Name
Abstract | ||
|---|---|---|
Remarkable progress in various fields of biology is leading in the direction of a complete map of the building blocks of biological systems. There is broad agreement among researchers that 21st century biology will focus on attempting to understand how component parts collaborate to create a whole. It is also well agreed that this transition of biology from identifying the building blocks (analysis) to integrating the parts into a whole (synthesis) should rely on the language of mathematics. In a recent publication, we described the results of a first attempt at confronting the above challenge using the visual formalism of statecharts. We presented a detailed model for T cell activation using statecharts within the general framework of object-oriented modeling. In this work, we compare the statechart-based modeling approach to a Boolean formalism presented by Thomas & D'Ari. This comparison was done by taking a model for T cell activation and anergy, which was constructed by Kaufman et al. using such a Boolean formalism, and translating it into the language of statecharts. Comparing these two representations of the same phenomena allows us to assess the advantages and disadvantages of each modeling approach. We believe that the results of this work, together with the results of our previous modeling work on T cell activation, should encourage the use of visual formalisms such as statecharts for modeling complex biological systems. A full version of this paper appeared in the proceedings of the Second International Conference on Systems Biology, Pasadena, CA, USA, 2001 [9]. |
Year | DOI | Venue |
|---|---|---|
2002 | 10.1145/1556262.1556318 | AVI |
Keywords | Field | DocType |
century biology,boolean formalism,biological system,biological reactivity,modeling approach,statechart-based modeling approach,cell activation,previous modeling work,object oriented modeling,building block,immunology,statecharts,visual formalism,object-oriented modeling,biological systems,system biology | Object-oriented modeling,Programming language,Computer science,State diagram,Systems biology,Language of mathematics,Boolean algebra,Formalism (philosophy),Rotation formalisms in three dimensions | Conference |
ISBN | Citations | PageRank |
1-58113-537-8 | 10 | 1.36 |
References | Authors | |
4 | 3 | |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Naaman Kam | 1 | 11 | 1.74 |
| Irun R. Cohen | 2 | 296 | 21.62 |
| David Harel | 3 | 9703 | 1953.76 |