This paper introduces the UbiManager, a tool for managing the ubichip reconfigurable circuit. The ubichip is a custom reconfigurable electronic device for implementing circuits featuring bio-inspired mechanisms like growth, learning, and evolution. The ubichip has been developed in the framework of Perplexus, a European project that aims to develop a scalable hardware platform made of bio-inspired custom reconfigurable devices for simulating large-scale complex systems. In this paper, we present the software tool used for designing, simulating, emulating, debugging, configuring, and monitoring the systems to be implemented in the ubichip. This paper also presents the dissemination plans of the UbiManager, that consist in a web platform allowing researchers to access the hardware platform from any remote base station.