Team:USTC Software/hoWIO

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SBML

The Systems Biology Markup Language (SBML) is a computer-readable format for representing models of biological processes. It's applicable to simulations of metabolism, cell-signaling, and many other topics. SBML has been evolving since mid-2000 thanks to an international community of software developers and users. Thus, we make SBML to access our software, which makes it more compatible to other biological projects.


To access the requirement, there must be a tool helps us to fetch the list of data from a SBML file. Fortunately, LibSBML assists us for all the SBML related staff. LibSBML is an open-source programming library to help you read, write, manipulate, translate, and validate SBML files and data streams. The Latest stable release of LibSBML is 4.0.0. In terms of our software, the following two major functions has been accomplished based on LibSBML.

1.ReadSBMLFile

The class ReadSBMLFile is used to extract all useful data from a SBML file and send them to the class “val_func”. Since each class represents one term of the the expression. all the terms will be push into a vector. In another word, another container has been created used to place a list of "val_func", of course you can realize that Nth list of "val_func" accommodates all the informations related to Nth species in this Biological system. Finally, all the containers will be package orderly and send to the Particle Swarm Optimization Algorithm (PSO) part or the Global Sensitivity Analysis (GSA) part for the next step. Here are the components of class “val_func”.

class val_func
{
public:
	val_func();
	~val_func();
	int type;                                             //the type of the kineticlaw
	int spec_num;                                         //number of species
	int para_num;                                         //number of parameters
	vector<int> spec;                                     //serial number of the species of the reaction
	vector <double> para;                                 //initial value of the parameters
	vector <string> para_name;                            //IDs/names of the parameters
	vector <string> var_name;                             //IDs/names of the species
	map<int,double> min_data;                             //N/A
	map<int , double> max_data;                           //N/A
	const ASTNode * head;                                 //ASTNode tree of the formula
	double value( const vector<double>& s);               //N/A
};

P.S: the type of the kineticlaw(the list of the readable function type has been stored in the cadidate_function.dat). Due to the ASTNode(a simple kind of data structure) used to store mathematical expressions in SBML(most of them is algebraic expression), it is hard to judge the type mentioned in the file. Usually we give a number 15 to this variable, which implies the expression will be execute by route “user define”.


2.WriteSBMLFile

The class WriteSBMLFile is used to output a SBML file base on the species and parameters selected from the database part.

In this part, the class WriteSBMLFile extract data from the two following file: “subs.dat”; ”dbt.dat”.