CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks

Funahashi, Akira; Matsuoka, Yoshikazu; Jouraku, Akiya; Morohashi, Mineo; Kikuchi, Norihiro; Kitano, Hiroaki

doi:10.1109/jproc.2008.925458

Cited by 414 publications

(311 citation statements)

References 28 publications

Supporting

Mentioning

308

Contrasting

Unclassified

Order By: Relevance

“…The TSHR, TPO, and NIS network models which include gene, RNA, protein, enzyme, receptor and ions were constructed with CellDesigner ver 4.1 and stored in system biology markup language (SBML) machine-readable model representation format (Funahashi et al 2007(Funahashi et al , 2008Hucka et al 2004;Funahashi et al 2003). CellDesigner tool is a process diagram editor for representation of genetic and biochemical pathways.…”

Section: Methodsmentioning

confidence: 99%

Modeling and simulation analysis of propyl-thiouracil (PTU), an anti-thyroid drug on thyroid peroxidase (TPO), thyroid stimulating hormone receptor (TSHR), and sodium iodide (NIS) symporter based on systems biology approach

Gupta

Misra

2013

Netw Model Anal Health Inform Bioinforma

View full text Add to dashboard Cite

The aim of metabolic modeling was to understand the cause effect interaction and reliance linked with the complex interactions of biological networks and molecular systems. Drugs that therapeutically modulate the biological processes of disease are often developed with limited knowledge of the underlying complexity of their specific targets. The robustness for systemic modulating behavior of thyroid hormone secretion during the course of different time unit simulation is explained in this study. In this work, a computational model has been developed which mimics the in vivo simulation. The model was constructed with the help of cell designer 4.1 used for analyzing the effect of perturbed amount of drugs at 0.1, 0.5, 1.0, 1.5, 2.0, 2.5, 3.0 amounts as a unit, targeting Thyroid Peroxidase (TPO), Thyroid Stimulating Hormone Receptor (TSHR), and Sodium Iodide Symporter (NIS). The rate kinetic equations were defined with each reaction to simulate the molecular species dynamic behavior. The modulating behavior of thyroid hormone secretion was analyzed by the process of activation and inactivation states of TPO, TSHR, and NIS at various amounts of drugs.Obtained results explain suitably the entire observable fact of the drug effects and are capable to proceed in response to the perturbations of the natural cell. TSHR was found as the most potent molecular therapeutic target in this study.

show abstract

Section: Methodsmentioning

confidence: 99%

Modeling and simulation analysis of propyl-thiouracil (PTU), an anti-thyroid drug on thyroid peroxidase (TPO), thyroid stimulating hormone receptor (TSHR), and sodium iodide (NIS) symporter based on systems biology approach

Gupta

Misra

2013

Netw Model Anal Health Inform Bioinforma

View full text Add to dashboard Cite

show abstract

“…In addition, several software platforms are available that enable the easy editing of SMBL maps using graphical user interfaces (Table 2) [33]. For example, CellDesigner TM is used to describe molecular events within cells [34] (Figure 2c). CellDesigner TM can be used to convert the activity flow diagram shown in Figure 2b to a pathway map, which is referred to as a process flow diagram (Figure 2c).…”

Section: Preparation Of Pathway Mapsmentioning

confidence: 99%

Systems‐based understanding of pharmacological responses with combinations of multidisciplinary methodologies

Kariya

Honma

Suzuki

2013

Biopharm & Drug Disp

View full text Add to dashboard Cite

The importance of systems-based pharmacological approaches to drug discovery and development has increasingly been recognized. This reviews summarizes recent advances in the development of systems pharmacology and introduces the methods used for analysis. To understand the cellular response at the molecular level, pathway maps must be prepared to show how the function of the constituent molecules within cells are linked and integrated to form molecular networks. First, the methods used to prepare these pathway maps, such as databases, knowledge bases and software platforms, are introduced. Then the mathematical theories used to analyse the behavior of molecular networks are summarized. To quantitatively predict cellular responses, simulations are performed that are based on the rate equations for each reaction within the pathway map. If the number of reactions described in the pathway map is small, and if the parameter values for the rate constants are available, it is possible accurately to simulate the behavior of the molecular networks. However, to analyse complex maps, mathematical abstraction is required. Such abstraction methods are important to integrate cellular responses and to understand tissue/organ and in vivo pharmacological/toxicological responses. The scope and limitations of the methods are also discussed.

show abstract

“…Unfortunately, hardly any tools exist that visualize these uncertainties. Tools, such as COPASI [14] or CellDesigner [12], support the simulation of BRN models and visualization of model predictions. While these tools are suitable given that we are interested in just one parameter value, they fail to provide visualizations of the prediction uncertainties.…”

Section: Related Workmentioning

confidence: 99%

Uncertainty-aware visual analysis of biochemical reaction networks

Vehlow

Hasenauer

Kramer

et al. 2012

2012 IEEE Symposium on Biological Data Visualization (BioVis)

View full text Add to dashboard Cite

We present a visual analytics system that supports an uncertaintyaware analysis of static and dynamic attributes of biochemical reaction networks (BRNs). These are often described by mathematical models, such as ordinary differential equations (ODEs), which enable the integration of a multitude of different data and data types using parameter estimation. Due to the limited amount of data, parameter estimation does not necessarily yield a single point in parameter space and many attributes of the model remain uncertain. Our system visualizes the model as a graph, where the statistics of the attributes are mapped to the color of edges and vertices. The graph view is combined with several linked views such as lineplots, scatterplots, and correlation matrices, to support the identification of uncertainties and the analysis of their mutual dependencies as well as their time dependencies. To assess the utility of the individual visualization approaches and multiple linked views, a qualitative user study with domain experts was performed. We found that all users were able to process analysis tasks using our system.

show abstract

CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks

Cited by 414 publications

References 28 publications

Modeling and simulation analysis of propyl-thiouracil (PTU), an anti-thyroid drug on thyroid peroxidase (TPO), thyroid stimulating hormone receptor (TSHR), and sodium iodide (NIS) symporter based on systems biology approach

Modeling and simulation analysis of propyl-thiouracil (PTU), an anti-thyroid drug on thyroid peroxidase (TPO), thyroid stimulating hormone receptor (TSHR), and sodium iodide (NIS) symporter based on systems biology approach

Systems‐based understanding of pharmacological responses with combinations of multidisciplinary methodologies

Uncertainty-aware visual analysis of biochemical reaction networks

Contact Info

Product

Resources

About