for what kind of application scenarios do you need these tools. NS2 also provides a lot of features and plugins to emulate / simulate biology-based computational plattforms.

Furthermore, you can try SimANet, a modular simulation framework for different types of networks:

https://www.ce.informatik.tu-chemnitz.de/forschung/demonstratoren/simanet/

I mean tools that is open source and applied in gene regulatory network reconstruction. 

Hi,

IMHO your application scenario is based on specific movement models for your network nodes. Starting from a given, "destroyed" structure, the nodes have to re-organise predefined patterns / topologies. You measure the time and the quality of the results. Is this right?

If yes, you can use several mobile ad hoc network simulators, which are able to integrate user-defined movement models (mobility models). So NS2, NS3, OMNet++ with the MiXiM or INETMANET extension as well as SimANet. Special nodes behaviour for your fields of application will be implemented in node-specifc classes or modules.

Cytoscape is the best choice for gene regulatory network analysis, since it includes plugins for many databases e.g. NCBI GEO.

http://www.cytoscape.org/

Thank you very much. I'll do my homework on Cytoscape. But the field is more concentrated on the reconstruction of Gene Regulatory Networks than just analysis. Do you know any tools in this field?

GeneNetWeaver and CytoScape are two usefull toos in Gene Regulatory Network. From GeneNettWeaver you can get Gene Expression Data for a given network. It is easy to learn and helpful.