A Geometric Relaxation Solver for Constraint-Based Models

2000 ◽  
pp. 251-268 ◽  
Author(s):  
Lluis Solano Albajes ◽  
Pere Brunet Crosa
Keyword(s):  
Constraint Based Models

Estimating optimal profiles of genetic alterations using constraint-based models

2004 ◽  
Vol 89 (2) ◽  
pp. 243-251 ◽  
Author(s):  
Kapil G. Gadkar ◽  
Francis J. Doyle III ◽  
Jeremy S. Edwards ◽  
Radhakrishnan Mahadevan
Keyword(s):  
Genetic Alterations ◽  
Constraint Based Models

scholarly journals Exploring the associations between transcript levels and fluxes in constraint-based models of metabolism

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Neeraj Sinha ◽  
Evert M. van Schothorst ◽  
Guido J. E. J. Hooiveld ◽  
Jaap Keijer ◽  
Vitor A. P. Martins dos Santos ◽  
...  
Keyword(s):  
Metabolic Flux ◽  
Transcript Levels ◽  
Proportionality Constant ◽  
Model Predictions ◽  
Physiological Information ◽  
Highly Expressed Genes ◽  
Transcriptomics Data ◽  
Genome Scale ◽  
The Impact ◽  
Constraint Based Models

Abstract Background Several computational methods have been developed that integrate transcriptomics data with genome-scale metabolic reconstructions to increase accuracy of inferences of intracellular metabolic flux distributions. Even though existing methods use transcript abundances as a proxy for enzyme activity, each method uses a different hypothesis and assumptions. Most methods implicitly assume a proportionality between transcript levels and flux through the corresponding function, although these proportionality constant(s) are often not explicitly mentioned nor discussed in any of the published methods. E-Flux is one such method and, in this algorithm, flux bounds are related to expression data, so that reactions associated with highly expressed genes are allowed to carry higher flux values. Results Here, we extended E-Flux and systematically evaluated the impact of an assumed proportionality constant on model predictions. We used data from published experiments with Escherichia coli and Saccharomyces cerevisiae and we compared the predictions of the algorithm to measured extracellular and intracellular fluxes. Conclusion We showed that detailed modelling using a proportionality constant can greatly impact the outcome of the analysis. This increases accuracy and allows for extraction of better physiological information.

scholarly journals IDENTIFYING CANCER SPECIFIC METABOLIC SIGNATURES USING CONSTRAINT-BASED MODELS

2016 ◽  
Author(s):  
A. SCHULTZ ◽  
S. MEHTA ◽  
C.W. HU ◽  
F.W. HOFF ◽  
T.M. HORTON ◽  
...  
Keyword(s):  
Constraint Based Models ◽  
Metabolic Signatures

scholarly journals Advances in the integration of transcriptional regulatory information into genome-scale metabolic models

2016 ◽  
Author(s):  
R.P. Vivek-Ananth ◽  
Areejit Samal
Keyword(s):  
Systems Biology ◽  
Metabolic Networks ◽  
Computational Models ◽  
Cellular Metabolism ◽  
Transcriptional Regulatory ◽  
Metabolic Systems ◽  
Regulatory Information ◽  
Domains Of Life ◽  
Genome Scale ◽  
Constraint Based Models

AbstractA major goal of systems biology is to build predictive computational models of cellular metabolism. Availability of complete genome sequences and wealth of legacy biochemical information has led to the reconstruction of genome-scale metabolic networks in the last 15 years for several organisms across the three domains of life. Due to paucity of information on kinetic parameters associated with metabolic reactions, the constraint-based modelling approach, flux balance analysis (FBA), has proved to be a vital alternative to investigate the capabilities of reconstructed metabolic networks. In parallel, advent of high-throughput technologies has led to the generation of massive amounts of omics data on transcriptional regulation comprising mRNA transcript levels and genome-wide binding profile of transcriptional regulators. A frontier area in metabolic systems biology has been the development of methods to integrate the available transcriptional regulatory information into constraint-based models of reconstructed metabolic networks in order to increase the predictive capabilities of computational models and understand the regulation of cellular metabolism. Here, we review the existing methods to integrate transcriptional regulatory information into constraint-based models of metabolic networks.

Model Checking of Constraint-Based Workflow Based on Linear Temporal Logic

2012 ◽  
Vol 601 ◽  
pp. 401-405
Author(s):  
Wen Bo Zhou ◽  
Shu Zhen Yao
Keyword(s):  
Model Checking ◽  
Temporal Logic ◽  
Business Processes ◽  
Workflow Management ◽  
Linear Temporal Logic ◽  
Management Systems ◽  
Workflow Management Systems ◽  
Model Based ◽  
Büchi Automaton ◽  
Constraint Based Models

The degree of flexibility of workflow management systems heavily influences the way business processes are executed. Constraint-based models are considered to be more flexible than traditional models because of their semantics: everything that does not violate constraints is allowed. More and more people use declarative languages to define workflow, such as linear temporal logic. But how to guarantee the correctness of the model based on the linear temporal logic is still a problem. This article proposes a way to verify the model based on Büchi automaton and gives the corresponding algorithms. Thus the verification of declarative workflow based on the linear temporal logic is solved.

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