Characteristics of mathematical modeling languages that facilitate model reuse in systems biology: a software engineering perspective

摘要

Each of the three code snippets contains the same information defining a variable y, which depends on another preexisting variable x. Antimony mainly focuses on how humans would write equations in text form, but requires a specialized parser. CellML Text—an intermediary editing language used by the tool OpenCOR69—adds some syntax that is easy to parse by a machine (due to using braces that do not conflict with other symbols in the code), but is not an intuitive representation of unit information for a human unfamiliar with the language. SBML focuses more on machine-readability, since XML can be parsed by the standard libraries of most modern programming languages, ensuring minimal barriers for tool support. However, while the SBML code is still readable and editable in a text editor, it takes some effort and familiarity with the language to decipher the meaning from the symbols.