LEMS Simulation files

For many users, the most obvious place that LEMS is used is in the LEMS Simulation file (usually LEMS_*.xml).

Specification of format

See here for definition of the main elements used in the file, including Display, OutputFile, etc.

Quantities and paths

Specifying the quantities to save/display in a LEMS Simulation file is an important and sometimes confusing process. There is a dedicated page on quantities and paths in LEMS and NeuroML2.

What about SED-ML?

The Simulation Experiment Description Markup Language (SED-ML) is used by a number of other initiatives such as SBML for specifying simulation setup, execution and basic analysis.

We chose to have a LEMS specific format for specifying simulations in NeuroML2 as opposed to natively supporting SED-ML, mainly because of the tight link to the LEMS language and jLEMS package, i.e. all of the NeuroML2 elements and elements in a LEMS simulation file have underlying definitions in the LEMS language. However it is possible to convert the LEMS simulation to the equivalent in SED-ML.

Exporting LEMS simulation descriptions to SED-ML

# Using jnml
jnml <LEMS simulation file> -sedml

# Using pynml
pynml <LEMS simulation file> -sedml