Leech heart interneuron network model (Hill et al 2001, 2002)

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Accession:19698
We have created a computational model of the timing network that paces the heartbeat of the medicinal leech, Hirudo medicinalis. In the intact nerve cord, segmental oscillators are mutually entrained to the same cycle period. Although experiments have shown that the segmental oscillators are coupled by inhibitory coordinating interneurons, the underlying mechanisms of intersegmental coordination have not yet been elucidated. To help understand this coordination, we have created a simple computational model with two variants: symmetric and asymmetric. See references for more details. Biologically realistic network models with two, six, and eight cells and a tutorial are available at the links to Calabrese's web site below.
References:
1 . Hill AA, Masino MA, Calabrese RL (2002) Model of intersegmental coordination in the leech heartbeat neuronal network. J Neurophysiol 87:1586-602 [PubMed]
2 . Hill AA, Lu J, Masino MA, Olsen OH, Calabrese RL (2001) A model of a segmental oscillator in the leech heartbeat neuronal network. J Comput Neurosci 10:281-302 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism: Leech;
Cell Type(s): Leech heart interneuron;
Channel(s): I Na,p; I Na,t; I K; I h; I Calcium; I Potassium;
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: GENESIS;
Model Concept(s): Activity Patterns; Bursting; Oscillations; Spatio-temporal Activity Patterns; Tutorial/Teaching; Action Potentials; Invertebrate;
Implementer(s): Hill, Andrew A [aavhill at yahoo.com];
Search NeuronDB for information about:  I Na,p; I Na,t; I K; I h; I Calcium; I Potassium;
# $Id: Usermake,v 1.12 1997/07/25 22:22:13 dhb Exp $
#
# Usermake - a Makefile template for compiling a new version of GENESIS
#
# GENESIS/XODUS : network simulator - top level user makefile
# this makefile compiles a version of the simulator containing
# additional user-defined libraries. See the document NewGenesis.doc
# in the genesis Doc directory (usually /home/genesis/Doc) for details
# on adding a new library.
#
#
# NOTE: This file should be copied into the directory from which you are
# compiling the new version of GENESIS and given the name 'Makefile'.
# Before doing a "make", you must edit the file as defined below:
#
#
#
# 1) set MACHINE= one of {sun3, sun4, Solaris, i386, mips, irix, hpux, Linux, FreeBSD}
# 2) set OS= one of {BSD,SYSV}
# 3) set XVERSION= one of {X11R4,X11R5,X11R6}
# 3) for mips or irix 4.x add '-G 6' (excluding quotes) to CFLAGS and LDFLAGS
# 5) check other macros in user configurable section
# 6) type 'make'
#

#
# Define "MACHINE" to be one of:
#
#	sun3			- for Sun 3's
#	sun4			- for Sun 4's and Sparcstations
#	Solaris			- for Sun's running Solaris 2.x
#	i386			- for Sun 386i's
#	MASSCOMP		- for Masscomp's
#	mips			- for decstation 3100's
#	hpux			- for Hewlett Packard HPUX's
#	irix			- for Silicon Graphics IRIX's
#	aix			- for IBM RS/6000's running AIX
#	Linux			- for PC's running Linux
#	FreeBSD			- for PC's running FreeBSD
#
#

MACHINE = 	Linux
OS	=	BSD
XVERSION=	X11R6

# GENINST should refer to the GENESIS 2.0 installation directory.

GENINST =	/usr/local/genesis

# Lex library.  Change to -lfl (or the library file) if using GNU flex.

LEXLIB  =	-lfl

# If you want to use the debug option (which will cost you in both
# speed and memory), use the alternate CFLAGS = -g and LDFLAGS = -g
# Otherwise use "-O" to optimize.  LDFLAGS are the final link flags.
#
# GENESIS is written in non-ANSI C.  If you have an ANSI C compiler
# add the option to compile K&R C to CFLAGS.
#
# Solaris users: cpp is usually in /usr/ccs/lib/cpp

CC	=	cc
CPP	=	/lib/cpp -P
CFLAGS	=	-O
LDFLAGS =

# Location of our X11 libraries

# XLIB 	= 	/usr/lib
XLIB =		/usr/X11/lib

# Name to give your new GENESIS executable.

SIMNAME =	agenesis

#
# the user should place the directories of any user library
# modules in the USERDIR variable
# e.g. USERDIR = newlib1 newlib2
#

USERDIR	= newlib1 newlib2

#
# The user should place the pathnames of any library object modules other
# than the basic system libraries in the USEROBJ variable.  These should be
# the same as those used for the TARGET_OBJ variable in the 'Libmake' file.
# e.g. USEROBJ = newlib1/newlib1.o newlib2/newlib2.o
#

USEROBJ	= newlib1/newconnlib.o newlib2/leechlib.o


#
# Add the library names of each user library to the USERLIB macro.  The
# library name is set in each library's Makefile as the variable name
# LIBRARY_NAME.
#

USERLIB	= newconnlib leech

#
# The user should place any additional system dependent libraries in the
# SYSLIBS variable.  Known system dependent libraries include:
#
# irix
#	SYSLIBS = -lmalloc
#

SYSLIBS =


#
# Optional GENESIS libraries
#

#
# oldconn
#
# These are the GENESIS 1.4 connection facility compatibility libraries.
# Comment the OLDCONN and OLDCONNLIB macros to exclude 1.4 style
# connections.  You must also remove the libraries from the liblist
# file.
#
# NOTE: Several of the simulations in the Scripts
# directory use the oldconn library (e.g. MultiCell, Piriform,
# etc.) and will not run without oldconn.
#

OLDCONN	=	$(SIMLIB)/axonlib.o $(SIMLIB)/synlib.o $(SIMLIB)/perlib.o $(SIMLIB)/simconnlib.o $(SIMLIB)/toolconnlib.o
OLDCONNLIB =	axon synapse personal simconn toolconn

#
# kinetics
#
# This library is for kinetic modeling.  Comment KINETICS and KINETICSLIB
# to exclude the kinetics library.
#
# NOTE: the kkit kinetics modeling kit requires the kinetics library.
#

KINETICS =	$(SIMLIB)/kinlib.o
KINETICSLIB =	kin

#
# diskio
#
# The diskio and related objects from this library provide a disk_in
# disk_out backward compatible interface for netCDF portable binary
# files.  Comment out the DISKIO and DISKIOLIB macros to exclude the
# diskio library.  There are currently no kits or tutorials which
# depend on this library.
#
# NOTE: The netCDF library is known not to compile on Linux a.out
# systems.  Any Linux 1.3 or later (and some 1.2 versions) will work.
#

DISKIO =	$(SIMLIB)/diskiolib.o $(SIMLIB)/libnetcdf.a
DISKIOLIB =	diskio

#
# Xodus
#
# This is the graphics widget and draw library.  It is needed by
# just about everything in the Scripts directory.  If you want to
# run GENESIS in batch mode without graphics, comment out XLIBS,
# XODUS and XODUSLIB to get a non-Xodus genesis.
#

XLIBS   =       -L$(XLIB)  -lXt  -lXmu  -lXext  -lX11
XODUS 	=	$(SIMLIB)/drawlib.o  $(SIMLIB)/widglib.o  $(SIMLIB)/xolib.o  $(SIMLIB)/libDraw.a  $(SIMLIB)/libWidg.a  $(SIMLIB)/libXo.a
XODUSLIB =	xo  draw  widg

# end of optional libraries


###################################################################
# nothing beyond this point should have to be modified by the user
###################################################################

SHELL	=	/bin/sh

SIMLIB 	= 	$(GENINST)/lib
SIMSRC 	= 	$(GENINST)/src

GENESIS = 	$(SIMLIB)/simlib.o \
		$(SIMLIB)/ss.o \
		$(SIMLIB)/shelllib.o \
		$(SIMLIB)/utillib.o \
		$(SIMLIB)/buflib.o \
		$(SIMLIB)/seglib.o \
		$(SIMLIB)/hhlib.o \
		$(SIMLIB)/devlib.o \
		$(SIMLIB)/outlib.o \
		$(SIMLIB)/olflib.o \
		$(SIMLIB)/toollib.o \
		$(SIMLIB)/conclib.o \
		$(SIMLIB)/userlib.o \
                $(SIMLIB)/hineslib.o \
                $(SIMLIB)/spikelib.o \
                $(SIMLIB)/porelib.o \
		$(OLDCONN) \
		$(SIMLIB)/newconnlib.o \
		$(KINETICS) \
		$(DISKIO) \
		loadlib.o


LIBS 	= 	$(XLIBS) $(LEXLIB) -lm $(SYSLIBS)

LIBLIST =	output \
		hh \
		devices \
		buffer \
		segment \
		user \
		$(XODUSLIB) \
		olf \
		tools \
		concen \
		hines \
		spike \
		pore \
		newconn \
		$(DISKIOLIB) \
		$(OLDCONNLIB) \
		$(KINETICSLIB) \
		$(USERLIB)

default: userlibs $(SIMNAME)

userlibs:
	@(for i in $(USERDIR); do echo cd $$i; cd $$i; make CPP="$(CPP)" CC="$(CC)" CFLAGS="$(CFLAGS) -D$(MACHINE) -D$(OS) -D$(XVERSION)" GENINST="$(GENINST)"; cd ..;done)

liblist: Makefile
	echo "# liblist - This file is generated automatically." > liblist
	echo "#           DO NOT EDIT.  Edit Makefile instead." >> liblist
	echo $(LIBLIST) | tr ' ' '\012' >> liblist

loadlib.c: liblist
	$(SIMSRC)/libsh < liblist > loadlib.c

clean:
	@(for i in $(USERDIR); do echo cd $$i; cd $$i; make clean; cd ..;done)
	@rm -f loadlib.[oc]

$(SIMNAME): $(GENESIS) $(XODUS) $(USEROBJ)
	$(CC) $(LDFLAGS) $(GENESIS) $(XODUS) $(USEROBJ) $(LIBS) -o $(SIMNAME)

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