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Suggested priorities for reimplementing GENESIS 2 objects and commands in MOOSE/GENESIS 3. Part 1: non-graphical objects Already implemented in MOOSE: Ca_concen compartment concchan enz
nernst neutral reac spikegen
synchan table Mg_block symcompartment pool (same as MOOSE Molecule) reaction enzyme tabchannel == HHChannel tabgate and vdep_channel are implemented by automatic conversion to tabchannels, but there are some aspects that don't convert. ksolve: The kinetics solver: Implemented with 9 numerical methods, but this needs the GNU Scientific Library to be installed. hsolve: Hines solver. Implemented with calcium handling, still needs Nernst. gsolve: the Gillespie solver for stochastic kinetic calculations
High Priority Solvers: Smoldyn solver: Needs updating because both MOOSE and Smoldyn are on more recent versions.
asc_file
closely related objects that aren't high priority, but should be implmenented at the same time as asc_file:
par_asc_file res_asc_file leakage randomspike voltage clamp circuitry: PID RC diffamp
other commonly used device objects: efield pulsegen
Medium Priority script_out tab2Dchannel table2D facsynchan hebbsynchan Other device objects:
autocorr calculator crosscorr event_tofile freq_monitor funcgen
interspike peristim spikehistory timetable File I/O objects - need to redo in context of NETCDF replacement:
disk_in disk_out par_disk_out
Low Priority (Note that this does not necessarily mean "unimportant" or "unlikely to be implemented". But, implementation will probably wait until someone needs them enough to volunteer to implement them, or other higher priority items are done first.) Leech library objects: SynE_object SynG_object SynS_object Kpores Napores (These are specialized markov channels that should be reimplemented in a more efficient and general manner.) izcell rarely used device objects:
playback sigmoid Misc olflib objects:
ddsyn receptor receptor2
hh_channel (should be considered obsolete, but is widely used. Implement as a derived class of tabchannel) vdep_gate [tabgate and vdep_channel are implemented by automatic conversion to tabchannels, but there are some aspects that don't convert.] (Widely used, although can generally be replaced with tabchannel or tab2Dchannel.) NOTE: The concen and param libraries are not really low priority, but will take a lot of work. Unless someone volunteers to implement these, they will have to wait until the other pieces of GENESIS 3 are in place. Concen library objects
concpool dif2buffer difbuffer fura2 ghk difshell fixbuffer
hillpump mmpump tabcurrent taupump
Parameter search objects
paramtableBF paramtableCG paramtableGA paramtableSA paramtableSS
(paramtableSA is the most commonly used)
Not to be implemented oldconn library:
axon axonlink channelA channelB
channelC channelC2 channelC3 defsynapse
random spike synapse synapseA synapseB
undocumented buffer objects and other obsolete or unused objects:
expthresh graded linear passive_buffer periodic print_out
manuelconduct site
synchan2 (unused alias for synchan) unit (An isolated compartment that receives INJECT messages) Objects related to NETCDF - replace with another way of implementing platform-independent binary files:
diskio metadata variable
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