In general biologists are not accustomed to formulating biological problems in the precise mathematical terms that are required to solve them analytically or numerically. Although many computational tools for systems biology have been developed recently, our observations indicate that many of these tools are powerful only in the hands of those who know a lot about how to use them. For most biologists, the tools have a protracted learning curve and unfriendly user interface that often diminish their likelihood of being used. Our long term goal is to build a knowledge system that allows biologists to synthesize complex biological systems via natural language interactions, and the system is able to generate the corresponding mathematical descriptions so that the often cumbersome communication process between biologists and mathematicians/engineers in formulating complex biological problems in mathematic terms can be performed more easily. To focus, the first goal in this research is to build a knowledge system prototype that focuses on transport related biological problems that occur from the cellular to tissue level. We address specifically two inter-related problems: (1) Provision of an intelligent system that is capable of automatically synthesizing smaller components into more complex systems; Provision of a user-friendly and natural language interface.