Models
What is a Model?Filters
Creator: Alan Williams
Submitter: Alan Williams
Model type: Not specified
Model format: Not specified
Environment: Not specified
Creators: None
Submitter: Nils Beyer
Model type: Not specified
Model format: Not specified
Environment: Not specified
Creators: None
Submitter: Nils Beyer
Model type: Not specified
Model format: SBML
Environment: Not specified
Creators: None
Submitter: Nils Beyer
Model type: Not specified
Model format: Not specified
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Creators: None
Submitter: Nils Beyer
Model type: Not specified
Model format: Not specified
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Creators: None
Submitter: Nils Beyer
Model type: Not specified
Model format: Not specified
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Creators: None
Submitter: Nils Beyer
Model type: Not specified
Model format: Not specified
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Creators: None
Submitter: Nils Beyer
Model type: Not specified
Model format: SBML
Environment: Not specified
Creator: Xiaoming Hu
Submitter: Xiaoming Hu
Model type: Not specified
Model format: SBML
Environment: Not specified
Creator: Ulrike Wittig
Submitter: Ulrike Wittig
Model type: Not specified
Model format: SBML
Environment: Not specified
Creator: Ulrike2 Wittig2
Submitter: Ulrike2 Wittig2
Model type: Not specified
Model format: SBML
Environment: Not specified
Creator: Stuart Owen
Submitter: Stuart Owen
Model type: Not specified
Model format: Not specified
Environment: Not specified
BACKGROUND: The behaviour of biological systems can be deduced from their mathematical models. However, multiple sources of data in diverse forms are required in the construction of a model in order to define its components and their biochemical reactions, and corresponding parameters. Automating the assembly and use of systems biology models is dependent upon data integration processes involving the interoperation of data and analytical resources. RESULTS: Taverna workflows have been developed ...
Creator: Stuart Owen
Submitter: Stuart Owen
Model type: Not specified
Model format: SBML
Environment: Not specified
Creator: Stuart Owen
Submitter: Stuart Owen
Model type: Not specified
Model format: SBML
Environment: JWS Online
Glycolytic model for Plasmodium falciparum; closed system
Creator: Stuart Owen
Submitter: Stuart Owen
Model type: Not specified
Model format: Not specified
Environment: Not specified
Creator: Stuart Owen
Submitter: Stuart Owen
Model type: Not specified
Model format: SBML
Environment: Not specified
Creator: Stuart Owen
Submitter: Stuart Owen
Model type: Not specified
Model format: Not specified
Environment: Not specified
Creator: Franco Boudrot
Submitter: Franco Boudrot
Model type: Not specified
Model format: Not specified
Environment: Not specified
Creator: Stuart Owen
Submitter: Stuart Owen
Model type: Not specified
Model format: Not specified
Environment: Not specified
Creator: Quyen Yamanaka
Submitter: Quyen Yamanaka
Model type: Not specified
Model format: Not specified
Environment: Not specified
Creator: Lihua Angel
Submitter: Lihua Angel
Model type: Not specified
Model format: Not specified
Environment: Not specified
Creator: Quyen Yamanaka
Submitter: Quyen Yamanaka
Model type: Not specified
Model format: Not specified
Environment: Not specified
Creator: Quyen Yamanaka
Submitter: Quyen Yamanaka
Model type: Not specified
Model format: Not specified
Environment: Not specified
Creator: Quyen Yamanaka
Submitter: Quyen Yamanaka
Model type: Not specified
Model format: SBML
Environment: Not specified
re-testing model picture after changes.
Creator: Stuart Owen
Submitter: Stuart Owen
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Copasi
Creator: Stuart Owen
Submitter: Stuart Owen
Model type: Not specified
Model format: SBML
Environment: Not specified
Creator: Stuey Owen
Submitter: Stuey Owen
Model type: Partial differential equations (PDE)
Model format: BioPAX
Environment: JWS Online
Potato model taken from JWS Online: http://jjj.mib.ac.uk/
Testing notification email
Creator: Stuart Owen
Submitter: Stuart Owen
Model type: Not specified
Model format: SBML
Environment: JWS Online
Creator: Quyen Yamanaka
Submitter: Quyen Yamanaka
Model type: Partial differential equations (PDE)
Model format: SBML
Environment: JWS Online
Creators: None
Submitter: Deleted submitter
Model type: Not specified
Model format: Not specified
Environment: Not specified
Creators: None
Submitter: Deleted submitter
Model type: Not specified
Model format: Not specified
Environment: Not specified
Creator: Quyen Yamanaka
Submitter: Abeer Cherry
Model type: Not specified
Model format: Not specified
Environment: Not specified
Creator: Quyen Yamanaka
Submitter: Quyen Yamanaka
Model type: Not specified
Model format: Not specified
Environment: Not specified
Model for testing
Creator: Stuart Owen
Submitter: Stuart Owen
Model type: Partial differential equations (PDE)
Model format: SBML
Environment: Not specified
Genomic data allow the large-scale manual or semi-automated assembly of metabolic network reconstructions, which provide highly curated organism-specific knowledge bases. Although several genome-scale network reconstructions describe Saccharomyces cerevisiae metabolism, they differ in scope and content, and use different terminologies to describe the same chemical entities. This makes comparisons between them difficult and underscores the desirability of a consolidated metabolic network that ...
Creator: Quyen Yamanaka
Submitter: Quyen Yamanaka
Model type: Not specified
Model format: SBML
Environment: Not specified
Creator: Stuey Owen
Submitter: Stuey Owen
Model type: Not specified
Model format: Not specified
Environment: Not specified
changed
Creator: Stuey Owen
Submitter: Stuey Owen
Model type: Not specified
Model format: Not specified
Environment: Not specified
Creator: Stuart Owen
Submitter: Stuart Owen
Model type: Not specified
Model format: SBML
Environment: Not specified
Creator: Quyen Yamanaka
Submitter: Quyen Yamanaka
Model type: Not specified
Model format: Not specified
Environment: Not specified
Creator: Stuart Owen
Submitter: Stuart Owen
Model type: Not specified
Model format: Not specified
Environment: Not specified
Genomic data allow the large-scale manual or semi-automated assembly of metabolic network reconstructions, which provide highly curated organism-specific knowledge bases. Although several genome-scale network reconstructions describe Saccharomyces cerevisiae metabolism, they differ in scope and content, and use different terminologies to describe the same chemical entities. This makes comparisons between them difficult and underscores the desirability of a consolidated metabolic network that ...
Creator: Quyen Yamanaka
Submitter: Quyen Yamanaka
Model type: Not specified
Model format: Not specified
Environment: Not specified
Genomic data allow the large-scale manual or semi-automated assembly of metabolic network reconstructions, which provide highly curated organism-specific knowledge bases. Although several genome-scale network reconstructions describe Saccharomyces cerevisiae metabolism, they differ in scope and content, and use different terminologies to describe the same chemical entities. This makes comparisons between them difficult and underscores the desirability of a consolidated metabolic network that ...
Creator: Quyen Yamanaka
Submitter: Quyen Yamanaka
Model type: Not specified
Model format: SBML
Environment: Not specified
Creator: Stuart Owen
Submitter: Stuart Owen
Model type: Not specified
Model format: Not specified
Environment: Not specified
Model from JWS Online
Creator: Stuart Owen
Submitter: Stuart Owen
Model type: Not specified
Model format: SBML
Environment: Not specified
Creator: Quyen Yamanaka
Submitter: Quyen Yamanaka
Model type: Not specified
Model format: SBML
Environment: Not specified
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Creators: None
Submitter: Stuart Owen
Model type: Not specified
Model format: Not specified
Environment: Not specified
Creator: Franco Boudrot
Submitter: Franco Boudrot
Model type: Not specified
Model format: Not specified
Environment: Not specified
Creator: Quyen Yamanaka
Submitter: Quyen Yamanaka
Model type: Not specified
Model format: Not specified
Environment: Not specified
Creator: Jacky Snoep
Submitter: Guest
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
Creator: Quyen Yamanaka
Submitter: Quyen Yamanaka
Model type: Not specified
Model format: Not specified
Environment: Not specified
The recognition of carbon sources and the regulatory adjustments to recognized changes are of particular importance for bacterial survival in fluctuating environments. Despite a thorough knowledge base of Escherichia coli's central metabolism and its regulation, fundamental aspects of the employed sensing and regulatory adjustment mechanisms remain unclear. In this paper, using a differential equation model that couples enzymatic and transcriptional regulation of E. coli's central metabolism, we ...
Creator: Quyen Yamanaka
Submitter: Quyen Yamanaka
Model type: Not specified
Model format: SBML
Environment: Not specified
Genomic data allow the large-scale manual or semi-automated assembly of metabolic network reconstructions, which provide highly curated organism-specific knowledge bases. Although several genome-scale network reconstructions describe Saccharomyces cerevisiae metabolism, they differ in scope and content, and use different terminologies to describe the same chemical entities. This makes comparisons between them difficult and underscores the desirability of a consolidated metabolic network that ...
Creator: Quyen Yamanaka
Submitter: Quyen Yamanaka
Model type: Not specified
Model format: SBML
Environment: Not specified
Creator: Quyen Yamanaka
Submitter: Quyen Yamanaka
Model type: Not specified
Model format: Not specified
Environment: Not specified
MCA of Glycerol Synthesis in Saccharomyces cerevisiae
Creators: Jacky Snoep, Garth R. Cronwright, Johann M. Rohwer, and Bernard A. Prior
Submitter: Katy Wolstencroft
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Creator: Quyen Yamanaka
Submitter: Quyen Yamanaka
Model type: Not specified
Model format: SBML
Environment: Not specified
Creator: Quyen Yamanaka
Submitter: Quyen Yamanaka
Model type: Not specified
Model format: Not specified
Environment: Not specified
Targeting persistent tubercule bacilli has become an important challenge in the development of anti-tuberculous drugs. As the glyoxylate bypass is essential for persistent bacilli, interference with it holds the potential for designing new antibacterial drugs. We have developed kinetic models of the tricarboxylic acid cycle and glyoxylate bypass in Escherichia coli and Mycobacterium tuberculosis, and studied the effects of inhibition of various enzymes in the M. tuberculosis model.
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Creator: Quyen Yamanaka
Submitter: Quyen Yamanaka
Model type: Not specified
Model format: Not specified
Environment: Not specified
The animal cell cycle is controlled by the periodic variation of two cyclin-dependent protein kinases, cdk1 and cdk2, which govern the entry into the M (mitosis) and S (DNA replication) phases, respectively. The ordered progression between these phases is achieved thanks to the existence of checkpoint mechanisms based on mutual inhibition of these processes. Here we study a simple theoretical model for oscillations in cdk1 and cdk2 activity, involving mutual inhibition of the two oscillators. ...
Creator: Stuart Owen
Submitter: Stuart Owen
Model type: Not specified
Model format: SBML
Environment: Not specified
Creator: Stuart Owen
Submitter: Stuart Owen
Model type: Not specified
Model format: Not specified
Environment: Not specified
Creator: Quyen Yamanaka
Submitter: Quyen Yamanaka
Model type: Not specified
Model format: Not specified
Environment: Not specified
Creator: Stuart Owen
Submitter: Stuart Owen
Model type: Not specified
Model format: SBML
Environment: Not specified
Genomic data allow the large-scale manual or semi-automated assembly of metabolic network reconstructions, which provide highly curated organism-specific knowledge bases. Although several genome-scale network reconstructions describe Saccharomyces cerevisiae metabolism, they differ in scope and content, and use different terminologies to describe the same chemical entities. This makes comparisons between them difficult and underscores the desirability of a consolidated metabolic network that ...
Creator: Stuart Owen
Submitter: Stuart Owen
Model type: Not specified
Model format: SBML
Environment: Not specified
Experimental evidence suggests that regional differences in action potential (AP) morphology can provide a substrate for initiation and maintenance of reentrant arrhythmias in the right atrium (RA), but the relationships between the complex electrophysiological and anatomical organization of the RA and the genesis of reentry are unclear. In this study, a biophysically detailed three-dimensional computer model of the right atrial tissue was constructed to study the role of tissue heterogeneity and ...
Creator: Stuart Owen
Submitter: Stuart Owen
Model type: Not specified
Model format: SBML
Environment: Not specified
The behaviour of biological systems can be deduced from their mathematical models. However, multiple sources of data in diverse forms are required in the construction of a model in order to define its components and their biochemical reactions, and corresponding parameters. Automating the assembly and use of systems biology models is dependent upon data integration processes involving the interoperation of data and analytical resources.
Originating from BioModels: ...
Creator: Stuart Owen
Submitter: Stuart Owen
Model type: Not specified
Model format: SBML
Environment: Not specified
Creator: Abeer Cherry
Submitter: Abeer Cherry
Model type: Not specified
Model format: Not specified
Environment: Not specified
The behaviour of biological systems can be deduced from their mathematical models. However, multiple sources of data in diverse forms are required in the construction of a model in order to define its components and their biochemical reactions, and corresponding parameters. Automating the assembly and use of systems biology models is dependent upon data integration processes involving the interoperation of data and analytical resources.
Originating from BioModels: ...
Creator: Abeer Cherry
Submitter: Abeer Cherry
Model type: Not specified
Model format: Not specified
Environment: Not specified
One of the most obvious phenotypes of a cell is its metabolic activity, which is defined by the fluxes in the metabolic network. Although experimental methods to determine intracellular fluxes are well established, only a limited number of fluxes can be resolved. Especially in eukaryotes such as yeast, compartmentalization and the existence of many parallel routes render exact flux analysis impossible using current methods. To gain more insight into the metabolic operation of S. cerevisiae we ...
Creator: Stuart Owen
Submitter: Stuart Owen
Model type: Not specified
Model format: SBML
Environment: Not specified
Detailed kinetic model for glycolysis of L. lactis. The model is basically the same model as that published by Hoefnagel et al 2002 (Mol. Biol. Reports 29, 157-161). The change made to the model is to make external glucose a variable such that a glucose pulse can be simulated.
Creators: Jacky Snoep, Ana Rute Neves
Submitter: Katy Wolstencroft
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified