We propose black box checking as a framework for analyzing biochemical networks. Black box checking was originally introduced by Peled, Yannakakis and Vardi in the context of formal verification of concurrent systems as a strategy that combines model checking and testing, as two main techniques in that area. Based on the natural analogy between biochemical networks and concurrent systems we argue that black box checking can be used to design and perform experiments in a systematic manner, and also to learn about the network underlying mechanisms. We also discuss potential applications with emphasis on forward engineering of biochemical networks.
|Title of host publication||Computational Methods in Systems Biology (2nd International Conference, CMSB 2004, Paris, France, May 26-28, 2004, Revised Selected Papers)|
|Editors||V. Danos, V. Schächter|
|Place of Publication||Berlin|
|Publication status||Published - 2005|
|Name||Lecture Notes in Computer Science|
Bosnacki, D. (2005). Black box checking for biochemical networks. In V. Danos, & V. Schächter (Eds.), Computational Methods in Systems Biology (2nd International Conference, CMSB 2004, Paris, France, May 26-28, 2004, Revised Selected Papers) (pp. 225-230). (Lecture Notes in Computer Science; Vol. 3082). Springer. https://doi.org/10.1007/b107287