Writing an AdvanceSyn Model Specification (Type 1)

AdvanceSyn Model (ASM) Specification is based on INI file, which is commonly used for software configuration.

In the simplest sense, a ASM file is a set of key-value pairs in the format of "key : value". For example, ip_address : 100.0.0.1 means that the IP address (ip_address) is set to 100.0.0.1. For organization purposes, key-value pairs can be grouped into sections. In this case, each key within a section must be unique.

Six sections are defined in ASM (Type 1):

1. Specification: Defining the ASM version.
2. Identifiers: Providing metadata about the model.
3. Objects: Defining the objects / entities in the model.
4. Initials: Defining the initial values of each object / entity.
5. Variables: Defining changeable variables used in the model.
6. Reactions: Defining the reactions / flows between each object / entity in the model.

Example Reaction

As an example, we will define a chemical reaction A + B = P + Q where the rate term can be defined as bAB. This means that the rate where substrates A and B forms products P and Q is bAB/second - b(concentration of A)(concentration of B).

Written in ordinary differential equations (ODEs),

• dA/dt = -bAB
• dB/dt = -bAB
• dP/dt = bAB
• dQ/dt = bAB

In another words, coefficient b is a rate variable.

Specification Section

Identifiers Section

Objects Section

Initials Section

Variables Section

Reactions Section