Figure 1.
Core OpenCL-based implementation for robustness calculation (left) and FBLs examination (right) in parallel.
It is shown how in parallel PANET computes converging attractors over all possible initial-states or all update-rules (left) and searches FBLs (right).
Figure 2.
User interface for a batch-mode simulation on RBNs.
There are three steps for configuring parameters of the batch-mode simulation: selecting an RBN generation model, setting the number of considered initial-states and the type of update-rule schemes, and specifying the maximal length of FBLs/FFLs to be searched.
Table 1.
Performance comparisons of PANET with NetDS.
Figure 3.
Relationship between the ratio of coherent FFLs and update-rule robustness in large-scale Boolean networks by BA and ER models.
(a) Result of BA-based RBNs of the same size with HSN. (b) Result of BA-based RBNs of the same size with CCSN. (c) Result of ER-based RBNs of the same size with HSN. (d) Result of ER-based RBNs of the same size with CCSN. The maximal length of examined FFLs is set to 4 or 6 for (a) and (c), or (b) and (d), respectively. For robustness against update-rule perturbation, |S| is set to 1,024. The slopes of the regression lines are 0.66315, 0.36297, 1.38296 and 1.01162 in (a), (b), (c) and (d), respectively (all P-values<0.0001 using t-test).
Table 2.
Comparison of the ratios of coherent FFLs between each of the real signaling networks (HSN and CCSN) and RBNs.
Table 3.
Comparison of the ratios of coherent FBLs between each of the real signaling networks (HSN and CCSN) and RBNs.
Figure 4.
Relationship between the ratio of coherent FBLs and initial-state robustness in Boolean networks by the BA model.
(a) Result of RBNs of the same size with the HSN. (b) Result of RBNs of the same size with the CCSN. (c) Result of RBNs with |V| = 50 and |A| = 97. (d) Result of RBNs with |V| = 50 and |A| = 117. The maximal length of examined FBLs is set to 6, 8, 50 and 12, in (a) through (d), respectively. For robustness against initial-state perturbation, |S| is set to 1,024. In (a), (b) and (c), the correlations are not significant (P-value = 0.645, P-value = 0.895 and P-value = 0.167, respectively). On the other hand, the correlation is significantly negative in (d) (P-value = 0.048).