scholarly journals A High-Level Petri Net Framework for Genetic Regulatory Networks

2007 ◽  
Vol 4 (3) ◽  
pp. 1-14 ◽  
Author(s):  
Richard Banks ◽  
L. Jason Steggles
Keyword(s):  
Regulatory Networks ◽  
Formal Analysis ◽  
Boolean Model ◽  
Genetic Regulatory Networks ◽  
Cellular Systems ◽  
Logic Minimization ◽  
Formal Framework ◽  
The Individual ◽  
High Level ◽  
Compare And Contrast

Summary To understand the function of genetic regulatory networks in the development of cellular systems, we must not only realise the individual network entities, but also the manner by which they interact. Multi-valued networks are a promising qualitative approach for modelling such genetic regulatory networks, however, at present they have limited formal analysis techniques and tools. We present a flexible formal framework for modelling and analysing multi-valued genetic regulatory networks using high-level Petri nets and logic minimization techniques. We demonstrate our approach with a detailed case study in which part of the genetic regulatory network responsible for the carbon starvation stress response in Escherichia coli is modelled and analysed. We then compare and contrast this multivalued model to a corresponding Boolean model and consider their formal relationship.

Evolving Boolean Networks with Structural Dynamism

2012 ◽  
Vol 18 (4) ◽  
pp. 385-397 ◽  
Author(s):  
Larry Bull
Keyword(s):  
Regulatory Networks ◽  
Boolean Model ◽  
Boolean Networks ◽  
Genetic Regulatory Networks ◽  
Short Article ◽  
Evolutionary Innovation ◽  
Current Cell ◽  
Cell Life ◽  
Node Connectivity ◽  
Asynchronous Updating

This short article presents an abstract, tunable model of genomic structural change within the cell life cycle and explores its use with simulated evolution. A well-known Boolean model of genetic regulatory networks is extended to include changes in node connectivity based upon the current cell state to begin to capture some of the effects of transposable elements. The evolvability of such networks is explored using a version of the NK model of fitness landscapes with both synchronous and asynchronous updating. Structural dynamism is found to be selected for in nonstationary environments with both update schemes and subsequently shown capable of providing a mechanism for evolutionary innovation when such reorganizations are inherited. This is also found to be the case in stationary environments with asynchronous updating.

ON EXPLORING EFFECTS OF MOLECULAR NOISE IN A SIMPLE VIRAL INFECTION MODEL

2010 ◽  
Vol 03 (01) ◽  
pp. 1-19 ◽  
Author(s):  
ZHI XIE ◽  
DON KULASIRI
Keyword(s):  
Viral Infection ◽  
Regulatory Networks ◽  
Virus Assembly ◽  
Intrinsic Noise ◽  
Genetic Regulatory Networks ◽  
Infection Model ◽  
Extrinsic Noise ◽  
Living Organisms ◽  
High Level ◽  
And Function

Intrinsic and extrinsic noises are all believed to be important in the development and function of many living organisms. In this study, we investigate the sources of the intrinsic noise and the influence of the extrinsic noise on an intracellular viral infection system. The contribution of the intrinsic noise from each reaction is measured by means of a special form of stochastic differential equations (SDEs), chemical Langevin equation. The intrinsic noise of the system is a linear sum of the noise in each of the reactions. The intrinsic noise mainly arises from the degradation of mRNA and the transcription processes. We then study the effects of extrinsic noise by the means of a general form of SDE. It is found that the noise of the viral components grows logarithmically with the increasing noise intensities. The system is most susceptible to the noise in the virus assembly process. A high level of noise in this process can even inhibit the growth of the viruses. This study also demonstrates the utility of SDEs in analyzing genetic regulatory networks perturbed by either inherent or parametric stochasticity.

scholarly journals GeneVis: Simulation and Visualization of Genetic Networks

2003 ◽  
Vol 2 (4) ◽  
pp. 201-217 ◽  
Author(s):  
Charles Baker ◽  
Sheelagh Carpendale ◽  
Przemyslaw Prusinkiewicz ◽  
Michael Surette
Keyword(s):  
Network Structure ◽  
Base Pair ◽  
Regulatory Networks ◽  
Protein Concentration ◽  
Genetic Network ◽  
Genetic Regulatory Networks ◽  
Genetic Networks ◽  
Structure Representation ◽  
Individual Protein ◽  
The Individual

GeneVis simulates genetic networks and visualizes the process of this simulation interactively, providing a visual environment for exploring the dynamics of genetic regulatory networks. The visualization environment supports several representational modes, which include: an individual protein representation, a protein concentration representation, and a network structure representation. The individual protein representation shows the activities of the individual proteins. The protein concentration representation illustrates the relative spread and concentrations of the different proteins in the simulation. The network structure representation depicts the genetic network dependencies that are present in the simulation. GeneVis includes several interactive viewing tools. These include animated transitions from the individual protein representation to the protein concentration representation and from the individual protein representation to the network structure representation. Three types of lenses are used to provide different views within a representation: fuzzy lenses, base pair lenses, and the network structure ring lens. With a fuzzy lens an alternate representation can be viewed in a selected region. The base pair lenses allow users to reposition genes for better viewing or to minimize interference during the simulation. The ring lens provides detail-in-context viewing of individual levels in the genetic network structure representation.

A Graph Grammar Approach to Artificial Life

2004 ◽  
Vol 10 (4) ◽  
pp. 413-431 ◽  
Author(s):  
Ole Kniemeyer ◽  
Gerhard H. Buck-Sorlin ◽  
Winfried Kurth
Keyword(s):  
Artificial Life ◽  
Regulatory Networks ◽  
Object Oriented ◽  
Graph Grammar ◽  
Lindenmayer Systems ◽  
Rewriting Systems ◽  
Flower Morphogenesis ◽  
Formal Framework ◽  
High Level ◽  
Rewriting Rules

We present the high-level language of relational growth grammars (RGGs) as a formalism designed for the specification of ALife models. RGGs can be seen as an extension of the well-known parametric Lindenmayer systems and contain rule-based, procedural, and object-oriented features. They are defined as rewriting systems operating on graphs with the edges coming from a set of user-defined relations, whereas the nodes can be associated with objects. We demonstrate their ability to represent genes, regulatory networks of metabolites, and morphologically structured organisms, as well as developmental aspects of these entities, in a common formal framework. Mutation, crossing over, selection, and the dynamics of a network of gene regulation can all be represented with simple graph rewriting rules. This is demonstrated in some detail on the classical example of Dawkins' biomorphs and the ABC model of flower morphogenesis: other applications are briefly sketched. An interactive program was implemented, enabling the execution of the formalism and the visualization of the results.

A Simple Computational Cell: Coupling Boolean Gene and Protein Networks

2012 ◽  
Vol 18 (2) ◽  
pp. 223-236 ◽  
Author(s):  
Larry Bull
Keyword(s):  
Information Processing ◽  
Protein Interaction ◽  
Protein Interaction Network ◽  
Regulatory Networks ◽  
Interaction Network ◽  
Boolean Model ◽  
Genetic Regulatory Networks ◽  
Simulated Evolution ◽  
Cell Coupling ◽  
Computational Cell

This article presents an abstract, tunable model containing two of the principal information-processing features of cells and explores its use with simulated evolution. The random Boolean model of genetic regulatory networks is extended to include a protein interaction network. The underlying behavior of the resulting two coupled dynamical networks is investigated before their evolvability is explored using a version of the NK model of fitness landscapes.

Territorial Distribution of Alcohol and Drug Addictions Mortality Concerning Regional Disparities in the Slovak Republic from Year 1996 to Year 2015

2020 ◽  
Keyword(s):  
Mortality Rate ◽  
Slovak Republic ◽  
Regional Disparities ◽  
Point Of View ◽  
Extreme Position ◽  
Data Set ◽  
Female Sex ◽  
Male Sex ◽  
The Individual ◽  
High Level

BACKGROUND: This paper deals with territorial distribution of the alcohol and drug addictions mortality at a level of the districts of the Slovak Republic. AIM: The aim of the paper is to explore the relations within the administrative territorial division of the Slovak Republic, that is, between the individual districts and hence, to reveal possibly hidden relation in alcohol and drug mortality. METHODS: The analysis is divided and executed into the two fragments – one belongs to the female sex, the other one belongs to the male sex. The standardised mortality rate is computed according to a sequence of the mathematical relations. The Euclidean distance is employed to compute the similarity within each pair of a whole data set. The cluster analysis examines is performed. The clusters are created by means of the mutual distances of the districts. The data is collected from the database of the Statistical Office of the Slovak Republic for all the districts of the Slovak Republic. The covered time span begins in the year 1996 and ends in the year 2015. RESULTS: The most substantial point is that the Slovak Republic possesses the regional disparities in a field of mortality expressed by the standardised mortality rate computed particularly for the diagnoses assigned to the alcohol and drug addictions at a considerably high level. However, the female sex and the male sex have the different outcome. The Bratislava III District keeps absolutely the most extreme position. It forms an own cluster for the both sexes too. The Topoľčany District bears a similar extreme position from a point of view of the male sex. All the Bratislava districts keep their mutual notable dissimilarity. Contrariwise, evaluation of a development of the regional disparities among the districts looks like notably heterogeneously. CONCLUSIONS: There are considerable regional discrepancies throughout the districts of the Slovak Republic. Hence, it is necessary to create a common platform how to proceed with the solution of this issue.

Ibn Khaldun’s Theory of Social Change

1998 ◽  
Vol 15 (2) ◽  
pp. 25-45 ◽  
Author(s):  
Fida Mohammad
Keyword(s):  
Industrial Revolution ◽  
Natural World ◽  
Social Knowledge ◽  
Philosophical Tradition ◽  
Historical Process ◽  
Ibn Khaldun ◽  
Historical Processes ◽  
The Will ◽  
The Individual ◽  
Compare And Contrast

In this article I shall compare and contrast Ibn Khaldun’s ideas aboutsociohistorical change with those of Hegel, Marx, and Durkheim. I willdiscuss and elaborate Ibn Khaldun’s major ideas about historical andsocial change and compare them with three important figures of modemWestern sociology and philosophy.On reading Ibn Khaldun one should remember that he was living in thefourteenth century and did not have the privilege of witnessing the socialdislocation created by the industrial revolution. It is also very difficult tocategorize Ibn Khaldun within a single philosophical tradition. He is arationalist as well as an empiricist, a historicist as well as a believer inhuman agency in the historical process. One can see many “modem”themes in his thinking, although he lived a hundred years beforeMachiavelli.Lauer, who considers Ibn Khaldun the pioneer of modem sociologicalthought, has summarized the main points of his philosophy.’ In his interpretationof Ibn Khaldun, he notes that historical processes follow a regularpattern. However, whereas this pattern shows sufficient regularity, itis not as rigid as it is in the natural world. In this regard the position ofIbn Khaldun is radically different from those philosophies of history thatposit an immutable course of history determined by the will of divineprovidence or other forces. Ibn Khaldun believes that the individual isneither a completely passive recipient nor a full agent of the historicalprocess. Social laws can be discovered through observation and datagathering, and this empirical grounding of social knowledge represents adeparture from traditional rational and metaphysical thinking ...

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