The Physiome Project needs to support both public good science and industry involvement. All software tools (including APIs, authoring tools, visualization tools, graphical user interfaces, and simulation tools) developed for the Physiome Project will be open source under a Mozilla or LGPL licence – i.e. modifications must be put back into the public domain, but apart from this there is no restriction on commercial use (a commercial package, for example, can link the open-source library).

The Auckland group has contributed its visualization package CMGUI to this open source effort and the University of Washington, Seattle, group similarly intends releasing its JSim systems modeling package under an open source licence.

The Auckland computational CMISS software is currently subject to commercial licence agreements which prevent it from being open source. CMISS is, however, freely available for academic use.