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¶
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