对“关于”代谢网络的正则化能力“的评论”的答复
Reply to ''Comment on 'Regularizing Capacity of Metabolic Networks' ''
摘要：
在最近的一篇论文[C。Marr，M. Mueller-Linow和M. T. Huett，Phys.Rev.E75，041917（2007）]，我们讨论了与随机对应物相比，真实代谢网络拓扑结构正则化复杂二元动力学的显著潜力。在他们的评论[P.霍姆和M。Huss，arXiv：0705.4084v1]，Holme和Huss批评了我们的方法，并用更现实的动力学重复了我们的研究，其中程式化的反应动力学是在成对反应集上实现的。作者发现从代谢网络和随机化对应物重建的反应集之间没有动态差异。我们重现作者的观察，并发现他们的算法导致一个动态的碎片，从而消除了包含在图中的拓扑信息。因此，他们的方法不能排除代谢网络的拓扑结构和稳态的普遍存在之间的联系。
英文摘要：
In a recent paper [C. Marr, M. Mueller-Linow, and M.-T. Huett, Phys. Rev. E 75, 041917 (2007)] we discuss the pronounced potential of real metabolic network topologies, compared to randomized counterparts, to regularize complex binary dynamics. In their comment [P. Holme and M. Huss, arXiv:0705.4084v1], Holme and Huss criticize our approach and repeat our study with more realistic dynamics, where stylized reaction kinetics are implemented on sets of pairwise reactions. The authors find no dynamic difference between the reaction sets recreated from the metabolic networks and randomized counterparts. We reproduce the author's observation and find that their algorithm leads to a dynamical fragmentation and thus eliminates the topological information contained in the graphs. Hence, their approach cannot rule out a connection between the topology of metabolic networks and the ubiquity of steady states.
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