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ByoDyn (http://cbbl.imim.es/ByoDyn) is a software tool for the study of biochemical networks within the framework of systems biology. SBML compatible, ByoDyn is a group effort of the Computational Biochemistry and Biophysics Lab.
PCSIM is a tool for distributed simulation of heterogeneous networks composed of different model neurons and synapses. The development of PCSIM was supported by the FACETS EU project.
CDNsim is a GNU/LINUX simulation tool for CDNs, written in C++ (core) and python (GUI wizard). It models: redirection policies, cache policies, TCP/IP, batch simulations, statistics extraction and more. CDNsim is uses the OMNet++ library
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pyomnet provide an object-oriented way to define the network topology.
It's a good way to illustrate network in an abstract way.
pyomnet could generate the NED scenario and configuration(latter) for OMNeT++ simulation tool.
Cellogica is a cellular logic analysis tool. It incorporates sequential logic and finite state machine to elucidate the relationship between transcription factors and corresponding gene expression.
Networked training tool for Air Traffic Controllers
Crujisim is a tool to allow Air Traffic Controllers trainees to practice in a radar environment. Different users connect to a hosting server to act either as controllers for adjacent positions or pseudopilots.
Distributions Networks Analyzer (DNA) is a tool for simulating (power flow) and analyzing electrical distribution networks. Users can easily implement and test their own power flow, optimal power flow and control algorithms.