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DOQCS specifications

Information


Unique identifier OMICS_08767
Name DOQCS
Alternative name Database Of Quantitative Cellular Signaling
Restrictions to use None
Maintained Yes

Maintainer


  • person_outline Upinder S. Bhalla

Publication for Database Of Quantitative Cellular Signaling

DOQCS citations

 (6)
library_books

In Silico Model driven Assessment of the Effects of Brain derived Neurotrophic Factor Deficiency on Glutamate and Gamma Aminobutyric Acid: Implications for Understanding Schizophrenia Pathophysiology

2017
PMCID: 5426484
PMID: 28449558
DOI: 10.9758/cpn.2017.15.2.115

[…] COPASI. Ordinary differential equations (ODE) were generated in COPASI, details of which are provided as supplementary material (). Values of global constants in network were set based on BRENDA and DOQCS.Optimization of unknown parameters was done for quantities that were not available in databases (). For optimization process combination of two algorithms was used—’random search’ for 10,000 ite […]

library_books

Comparison of human cell signaling pathway databases—evolution, drawbacks and challenges

2015
PMCID: 4309023
PMID: 25632107
DOI: 10.1093/database/bau126

[…] rs as it manually curates the model-related data, such as kinetic rate parameters, protein concentration, and dynamic rate equations, from the published literatures. There is another useful database, DOQCS, which serves as the in silico quantitative model repository for neuron and other signaling pathways. The models provided in this database are collated from peer-reviewed journals and are freely […]

library_books

Modeling Signal Transduction Leading to Synaptic Plasticity: Evaluation and Comparison of Five Models

2011
EURASIP J Bioinform Syst Biol
PMCID: 3171304
PMID: 21559300
DOI: 10.1155/2011/797250

[…] be used either from command line or from graphical user interface which is useful since many times different users prefer different ways of simulation.The model by Hayer and Bhalla [] can be found in database of quantitative cellular Signaling (DOQCS) (http://doqcs.ncbs.res.in/, []) in several formats from which we have used the MATLAB format. However, the MATLAB implementation of the model is har […]

library_books

KID an algorithm for fast and efficient text mining used to automatically generate a database containing kinetic information of enzymes

2010
BMC Bioinformatics
PMCID: 2912889
PMID: 20626859
DOI: 10.1186/1471-2105-11-375

[…] bout enzymes and their characteristics like e.g. BRENDA [-] with currently 92,291 entries for KM, 32,484 for kcat, 21,833 for Ki and 33,372 for specific activity [], Kinetikon [], KMedDB [], KDBI [], DOQCS [], SABIO-RK [] and IUPAC-kinetic [], respectively. However, these databases are far from complete, forcing scientists to a time consuming manual extraction of values from the literature if a sy […]

library_books

Mathematical modeling of intracellular signaling pathways

2006
BMC Neurosci
PMCID: 1775040
PMID: 17118154
DOI: 10.1186/1471-2202-7-S1-S10

[…] ortant ingredients for coupling of models are (1) the development of standardized model exchange formats such as SBML [], (2) the emergence of model databases such as JWS online [], Biomodels or the Database of Quantitative Cellular Signaling (DOQCS, ), and (3) quality standards for model description in publications, such as MIRIAM []. As an alternative, it has been proposed to construct signalin […]

library_books

Parameter estimate of signal transduction pathways

2006
BMC Neurosci
PMCID: 1775046
PMID: 17118160
DOI: 10.1186/1471-2202-7-S1-S6

[…] main contributors to the new Biomodels.Net databases and to the MIRIAM initiative;• CellML: repository of biochemicals models in CellML format [,]. The CellML team contributes to the MIRIAM project;• DOQCS: this is a large repository of signalling pathways, where all the reactions and kinetic parameters are directly shown, furthermore the models can be downloaded in the Genesis language [,]. Also […]

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DOQCS institution(s)
National Centre for Biological Sciences, GKVK Campus, Bangalore, India

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