[Moose-g3-devel] GENESIS 3 object and command priorities (Part 1)

[Dave B. <db...@do...>]

Dear GENESIS Developers,

At the WAM-BAMM*06 GENESIS developers meeting, we decided to assign
priorities to the GENESIS 2 objects and commands that, for backwards
compatibility, will need to be reimplemented in MOOSE/GENESIS 3.  (You can
read the full summary of the discussions on the GENESIS Developers web
site.)  Of course, there will also be new object types (classes) and
commands in GENESIS 3, in order to take advantage of new capabilities in
GENESIS 3.

As a first step, I am circulating my first pass at assigning priorities.
I urge you see if you use any objects or commands that I have listed
as "Low priority" or "Not to be implemented".  There are also a number
in the "Not sure" category.  These are ones that might not exist in
MOOSE because of differences in the way that solvers, scheduling,
messaging, and OS-independence are handled in MOOSE.  I would particularly
like to hear your commments and suggestions on these.  Of course, the
GENESIS Reference Manual or "help" within GENESIS can remind you what
some of these are used for.

(To be sure that everyone gets this, I am sending it to both the
Moo...@li... mailing list and the genesis-dev
mailing list. For most of you, this means that you will get it twice.)

After arriving af some consensus on which ones to reimplement first, we
can assign manpower to do the work, and solicit GENESIS users with
programming skills to reimplement the many objects and commands that
are very loosely coupled to the core simulator code.  The current
version of MOOSE has fairly good documentation on writing new  MOOSE
objects in C++.  You can download it from the MOOSE-G3 Sourceforge
Development site at http://sourceforge.net/projects/moose-g3

I will do this in four parts, tackling the non-graphical objects
and  commands first.

Dave Beeman

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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

pool  (same as MOOSE Molecule?)
tabchannel  == HHChannel

What is MOOSE HHgate?


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High Priority

asc_file
closely elated objects that aren't high priority, but should be
implemnented at the same time as asc_file: par_asc_file    res_asc_file

Mg_block    symcompartment    leakage    randomspike         

voltage clamp circuitry: PID   RC    diffamp
other commonly used device objects: efield    pulsegen

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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

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Low Priority   (Note that this does not necessarily mean "unimportant"
or "unlikely to be implemented".   But, implemenation 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 special case of tabchannel, or force users to change to tabchannels?)

tabgate vdep_channel vdep_gate (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)

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"Not sure" - these may be implemented in MOOSE under different names,
implemented implicitly without need for a class, or not needed, due
to differences between MOOSE and GENESIS 2 -- Comments are requested!

gsolve/hsolve - will these be handled transparently in MOOSE?

text (Used only in kkit - breaks the separation between Xodus and
non-Xodus objects)

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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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