Petri Net representations in systems biology

2003 ◽  
Vol 31 (6) ◽  
pp. 1513-1515 ◽  
Author(s):  
J.W. Pinney ◽  
D.R. Westhead ◽  
G.A. McConkey
Keyword(s):  
Quantitative Analysis ◽  
Systems Biology ◽  
Petri Nets ◽  
Petri Net ◽  
Biological Networks ◽  
Research Effort ◽  
Research Directions ◽  
Mathematical Structures ◽  
New Research

The mathematical structures known as Petri Nets have recently become the focus of much research effort in both the structural and quantitative analysis of all kinds of biological networks. This review provides a very brief summary of these interesting new research directions.

scholarly journals PetriScape - A plugin for discrete Petri net simulations in Cytoscape

2016 ◽  
Vol 13 (1) ◽  
pp. 1-6 ◽  
Author(s):  
Diogo Almeida ◽  
Vasco Azevedo ◽  
Artur Silva ◽  
Jan Baumbach
Keyword(s):  
Petri Nets ◽  
Petri Net ◽  
Biological Networks ◽  
Computational Analysis ◽  
Biological Network ◽  
Global Network ◽  
Data Sets ◽  
Biological Network Analysis ◽  
Network Properties ◽  
Sbml Format

SummarySystems biology plays a central role for biological network analysis in the post-genomic era. Cytoscape is the standard bioinformatics tool offering the community an extensible platform for computational analysis of the emerging cellular network together with experimental omics data sets. However, only few apps/plugins/tools are available for simulating network dynamics in Cytoscape 3. Many approaches of varying complexity exist but none of them have been integrated into Cytoscape as app/plugin yet. Here, we introduce PetriScape, the first Petri net simulator for Cytoscape. Although discrete Petri nets are quite simplistic models, they are capable of modeling global network properties and simulating their behaviour. In addition, they are easily understood and well visualizable. PetriScape comes with the following main functionalities: (1) import of biological networks in SBML format, (2) conversion into a Petri net, (3) visualization as Petri net, and (4) simulation and visualization of the token flow in Cytoscape. PetriScape is the first Cytoscape plugin for Petri nets. It allows a straightforward Petri net model creation, simulation and visualization with Cytoscape, providing clues about the activity of key components in biological networks.

scholarly journals VANESA - A Software Application for the Visualization and Analysis of Networks in Systems Biology Applications

2014 ◽  
Vol 11 (2) ◽  
pp. 43-57 ◽  
Author(s):  
Christoph Brinkrolf ◽  
Sebastian Jan Janowski ◽  
Benjamin Kormeier ◽  
Martin Lewinski ◽  
Klaus Hippe ◽  
...  
Keyword(s):  
Systems Biology ◽  
Petri Net ◽  
Biological Networks ◽  
Life Science ◽  
Experimental Results ◽  
Biological Processes ◽  
Molecular Systems ◽  
Software Application ◽  
Theoretical Approaches ◽  
Modeling Software

Summary VANESA is a modeling software for the automatic reconstruction and analysis of biological networks based on life-science database information. Using VANESA, scientists are able to model any kind of biological processes and systems as biological networks. It is now possible for scientists to automatically reconstruct important molecular systems with information from the databases KEGG, MINT, IntAct, HPRD, and BRENDA. Additionally, experimental results can be expanded with database information to better analyze the investigated elements and processes in an overall context. Users also have the possibility to use graph theoretical approaches in VANESA to identify regulatory structures and significant actors within the modeled systems. These structures can then be further investigated in the Petri net environment of VANESA. It is platform-independent, free-of-charge, and available at http://vanesa.sf.net.

Vulnerability, Uncertainty and Probability (VUP) Quantification of a Network of Interacting Satellites Using Stochastic Petri Nets (SPN)

2013 ◽  
Author(s):  
Atefeh Einafshar ◽  
Farrokh Sassani
Keyword(s):  
Markov Chain ◽  
Quantitative Analysis ◽  
Petri Nets ◽  
State Space ◽  
Petri Net ◽  
Stochastic Petri Nets ◽  
Discrete State ◽  
New Approach ◽  
Stochastic Petri Net ◽  
Discrete State Space

A new approach to Vulnerability, Uncertainty and Probability (VUP) quantification procedure using Stochastic Petri Nets within a network of interacting satellites is presented. A Stochastic Petri Net based model is developed to quantify VUP in a network of interacting satellites. Three indicators are proposed to determine the VUP definitions in interacting network of satellites. The proposed VUP quantification scheme addresses a methodology which employs a Stochastic Petri Net for quantitative analysis of the behavior of the network. With the random variables associated with the Petri Net transitions, the dynamic behavior of the cooperating satellites in a SPN model can be mapped onto a time-continuous Markov chain with discrete state space. After generating a Markov Stochastic Petri Net model, the probability of a given condition in the network at a specified time can be computed and quantified as well as the vulnerability and uncertainty of the system using the identified indicators.

Compositional colored Petri net approach to multiscale modeling for systems biology

2014 ◽  
Vol 05 (04) ◽  
pp. 1450017 ◽  
Author(s):  
Fei Liu ◽  
Ming Yang
Keyword(s):  
Systems Biology ◽  
Petri Nets ◽  
Multiscale Modeling ◽  
Petri Net ◽  
Multiscale Model ◽  
Hierarchical Organization ◽  
Colored Petri Nets ◽  
Colored Petri Net ◽  
Multiscale Models ◽  
Multiscale Systems

Colored Petri nets have been demonstrated as a powerful tool for modeling multiscale systems biology. However, the construction of colored Petri nets for biological systems requires prior knowledge about colored Petri nets and is often error-prone and cumbersome for biologists, especially when the communication between components and hierarchical organization of components in a multiscale model are an issue. To address this problem, an established way is to develop small components and then compose them into bigger models. In this paper, we present a compositional colored Petri net approach to aid automatic modeling of systems biology, and demonstrate it with two case studies. We focus on the modeling of communication between components and hierarchical organization of components as they are key to build multiscale models.

INNOVATION CAPABILITY, ABSORPTIVE CAPACITY AND SMES PERFORMANCE IN PAKISTAN: THE MODERATING EFFECT OF BUSINESS STRATEGY

2018 ◽  
Vol 13 (Number 2) ◽  
pp. 1-11
Author(s):  
Muhammad Zulqarnain Arshad ◽  
Darwina Arshad
Keyword(s):  
Economic Growth ◽  
Absorptive Capacity ◽  
Business Strategy ◽  
Innovation Capability ◽  
Research Directions ◽  
Conceptual Paper ◽  
And Performance ◽  
New Research ◽  
The Relationship ◽  
Crucial Part

The small and medium-sized enterprises (SMEs) play a crucial part in county’s economic growth and a key contributor in country’s GDP. In Pakistan SMEs hold about 90 percent of the total businesses. The performance of SMEs depends upon many factors. The main aim for the research is to examine the relationship between Innovation Capability, Absorptive Capacity and Performance of SMEs in Pakistan. This conceptual paper also extends to the vague revelation on Business Strategy in which act as a moderator between Innovation Capability, Absorptive Capacity and SMEs Performance. Conclusively, this study proposes a new research directions and hypotheses development to examine the relationship among the variables in Pakistan’s SMEs context.

MATERIAL HANDLING MACHINES AND SYSTEMS – UMI-TWINN PROJECT CONTRIBUTION

2019 ◽  
Vol 12 (1) ◽  
pp. 7-20
Author(s):  
Péter Telek ◽  
Béla Illés ◽  
Christian Landschützer ◽  
Fabian Schenk ◽  
Flavien Massi
Keyword(s):  
Material Handling ◽  
Digital Data ◽  
Flow Process ◽  
Research Directions ◽  
Scientific Excellence ◽  
Research Activities ◽  
New Research ◽  
Eu Project ◽  
The University

Nowadays, the Industry 4.0 concept affects every area of the industrial, economic, social and personal sectors. The most significant changings are the automation and the digitalization. This is also true for the material handling processes, where the handling systems use more and more automated machines; planning, operation and optimization of different logistic processes are based on many digital data collected from the material flow process. However, new methods and devices require new solutions which define new research directions. In this paper we describe the state of the art of the material handling researches and draw the role of the UMi-TWINN partner institutes in these fields. As a result of this H2020 EU project, scientific excellence of the University of Miskolc can be increased and new research activities will be started.

scholarly journals Antimicrobial and Amyloidogenic Activity of Peptides Synthesized on the Basis of the Ribosomal S1 Protein from Thermus Thermophilus

2020 ◽  
Vol 21 (17) ◽  
pp. 6382 ◽  
Author(s):  
Stanislav Kurpe ◽  
Sergei Grishin ◽  
Alexey Surin ◽  
Olga Selivanova ◽  
Roman Fadeev ◽  
...  
Keyword(s):  
Antimicrobial Activity ◽  
Thermus Thermophilus ◽  
Antibacterial Properties ◽  
Cell Penetration ◽  
Research Directions ◽  
Bacterial Proteins ◽  
Hiv Transcription ◽  
Parent Protein ◽  
Amyloidogenic Peptides ◽  
New Research

Controlling the aggregation of vital bacterial proteins could be one of the new research directions and form the basis for the search and development of antibacterial drugs with targeted action. Such approach may be considered as an alternative one to antibiotics. Amyloidogenic regions can, like antibacterial peptides, interact with the “parent” protein, for example, ribosomal S1 protein (specific only for bacteria), and interfere with its functioning. The aim of the work was to search for peptides based on the ribosomal S1 protein from T. thermophilus, exhibiting both aggregation and antibacterial properties. The biological system of the response of Gram-negative bacteria T. thermophilus to the action of peptides was characterized. Among the seven studied peptides, designed based on the S1 protein sequence, the R23I (modified by the addition of HIV transcription factor fragment for bacterial cell penetration), R23T (modified), and V10I (unmodified) peptides have biological activity that inhibits the growth of T. thermophilus cells, that is, they have antimicrobial activity. But, only the R23I peptide had the most pronounced activity comparable with the commercial antibiotics. We have compared the proteome of peptide-treated and intact T. thermophilus cells. These important data indicate a decrease in the level of energy metabolism and anabolic processes, including the processes of biosynthesis of proteins and nucleic acids. Under the action of 20 and 50 μg/mL R23I, a decrease in the number of proteins in T. thermophilus cells was observed and S1 ribosomal protein was absent. The obtained results are important for understanding the mechanism of amyloidogenic peptides with antimicrobial activity and can be used to develop new and improved analogues.

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