Team:iBowu-China/Software
We write a simple modeling tool for synthetic biology——SynBioModerler. The program is written with C + + and QT framework. And the software takes a simple XML file as the input, according to the description of the synthetic biology system in the XML file, constructs the model of the system, and draws the kinetic curve of the target compound. The interface after program execution is as follows:
Click “File->Open” in the upper right corner of the program interface, and a file browser will be opened to select the target xml file. After selecting the file, the program will automatically parse the content of the XML file, then build the model according to the description, solve the model and draw the dynamic curve. The dynamic curve of GFP protein of cell free system is as follows:
The content of the XML file of the cell free system is:
The XML file is defined as “< description >” “< /description >”, and the specific content of the description is contained between the two “< >”. Parameters can also be defined in “<>”. Each system must start with the < system > label, and the definition of all compounds must be included between the < system > and < /system >. The “name” attribute in the system node represents the name of the node, “dt” represents the time interval that the system will be solved, “start” represents the start time of the solution, and “end” represents the end time. Genes, mRNA, protein and small molecules in the system are defined in “< gene >”, “< mrna >”, “< protein >” and “< smol >” tags respectively. The “type”, “commit” and “con” in the “< gene >” tag indicate the regulation type, commit information and concentration of the gene. If “type” attribution is not 0, than the “by”, “coef” and “k” attrubutions must be given. The “by” attribution indicates which substances regulate the gene and “coef” is the coefficient of regulation of these genes. Multiple parameters are connected using the "+" symbol. “k” represents the binding strength of these substances to genes during regulation. The < mrna > label indicates the mRNA component in the system. The “from” tag indicates which gene the mRNA comes from. “con”, “commit”, “alpha” and “deg” represent concentration, submission information, rate of transcription, and degradation coefficient, respectively. If the gene is regulated by other substances, then the leaky expression rate needs to be given. The < protein > tag represents the proteins involved in the system. “from”, “con”, “commit”, “alpha” and “deg” represent mRNA source, initial concentration, submitted information, translation rate constant and degradation coefficient, respectively. And the < SMOL > label indicates the small molecule involved. At last, "< show >" tag represent which component's kinetic curve you want to display.