Adding Built-in Catalogues to Arbor

There are two ways new mechanisms catalogues can be added to Arbor, statically or dynamically. If you have a set of mechanisms to use with Arbor, you are in all likelihood interested in the former.

Warning

If you are coming from NEURON and looking for the equivalent of nrnivmodl, please read on here.

Following the below instructions is for developers rather than end-users.

This requires a copy of the Arbor source tree and the compiler toolchain used to build Arbor in addition to the installed library. Following these steps will produce a catalogue of the same level of integration as the built-in catalogues (default, bbp, and allen). The required steps are as follows

1. Go to the Arbor source tree.

2. Create a new directory under mechanisms.

   1. Add any .mod files you wish to integrate.

   2. Add any raw C++ files to be included in the catalogue.

4. Edit mechanisms/CMakeLists.txt to add a definition like this (example from default catalogue)

   make_catalogue(
     NAME default                                                   # Name of your catalogue
     SOURCES "${CMAKE_CURRENT_SOURCE_DIR}/default"                  # Directory name (added above)
     OUTPUT "CAT_DEFAULT_SOURCES"                                   # Variable name to store C++ files into (see below)
     MOD exp2syn expsyn expsyn_stdp hh kamt kdrmt nax nernst pas    # Space separated list of NMODL mechanism names
     CXX                                                            # Space separated list of raw C++ mechanism names
     PREFIX "${PROJECT_SOURCE_DIR}/mechanisms"                      # where does 'generate_catalogue' live, do not change
     STANDALONE FALSE                                               # build as shared object, must be OFF
     VERBOSE OFF)                                                   # Print debug info at configuration time
   

5. Add your output-name to the arbor_mechanism_sources list.

   set(arbor_mechanism_sources
     ${CAT_BBP_SOURCES}
     ${CAT_ALLEN_SOURCES}
     ${CAT_DEFAULT_SOURCES}                                          # from above
     PARENT_SCOPE)
   

6. Add a global_NAME_catalogue function in mechcat.hpp and mechcat.cpp

7. Bind this function in python/mechanisms.cpp.

All steps can be directly adapted from the surrounding code.

Note

If you have special requirements, you can write mechanisms in C/C++ directly against Arbor’s ABI. These need to adhere to the calling convention of the ABI. See here for more.