PharmML
PharmML - Pharmacometrics Markup Language - is a new standard for encoding of models, associated tasks and their annotation as used in pharmacometrics.
It was developed by DDMoRe consortium.
The current version supports non-linear mixed effect models as used in analysis of continuous longitudinal population PK/PD data with:
- A structural model defined as a system of ordinary differential equation (ODE) and/or algebraic equations.
- A flexible parameter model allowing for implementation of virtually any parameter type used in the majority of models.
- Discrete or continuous covariates.
- A nested hierarchical variability model capable of expressing very complex random error structures.
- An observation model with flexible residual error model supporting untransformed or transformed data.
- A novel trial design model allowing for
- definition of many common design and drug administration types
- encoding of experimental data needed for typical simulation or estimation tasks, such as dosing, observations and covariates.
- Typical modelling steps such as estimation or simulation.
libPharmML
There is special Java library libPharmML that provides a convenient way to read and write PharmML. It also provides basic schema based validation.
The project is hosted on SourceForge:
The API should hopefully be intuitive. It can read a PharmML document,
write a DOM to a PharmML document, create a stub DOM and validate a DOM.
The PharmML DOM is generated using JAXB (see https://jaxb.java.net/) to convert the XML Schema into a set of Java classes. Each schema maps to a separate java package.
Currently the library only validates against the XML Schema definition. Addition rules such as type checking, checking for duplicate symbols or dangling symbol references are not yet checked.
