterium and common human pathogen. The M. genitalium database is the most comprehensive description of any single organism to date, and was used to develop the first whole-cell computational model. The M. genitalium database was curated from over 900 primary research articles, reviews, books, and databases. The M. genitalium database is extensively cross-referenced to external resources including BioCyc, KEGG, and UniProt. WholeCellKB is also an open-source web-based software program for constructing model organism databases. The WholeCellKB software provides an extensive and fully customizable data model that fully describes individual species including the structure and function of each gene, protein, reaction, and pathway. WholeCellKB is freely accessible via a web-based user interface as well as via a RESTful web service.
metasource: Fairsharing.orgversion: FAIRsharing.org: WholeCellKB; Whole-Cell Knowledge Base; DOI: https://doi.org/10.25504/FAIRsharing.4dfs3p; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Webpage:
http://www.wholecellkb.orgWebpage
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http://www.wholecellkb.org
metasource: Fairsharing.orgversion: FAIRsharing.org: WholeCellKB; Whole-Cell Knowledge Base; DOI: https://doi.org/10.25504/FAIRsharing.4dfs3p; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Licence:
Name: Wholecells DB MIT LicenceLicence name
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Wholecells DB MIT Licence
metasource: Fairsharing.orgversion: FAIRsharing.org: WholeCellKB; Whole-Cell Knowledge Base; DOI: https://doi.org/10.25504/FAIRsharing.4dfs3p; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Licence URL
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http://www.wholecellsimdb.org/about
metasource: Fairsharing.orgversion: FAIRsharing.org: WholeCellKB; Whole-Cell Knowledge Base; DOI: https://doi.org/10.25504/FAIRsharing.4dfs3p; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Publications:
Publications
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WholeCellKB: model organism databases for comprehensive whole-cell models
PMID: 23175606
metasource: Fairsharing.org
version: FAIRsharing.org: WholeCellKB; Whole-Cell Knowledge Base; DOI: https://doi.org/10.25504/FAIRsharing.4dfs3p; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Publications
More detailed information about this field from each metasource.
WholeCellKB: model organism databases for comprehensive whole-cell models
PMID: 23175606
metasource: Fairsharing.org
version: FAIRsharing.org: WholeCellKB; Whole-Cell Knowledge Base; DOI: https://doi.org/10.25504/FAIRsharing.4dfs3p; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
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WholeCellKB: model organism databases for comprehensive whole-cell models
PubMed citations: 20.
20 articles citing: WholeCellKB: model organism databases for comprehensive whole-cell models
Construction of Multiscale Genome-Scale Metabolic Models: Frameworks and Challenges. PMID:35625648
Building Structural Models of a Whole Mycoplasma Cell. PMID:34774566
Bayesian metamodeling of complex biological systems across varying representations. PMID:34453000
Datanator: an integrated database of molecular data for quantitatively modeling cellular behavior. PMID:33174603
Computer-Aided Whole-Cell Design: Taking a Holistic Approach by Integrating Synthetic With Systems Biology. PMID:32850764
A biochemical network modeling of a whole-cell. PMID:32764598
Emerging whole-cell modeling principles and methods. PMID:29275251
Automated visualization of rule-based models. PMID:29131816
Evolvix BEST Names for semantic reproducibility across code2brain interfaces. PMID:27918836
Guidelines for Reproducibly Building and Simulating Systems Biology Models. PMID:27429432
Toward Community Standards and Software for Whole-Cell Modeling. PMID:27305665
Potentials of single-cell biology in identification and validation of disease biomarkers. PMID:27113384
Facing the challenges of multiscale modelling of bacterial and fungal pathogen-host interactions. PMID:26857943
Databases for Microbiologists. PMID:26013493
Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology. PMID:25765281
WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions. PMID:25231498
The future of whole-cell modeling. PMID:24556244
Reaching new levels of realism in modeling biological macromolecules in cellular environments. PMID:24036504
WholeCellViz: data visualization for whole-cell models. PMID:23964998
Computational approaches for understanding energy metabolism. PMID:23897661
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curated information
metasource: Fairsharing.org
version: FAIRsharing.org: WholeCellKB; Whole-Cell Knowledge Base; DOI: https://doi.org/10.25504/FAIRsharing.4dfs3p; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
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curated information
metasource: Fairsharing.orgversion: FAIRsharing.org: WholeCellKB; Whole-Cell Knowledge Base; DOI: https://doi.org/10.25504/FAIRsharing.4dfs3p; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
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