Team:USTC SOFTWARE/Notebook/Meetings/10 May 2010


Zhen Wang

We decide to realize the database and simulation of a biological oscillator first, the model was presented in article “A synthetic oscillatory network of transcriptional regulators”, Nature 2000.

Kun Jiang

After meeting difficulty of developing a sbml ode solver from scratch, We turn to the existing library. At last, soslib v1.6.0, a library covered by the LGPL license, was choose to be as a part of our software. Add simple data display function to the soslib to get curve representation of the output data. And also need be noticed is that the soslib only support sbml version 2 level 1.

Shangyu Luo

Read the source code of TinkerCell and place emphasis on the simulation parts. Try to detail how it operate its modeling in sequence and detect that they use ODE and some mathematic API to simulate the biological reactions.