formal matrix based description of metabolic networks
Multi agent based modeling and simulation of metabolic networks
Ngày tải lên :
26/11/2015, 13:02
... Simulation and Emergence of Metabolic Network using the agent -based model 37 3.2 Illustration of Agent -based Execution of Metabolic Network 41 3.3 Application of Agent -based Model to Identifying ... to JADE 25 Reconstruction of metabolic network model 27 2.5 Scope of the thesis 29 2.2 2.3 Chapter Agent Based Modeling of Metabolic Networks 30 3.1 Model Architecture ... process of network characterization and re-annotation Though the main interest of this thesis relates to the analysis of metabolic networks, the basic practice of developing any other biological networks...
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Báo cáo khoa học:The principle of flux minimization and its application to estimate stationary fluxes in metabolic networks docx
Ngày tải lên :
07/03/2014, 15:20
... kinetic modelling of metabolic networks needs detailed rate equations for each of the participating metabolic processes Derivation of a reliable rate equation requires detailed knowledge of all physiological ... and control of the metabolic system studied [2] Moreover, kinetic simulations of metabolic networks may partially replace time-consuming and expensive experiments to explore possible metabolic ... topology of the metabolic network is given in terms of the so-called stoichiometric matrix, relating the time-dependent variation of the metabolite concentrations to the fluxes through all metabolic...
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Báo cáo khoa học: Antibody-based proteomics Analysis of signaling networks using reverse protein arrays pdf
Ngày tải lên :
16/03/2014, 00:20
... modulation of regulatory networks [5,6] A direct benefit of such an approach would be the early recognition of ‘off target’ and side effects of drug candidates [7], as well as the identification of putative ... Analysis of signaling networks using protein arrays H Voshol et al a contextual understanding of the molecular mechanisms of disease, but also has the potential to facilitate the validation of therapeutic ... Profiling of kinase inhibitors can be useful to assess the promiscuity of the inhibitor and how much of a problem that might present The first published screens of that kind emphasized the importance of...
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Báo cáo khoa học: Kinetic hybrid models composed of mechanistic and simplified enzymatic rate laws – a promising method for speeding up the kinetic modelling of complex metabolic networks pptx
Ngày tải lên :
23/03/2014, 06:20
... stationary reference state of the network at an ATP consumption rate of 20.8 lmặs)1 and a GTP consumption rate of 0.19 lmặs)1 On the basis of the stoichiometric matrix of the network and the ux ... of mechanistic and simplied rate laws available on request The stability of each solution was determined by evaluation of the eigenvalues of the Jacobian matrix [J = dv(S) dS] Identication of ... accessed free of charge at http:// jjj.biochem.sun.ac.za/database/bulik/index.html Results Test case a metabolic network of erythrocytes To investigate the suitability of different variants of kinetic...
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Báo cáo hóa học: " Research Article Functional Classification of Genome-Scale Metabolic Networks" potx
Ngày tải lên :
22/06/2014, 00:20
... that all three ways to describe metabolic networks contain fundamentally different pieces of information and that taxonomy, structure, and function of metabolic networks are only weakly correlated ... constructed by comparing the structure of selected metabolic pathways, we attempt to build phylogenies based on functional properties of the complete organism-wide metabolic network We generalize the ... characterizations of networks may be put into relation with the particular lifestyles of the corresponding organisms Carbon Utilization Spectra For a given metabolic network, the scope of a particular...
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Báo cáo y học: "Comparison of prevalence of metabolic syndrome in hospital and community-based Japanese patients with schizophrenia" potx
Ngày tải lên :
09/08/2014, 01:21
... Sugawara et al.: Comparison of prevalence of metabolic syndrome in hospital and community -based Japanese patients with schizophrenia Annals of General Psychiatry 2011 10:21 Page of Submit your next manuscript ... 0.46, df = 1, P = 0.50) The effect of type of care on the odds ratio for MetS To examine the independent effect of type of care for schizophrenia on the odds ratio of for MetS, two logistic regression ... differ based on the type of care, such as hospital or community -based care The type of care could be a large environmental factor However, there have been few studies that compare the prevalence of...
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Báo cáo khoa học: "A catalytically and genetically optimized β-lactamase-matrix based assay for sensitive, specific, and higher throughput analysis of native henipavirus entry characteristics" doc
Ngày tải lên :
12/08/2014, 04:21
... NiV matrix- based VLPs will likely better reflect the biological properties of their live-virus counterparts in entry assays Here, we developed a VLP -based assay that can be used for analyses of ... diffusing out of the cells), and permits loading of a variety of cell types including primary neuron or microvascular endothelial cells, the main targets of NiV infection Thus, virus-cell fusion of envelope ... steps in viral entry, such as matrix uncoating, may also not be resolved by either of these assays Many viruses form virus-like particles (VLPs) via expression of their matrix alone (e.g Sendai,...
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Báo cáo y học: " Bringing metabolic networks to life: integration of kinetic, metabolic, and proteomic data" pptx
Ngày tải lên :
13/08/2014, 16:21
... self-evident An intention of systems biology is to predict them by computer simulations, which requires mathematical models of the biochemical networks The structure of metabolic networks has been characterised ... increased by a factor of 50 We found that the accuracy of the predictions increased considerably between the kinetics -based and the metabolics -based posterior Hence, the fit to metabolic data adds ... analysis of complex metabolic networks Biophys J 2002, 83:79-86 Kacser H, Burns J: The control of flux Symp Soc Exp Biol 1973, 27:65-104 Fell DA: Metabolic control analysis: a survey of its theoretical...
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Báo cáo y học: "Computational identification of obligatorily autocatalytic replicators embedded in metabolic networks" docx
Ngày tải lên :
14/08/2014, 08:20
... accurate information on cofactor usage and transport processes might be Table List of investigated metabolic networks and their main properties Total number of metabolites Number of producible metabolites ... none of the 11 investigated metabolic networks did the scope of the externally available molecules include all producible compounds (Table 1), therefore providing evidence that the metabolic networks ... theoretical studies of the dynamics of energy metabolism [20,32] Thus, although it is out of the scope of our current analysis to analyze the dynamic behavior of autocatalyic subnetworks embedded...
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Báo cáo y học: "A classification based framework for quantitative description of large-scale microarray data" ppsx
Ngày tải lên :
14/08/2014, 16:21
... negative rate of about 50% The SA performed consistently well in identifying a subset of profiles (three out of seven profiles tested), but it did not identify the remaining profiles in which ... division FNR targets OxyR Cofactor synthesis RNA modification ATPases Heat shock response Figure Expression profiles of top-scoring classes for drug treatments Expression profiles of top-scoring classes ... correlated profiles of subsets of genes, we observed that genes related to tryptophan biosynthesis (aroM, trpCDE, aroH, tyrA) [18] make up a profile that is anti-correlated with that of the ribosomal...
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Dynamic based structure measures of complex networks
Ngày tải lên :
09/09/2015, 10:06
... concepts of complex networks in Section 1.2, and also give the explanation of dynamicbased structure measure of complex network in Section 1.3 1.2 General Description of Complex Networks Complex networks ... spectral rigidity of the complex networks follows RMT prediction, with scale depending upon the properties of the networks 1.3.2 Evolution of Complex Networks Evolving networks are networks whose ... model networks and real world networks using tools from Random Matrix Theory(RMT)[15] and nonlinear dynamics Our studies of spectra analysis of the systematic level dynamics of these large scale networks...
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A combined statistical and in silico framework for analysis and characterization of microbial and mammalian metabolic networks
Ngày tải lên :
11/09/2015, 21:27
... organisms 20 3.1 List of public resources available for reconstruction of genome-scale metabolic models* 47 4.1 Comparison of metabolic reaction fluxes of amino acids biosynthetic ... Algorithms available for characterizing metabolic networks MOMA (Minimization Of Metabolic Adjustment): This aims at understanding the metabolic flux states of mutant phenotypes (Segre et al 2002) ... issues in different chapters of the thesis 13 2.1 Genome-scale reconstruction of metabolic network and elucidation of the systemic properties using constraints -based analysis approach ...
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The study of TCP performance in IEEE 802 11 based mobile ad hoc networks
Ngày tải lên :
13/09/2015, 21:25
... THE STUDY OF TCP PERFORMANCE IN IEEE 802.11 BASED MOBILE AD HOC NETWORKS LI XIA (B Sc., Nan Jing University, PRC ) A THESIS SUBMITTED FOR THE DEGREE OF DOCTOR OF PHILOSOPHY DEPARTMENT OF ELECTRICAL ... purpose of which is to minimize the frequency of route re-computation Unfortunately, this sometimes results in a significant number of out -of- sequence packets arriving at the receiver The effect of ... sender limits the size of its maximum transmission window to the BDP of the path in multihop networks Though the maximum transmission window is limited at the value of BDP based on the path length,...
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Implementation and performance study of opportunistic network coding in 802 11 based wireless ad hoc networks using qualnet
Ngày tải lên :
16/10/2015, 11:59
... performance of COPE in large scale networks is also much worse than that of single-hop topologies One of the main reasons could be that the impact of COPE’s control messages on the overall performance of ... (P2P) file distribution networks to wireless ad-hoc networks, from the improvement of network capacity to increase of network security 1.5 Thesis Organization The rest of this thesis is organized ... Further in-depth study of the impact of T is a part of the future work The queue threshold of waiting scheme N increases from to 37 which is a bit larger than the default setting of the output queue...
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Economics of Wireless Networks
Ngày tải lên :
29/09/2013, 21:20
... content -based charging The novelty of this approach is that users are not charged based on usage, but rather on the type of content they access Some examples of the significance of content -based ... several economic aspects of wireless networks, including economic benefits of wireless networks, facts that affect the economics of the wireless industry, a forecast for the growth of wireless mobile ... Department of Microelectronics and Information Technology Royal Institute of Technology of Sweden, 2001 Economics of Wireless Networks 397 [3] Cushnie J., Hutchison D and Oliver H Evolution of Charging...
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Jini- Sun''s Technology of Impromptu Networks
Ngày tải lên :
06/10/2013, 14:20
... greater the frequency of polling, the smaller the period of uncertainty about the status of a service and the quicker the response of the Djinn as a whole in dealing with the loss of a service This ... promotional literature is full of interesting examples, and examples of the technology aren't hard to dream up The most common example is that of a printer Figure 10-1 The layers of architecture needed ... recently doubled the size of its office staff from 12 people, to 24 Laura Cogswell, ABC Industries office manager, noticed a situation brewing over the limited printing resource of their single laser...
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Statistical Description of Data part 1
Ngày tải lên :
20/10/2013, 17:15
... sums of integer powers of the values Best known is the mean of the values x1 , , xN , x= N N xj (14.1.1) j=1 which estimates the value around which central clustering occurs Note the use of ... 1974, Applied Statistics: Analysis of Variance and Regression (New York: Wiley) 14.1 Moments of a Distribution: Mean, Variance, Skewness, and So Forth When a set of values has a sufficiently strong ... tendency, the moments of a distribution, the median and mode In §14.2 we learn to test whether different data sets are drawn from distributions with different values of these measures of central tendency...
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Sensor-based navigation of a mobile robot in an indoor environment
Ngày tải lên :
23/10/2013, 15:15
... at the University of Paris XI, Orsay in 1981 Since 1986, he is Professor at the University of Evry and he was the Head of Electrical Engineering Department of the Institute of Technology from ... approximated by the sign of the terms of the Jacobian matrix of the plant (in the assumption that these signs are fixed on the working space, which is valid for a lot of real systems) These results ... the maximum angular speed of each wheel of the robot (1.58 rad/s) By applying this method, a saturation of the growth of the weights is obtained without any degradation of the residual quadratic...
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Statistical Description of Data part 2
Ngày tải lên :
24/10/2013, 15:15
... significance of a difference of means is not the number of standard deviations that they are apart, but the number of so-called standard errors that they are apart The standard error of a set of values ... definitions into sums of various powers of the data, e.g., the familiar N x2 − N x2 ≈ x2 − x2 (14.1.7) Var(x1 xN ) = j N −1 614 Chapter 14 Statistical Description of Data Semi-Invariants ... the first moment of the tails is large; it is easy to construct examples where the first moment of the tails is large even though their area is negligible To find the median of a set of values, one...
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Statistical Description of Data part 3
Ngày tải lên :
24/10/2013, 15:15
... *prob=betai(0.5*df,0.5,df/(df+(*t)*(*t))); Degrees of freedom Pooled variance See equation (6.4.9) } which makes use of the following routine for computing the mean and variance of a set of numbers, Sample page from ... of research: Are the visible stars distributed uniformly in the sky? (That is, is the distribution of stars as a function of declination — position in the sky — the same as the distribution of ... function of declination?) Are educational patterns the same in Brooklyn as in the Bronx? (That is, are the distributions of people as a function of last-grade-attended the same?) Do two brands of fluorescent...
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