This paper presents a new unified design flow developed within the Perplexus project that aims to accelerate parallelizable data-intensive applications in the context of ubiquitous computing. This contribution relies on the JubiTool: a set of integrated tools (JubiSplitter, JubiCompiler, UbiAssembler), allowing respectively to extract, compile and assemble parallelizable parts of applications described in Jubi language. Jubi is a modified Java agent based language (JADE) dedicated to the Ubichip (the bio-inspired chip developed within the confines of the Perplexus project). By appending hardware directives to a software agent description, the inherent flexibility of software is combined with the runtime performance of a hardware execution. In the case of typical Perplexus applications such as the Spiking Neural Network Simulator, this contribution takes profit of the intrinsic property of the Ubichip in terms of parallelism resulting in an expected speedup of at least one order of magnitude. Finally, this hybrid (SW/HW) flow could be easily modified and adapted to support other kind of distributed platforms.