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Ammonium assimilation model (AmtB transporter and protein level regulation) |
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Modelling is an important methodology in systems biology research. In this paper, we presented a kinetic model for the complex ammonium assimilation regulation system of E. coli. Based on a previously published model, the new model included the AmtB mediated ammonium transport and its protein level regulation by GlnK. Protein concentrations and several parameter values were determined or refined based on new experimental data. Steady-state analysis of the model showed that the expression of AmtB increased the ammonium assimilation rate by 4-5 fold at external ammonium concentrations as low as 5 µM. Model analysis also suggested that AmtB and GS levels were coupled to maximize the assimilation flux and to avoid a possible negative ammonia diffusion flux. In addition, model simulation of the short term dynamic response to increased external ammonium concentrations implied that the maximal rate for GlnB/GlnK uridylylation/deuridylylation should be higher for a quick response to environmental changes. dx.doi.org/10.1016/j.jbiotec.2009.09.003 |
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BioDiVinE - Parallel Model-Checker for Multi-Affine ODE Models |
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BioDiVinE tool adapts parallel LTL model checking algorithms for rectangular abstraction of multi-affine ODE models. Biological models described in terms of mass action kinetics are supported. The tool is accompanied with a simple GUI that allows specification of reactions. The tool package includes a visualisation utility Simaff that allows untimed simulation and 2D depiction of rectangular phase spaces. [ link ] |
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BioDiVinE GUI |
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Stand-alone Java GUI for graphical specification of biological reaction networks. This prototype tool allows both graphical and textual editing of biological models which can be exported into .bio format readable by BioDiVinE. The tool is planned to serve also as an interface for BioDiVinE. As an example, visualization of reachable concentration levels is currently supported. [ link ] |
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CADP |
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CADP (Construction and Analysis of Distributed Processes) is a popular toolbox for the design of communication protocols and distributed systems. CADP is developed by the VASY team at INRIA Rhone-Alpes and connected to various complementary tools. CADP is maintained, regularly improved, and used in many industrial projects. The toolbox offers a wide range of functionalities assisting the user throughout the design process: compilation and rapid prototyping, interactive step-by-step and guided simulation, model checking and equivalence checking, test case generation, and performance evaluation. Several verification techniques (on-the-fly, compositional, and massively parallel) are provided by CADP and can be combined in order to fight against state explosion. [ link ] |
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Central carbon metabolic models |
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Central carbon metabolic models A model of the phosphotransferase system (PTS) was constructed by Rohwer et al. and a model of glycolysis, pentose phosphate pathway and biosynthesis was constructed by Chassagnole et al. The two models are available on JWS online, a on-line repository. These two models were connected in a large kinetic model. This model will be available on JWS online after publication. http://jjj.biochem.sun.ac.za/index.html |
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Central nitrogen metabolic models |
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Central nitrogen metabolic models A model of the central nitrogen assimilation network was constructed by Bruggeman et al. and this model is available on JWS online. The extended model of ammonium transport and assimilation will be available on JWS online soon. http://jjj.biochem.sun.ac.za/index.html |
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GeNeSim GUI: Web Interface for Biological Models |
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GeNeSim GUI is a web interface which currently allows managing of piece-wise linear and multi-affine models, it supports import of models from GNA and SBML, and export to GNA and BioDiVinE tools. The models are represented in an internal XML format. [ link ] |
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GeNeSim-DiVinE - prototype of a distributed LTL model checker for genetic regulatory networks |
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GeNeSim/DiVinE is an experimental prototype extension of the parallel model-checker DiVinE which implements implicit representation of qualitative automata for piece-wise linear models. [ link ] |
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Genetic Network Analyzer (GNA) |
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Genetic Network Analyzer (GNA) Genetic Network Analyzer (GNA) is a computer tool for the modeling and simulation of genetic regulatory networks. The aim of GNA is to assist biologists and bioinformaticians in constructing a model of a genetic regulatory network using knowledge about regulatory interactions in combination with gene expression data. [ link ] |
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LTSmin LTSmin - Minimization and Instantiation of Labelled Transition Systems |
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LTSmin is a toolset for manipulating large labelled transition systems.This can be done in two ways: by means of symbolic (BDD based) state space exploration or by means of distributed state space generation and reduction. [ link ] |
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Qualitative model of network of global regulators in E. coli |
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The adaptation of the bacterium Escherichia coli to carbon starvation is controlled by a large network of biochemical reactions involving genes, mRNAs, proteins, and signalling molecules. The dynamics of these networks is difficult to analyze, notably due to a lack of quantitative information on parameter values. To overcome these limitations, model reduction approaches based on quasi-steady-state (QSS) and piecewise-linear (PL) approximations have been proposed, resulting in models that are easier to handle mathematically and computationally. These approximations are not supposed to affect the capability of the model to account for essential dynamical properties of the system, but the validity of this assumption has not been systematically tested. In this paper we carry out such a study by evaluating a large and complex PL model of the carbon starvation response in E. coli using an ensemble approach. The results show that, in comparison with conventional nonlinear models, the PL approximations generally preserve the dynamics of the carbon starvation response network, although with some deviations concerning notably the quantitative precision of the model predictions. This encourages the application of PL models to the qualitative analysis of bacterial regulatory networks, in situations where the reference time-scale is that of protein synthesis and degradation. [ link1 link2 ] |
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Tools & Models