scholarly journals Petri Net-Based Graphical and Computational Modelling of Biological Systems

2016 ◽  
Author(s):  
Alessandra Livigni ◽  
Laura O’Hara ◽  
Marta E. Polak ◽  
Tim Angus ◽  
Lee B. Smith ◽  
...  
Keyword(s):  
Graphical Representation ◽  
Computational Modelling ◽  
Dynamic Activity ◽  
Metabolic Signalling ◽  
Graphical Modelling ◽  
Notation Scheme ◽  
Pathway Models ◽  
Process Diagrams ◽  
Transcriptional Pathway ◽  
Modelling System

AbstractIn silico modelling of biological pathways is a major endeavour of systems biology. Here we present a methodology for construction of pathway models from the literature and other sources using a biologist-friendly graphical modelling system. The pathway notation scheme, called mEPN, is based on the principles of the process diagrams and Petri nets, and facilitates both the graphical representation of complex systems as well as dynamic simulation of their activity. The protocol is divided into four sections: 1) assembly of the pathway in the yEd software package using the mEPN scheme, 2) conversion of the pathway into a computable format, 3) pathway visualisation and in silico simulation using the BioLayout Express3D software, 4) optimisation of model parameterisation. This method allows reconstruction of any metabolic, signalling and transcriptional pathway as a means of knowledge management, as well as supporting the systems level modelling of their dynamic activity.

Using process diagrams for the graphical representation of biological networks

2005 ◽  
Vol 23 (8) ◽  
pp. 961-966 ◽  
Author(s):  
Hiroaki Kitano ◽  
Akira Funahashi ◽  
Yukiko Matsuoka ◽  
Kanae Oda
Keyword(s):  
Biological Networks ◽  
Graphical Representation ◽  
Process Diagrams

scholarly journals Computational Modelling and Prediction of Consequences in Case of Accidental Releases of Hazardous Substances in an Industrial Plant

2021 ◽  
Vol 241 ◽  
pp. 03003
Author(s):  
Vlad Mihai Pasculescu ◽  
Marius Simion Morar ◽  
Cristian Raul Cioara ◽  
Ligia Ioana Tuhut ◽  
Andrada Denisa Babut
Keyword(s):  
Computational Modelling ◽  
Hazardous Materials ◽  
Hazardous Substances ◽  
Industrial Plant ◽  
Toxic Substances ◽  
Specialized Software ◽  
Graphical Modelling ◽  
Industrial Unit ◽  
Accident Scenarios ◽  
Main Activity

Storing relatively large amounts of hazardous materials under certain conditions can lead to high-risk situations. In industrial units, the assessment of the amplitude and severity of the consequences of the identified major accidents is done in order to provide data on site intervention and emergency planning. This study aims to assess the consequences of untimely releases of hazardous explosive / toxic substances in an industrial unit by graphical modelling and analysis of such accident scenarios using specialized software tools. The main activity of the industrial unit under study consists in the manufacture, processing and marketing of essential oils and their derived products.

HIPPO — A Declarative Graphical Modelling System

1999 ◽  
pp. 154-168
Author(s):  
Chris J. Hinde ◽  
Richard J. Reader ◽  
Kath Phelps
Keyword(s):  
Graphical Modelling ◽  
Modelling System

Metabolic signalling and the partitioning of resources in plant storage organs

1999 ◽  
Vol 133 (3) ◽  
pp. 243-249 ◽  
Author(s):  
NIGEL G. HALFORD
Keyword(s):  
Dry Weight ◽  
Wild Relatives ◽  
Crop Plants ◽  
Wild Plants ◽  
Young Plant ◽  
Carbon And Nitrogen ◽  
Cultivated Potato ◽  
Metabolic Signalling ◽  
Storage Organs ◽  
Plant Storage

The most important harvested organs of crop plants, such as seeds, tubers and fruits, are often described as assimilate sinks. They play little or no part in the fixation of carbon through the production of sugars through photosynthesis, or in the uptake of nitrogen and sulphur, but import these assimilated resources to support metabolism and to store them in the form of starch, oils and proteins. Wild plants store resources in seeds and tubers to later support an emergent young plant. Cultivated crops are effectively storing resources to provide us with food and many have been bred to accumulate much more than would be required otherwise. For example, approximately 80% of a cultivated potato plant's dry weight is contained in its tubers, ten times the proportion in the tubers of its wild relatives (Inoue & Tanaka 1978). Cultivation and breeding has brought about a shift in the partitioning of carbon and nitrogen assimilate between the organs of the plant.

Innovative Methods for Graphical Representation of System State Information

1995 ◽  
Author(s):  
Richard E. Maisano ◽  
Mark Y. Czarnolewski
Keyword(s):  
Graphical Representation ◽  
System State ◽  
State Information ◽  
Innovative Methods

Missing Data - Better "Not to Have Them", but What If You Do? (Part 1)

Marketing ZFP ◽  
2019 ◽  
Vol 41 (4) ◽  
pp. 21-32
Author(s):  
Dirk Temme ◽  
Sarah Jensen
Keyword(s):  
Missing Data ◽  
Statistical Power ◽  
Missing Values ◽  
Graphical Representation ◽  
Marketing Research ◽  
Likelihood Estimation ◽  
Parameter Estimates ◽  
Full Information Maximum Likelihood ◽  
Definition Of ◽  
Traditional Approaches

Missing values are ubiquitous in empirical marketing research. If missing data are not dealt with properly, this can lead to a loss of statistical power and distorted parameter estimates. While traditional approaches for handling missing data (e.g., listwise deletion) are still widely used, researchers can nowadays choose among various advanced techniques such as multiple imputation analysis or full-information maximum likelihood estimation. Due to the available software, using these modern missing data methods does not pose a major obstacle. Still, their application requires a sound understanding of the prerequisites and limitations of these methods as well as a deeper understanding of the processes that have led to missing values in an empirical study. This article is Part 1 and first introduces Rubin’s classical definition of missing data mechanisms and an alternative, variable-based taxonomy, which provides a graphical representation. Secondly, a selection of visualization tools available in different R packages for the description and exploration of missing data structures is presented.

A Problem of Long - Term Digital Preservation: Difference in Humanities and Natural Sciences

2014 ◽  
Vol 3 ◽  
pp. 183-195
Author(s):  
Elena Macevičiūtė
Keyword(s):  
Social Sciences ◽  
Digital Preservation ◽  
Dynamic Activity ◽  
Private Companies ◽  
Time Line ◽  
Digital Documents ◽  
Whole Process ◽  
The Difference ◽  
Technological Science

The article deals with the requirements and needs for long-term digital preservation in different areas of scholarly work. The concept of long-term digital preservation is introduced by comparing it to digitization and archiving concepts and defined with the emphasis on dynamic activity within a certain time line. The structure of digital preservation is presented with regard to the elements of the activity as understood in Activity Theory. The life-cycle of digitization processes forms the basis of the main processing of preserved data in preservation archival system.The author draws on the differences between humanities and social sciences on one hand and natural and technological science on the other. The empirical data characterizing the needs for digital preservation within different areas of scholarship are presented and show the difference in approaches to long-term digital preservation, as well as differences in selecting the items and implementing the projects of digital preservation. Institutions and organizations can also develop different understanding of preservation requirements for digital documents and other objects.The final part of the paper is devoted to some general problems pertaining to the longterm digital preservation with the emphasis of the responsibility for the whole process of safe-guarding the cultural and scholarly heritage for the re-use of the posterior generations. It is suggested that the longevity of the libraries in comparison with much shorter life-span of private companies strengthens the claim of memory institutions to playing the central role in the long-term digital preservation.

The properties of Bessel-type fractional derivatives and integrals

2016 ◽  
pp. 3973-3982
Author(s):  
V. R. Lakshmi Gorty
Keyword(s):  
Fractional Order ◽  
Real Line ◽  
Computer Algebra System ◽  
Fractional Derivatives ◽  
Graphical Representation ◽  
Fractional Integrals ◽  
The Real ◽  
Fractional Derivatives And Integrals ◽  
Half Axis ◽  
Derivatives Of

The fractional integrals of Bessel-type Fractional Integrals from left-sided and right-sided integrals of fractional order is established on finite and infinite interval of the real-line, half axis and real axis. The Bessel-type fractional derivatives are also established. The properties of Fractional derivatives and integrals are studied. The fractional derivatives of Bessel-type of fractional order on finite of the real-line are studied by graphical representation. Results are direct output of the computer algebra system coded from MATLAB R2011b.

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