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APPLICATIONS OF MATLAB IN SCIENCE AND ENGINEERING - PART 3

Có hai cách xác định cùng một mô hình Boolean. Một đại diện đồ họa tương tác quản lý được tạo ra trong trình soạn thảo đồ thị yEd. Lưu ý việc sử dụng "&" nút dán nhãn để tạo ra và cửa. Mũi tên thường xuyên đại diện cho kích hoạt trong khi kim cương đầu mũi tên đứng cho sự ức chế. | 42 Applications of MATLAB in Science and Engineering Fig. 5. Two ways of defining the same Boolean model. A Graphical representation of the regulatory interactions created in the yEd graph editor. Note the usage of labeled nodes in order to create AND gates. Regular arrows represent activation whereas diamond head arrows stand for inhibition. B Boolean equations for the same model. We use to indicate input species with no regulators and MATLAB Boolean operators and to define the Boolean equations. 4.1 Definition of tHe Boolean model The most convenient methods to define Boolean models in the Odefy toolbox are Boolean equations and the yEd graph editor3. A simple graph where each node represents a factor of the system and each edge represents a regulatory interaction is not sufficient to define a Boolean model since we cannot distinguish between AND and OR gates of different inputs. Therefore we adapted the intuitive hypergraph representation proposed by Klamt et al. 2006 as exemplarily demonstrated in Figure 5A. All incoming edges into a factor are interpreted as OR gates for instance C will be active when B or E is present. AND gates are created by using a special node labeled e.g. E will be active when I2 is present and I1 is not present. We now load this model from a pre-created .graphml file which is contained in the Odefy materials download package. Ensure that Odefy is initialized first InitOdefy We can now call the LoadModelFile command which automatically detects the underlying file format model LoadModelFilef cnatoy.graphml As mentioned previously in this chapter Boolean equations are a convenient alternative for constructing a Boolean model. While obviously the graphical depiction of the network is lost Boolean equations can be rapidly setup and altered Figure 5B . We can either load them from a text file containing one equation per line or directly enter them into the MATLAB command line model LoadModelFilef cnatoy.txt or model ExpressionsToOdefy I1 I2 A