A graphical notation for biochemical networks

BIOSILICO ◽  
2003 ◽  
Vol 1 (5) ◽  
pp. 169-176 ◽  
Author(s):  
Hiroaki Kitano
2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Harrison B. Smith ◽  
Hyunju Kim ◽  
Sara I. Walker

AbstractBiochemical reactions underlie the functioning of all life. Like many examples of biology or technology, the complex set of interactions among molecules within cells and ecosystems poses a challenge for quantification within simple mathematical objects. A large body of research has indicated many real-world biological and technological systems, including biochemistry, can be described by power-law relationships between the numbers of nodes and edges, often described as “scale-free”. Recently, new statistical analyses have revealed true scale-free networks are rare. We provide a first application of these methods to data sampled from across two distinct levels of biological organization: individuals and ecosystems. We analyze a large ensemble of biochemical networks including networks generated from data of 785 metagenomes and 1082 genomes (sampled from the three domains of life). The results confirm no more than a few biochemical networks are any more than super-weakly scale-free. Additionally, we test the distinguishability of individual and ecosystem-level biochemical networks and show there is no sharp transition in the structure of biochemical networks across these levels of organization moving from individuals to ecosystems. This result holds across different network projections. Our results indicate that while biochemical networks are not scale-free, they nonetheless exhibit common structure across different levels of organization, independent of the projection chosen, suggestive of shared organizing principles across all biochemical networks.


2014 ◽  
Vol 8 (1) ◽  
pp. 20 ◽  
Author(s):  
Joep Vanlier ◽  
Christian A Tiemann ◽  
Peter AJ Hilbers ◽  
Natal AW van Riel

2001 ◽  
Vol 16 (4) ◽  
pp. 295-329 ◽  
Author(s):  
ANTHONY HUNTER

Numerous argumentation systems have been proposed in the literature. Yet there often appears to be a shortfall between proposed systems and possible applications. In other words, there seems to be a need for further development of proposals for argumentation systems before they can be used widely in decision-support or knowledge management. I believe that this shortfall can be bridged by taking a hybrid approach. Whilst formal foundations are vital, systems that incorporate some of the practical ideas found in some of the informal approaches may make the resulting hybrid systems more useful. In informal approaches, there is often an emphasis on using graphical notation with symbols that relate more closely to the real-world concepts to be modelled. There may also be the incorporation of an argument ontology oriented to the user domain. Furthermore, in informal approaches there can be greater consideration of how users interact with the models, such as allowing users to edit arguments and to weight influences on graphs representing arguments. In this paper, I discuss some of the features of argumentation, review some key formal argumentation systems, identify some of the strengths and weaknesses of these formal proposals and finally consider some ways to develop formal proposals to give hybrid argumentation systems. To focus my discussions, I will consider some applications, in particular an application in analysing structured news reports.


1999 ◽  
Vol 76 (1) ◽  
pp. 1-11 ◽  
Author(s):  
Soumalee Basu ◽  
Chitra Dutta ◽  
Jyotirmoy Das

2018 ◽  
Vol 14 (2) ◽  
pp. e1005740 ◽  
Author(s):  
Vasundra Touré ◽  
Nicolas Le Novère ◽  
Dagmar Waltemath ◽  
Olaf Wolkenhauer

2007 ◽  
Vol 1 (1) ◽  
Author(s):  
Tommi Aho ◽  
Olli-Pekka Smolander ◽  
Jari Niemi ◽  
Olli Yli-Harja

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