Index

_ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z

_

A

ab() (KSTrans method)
abs()
- built-in function
abs() (Vector method)
accept_action() (List method)
- (SectionBrowser method)
acor() (CVode method)
action() (MechanismStandard method)
- (MechanismType method)
- (Shape method)
active() (CVode method)
- (NetCon method)
Adapting MOD files for C++ with |neuron_with_cpp_mechanisms|
- guide
add() (Matrix method)
- (Vector method)
add_hhstate() (KSChan method)
add_ksstate() (KSChan method)
add_transition() (KSChan method)
addexpr() (Graph method)
addobject() (Graph method)
addrand() (Vector method)
addvar() (Graph method)
adjust() (VBox method)
adjuster() (VBox method)
alias() (StringFunctions method)
alias_list() (StringFunctions method)
align() (Graph method)
allgather() (ParallelContext method)
allobjects()
- built-in function

allobjectvars()
- built-in function
allprint() (FInitializeHandler method)
allreduce() (ParallelContext method)
allroots() (SectionList method)
alltoall() (ParallelContext method)
AlphaSynapse (built-in class)
amp() (Electrode method)
amp0() (Electrode method)
aopen() (File method)
APCount (built-in class)
append() (List method)
- (SectionList method)
- (Vector method)
apply() (Vector method)
area()
- built-in function
as_numpy() (Vector method)
assign() (Pointer method)
at() (Vector method)
atan()
- built-in function
atan2()
- built-in function
atol() (CVode method)
atolscale() (CVode method)
attr_praxis()
- built-in function
axis()
- built-in function

B

b_rate (rxd.Reaction property), [1]
barrier() (ParallelContext method)
batch_run()
- built-in function
batch_save()
- built-in function
BBSaveState (built-in class)
bcopy() (Matrix method)
begin() (Graph method)
- (RangeVarPlot method)
beginline() (Graph method)
- (PlotShape method)
- (Shape method)
binomial() (Random method)
Biology Modeling FAQ
- guide
boolean_dialog()
- built-in function
broadcast() (ParallelContext method)
browser() (List method)
brush() (Graph method)
buffer_size() (Vector method)
built-in function

C

concentration (rxd.node.Node property)
- (rxd.nodelist.NodeList property)
concentrations() (rxd.Species method)
condition_order() (CVode method)
connect (keyword)
connect() (Section method)
contains() (Vector method)
context() (ParallelContext method)
continue_dialog()
- built-in function
convlv() (Vector method)
copy() (Vector method)
coredump_on_error()
- built-in function
correl() (Vector method)
cos()
- built-in function
count() (List method)
- (MechanismStandard method)
- (MechanismType method)
- (PWManager method)
cpt() (Glyph method)
create (keyword)
create_cell() (ParallelNetManager method)
create_nrnmech
- command
Creating a stylized ("stick-figure") model cell
- guide
crosshair_action() (Graph method)
current_method() (CVode method)
curve() (Glyph method)
CVode (built-in class)

D

diff (rxd.nodelist.NodeList property)
Differences between idraw and CorelDraw
- guide
differentiate2c() (in module neuron.nmodl.ode)
dir() (File method)
disconnect()
- built-in function
disconnect() (Section method)
discretize_derivative() (in module neuron.nmodl.ode)
discunif() (Random method)
dismiss_action() (VBox method)
distance()
- built-in function
div() (Vector method)
doEvents()
- built-in function
done() (ParallelContext method)
doNotify()
- built-in function
dot() (Vector method)
dstates() (CVode method)
dt (built-in variable)
dt() (ParallelContext method)
dur() (Electrode method)
dur0() (Electrode method)

E

event_time() (ParallelContext method)
Example of a Hybrid Network
- guide
Example of a Simple Network
- guide
exec_menu() (Graph method)
- (PlotShape method)
- (Shape method)
execerror()
- built-in function
execute()
- built-in function
execute() (neuron.hoc method)
execute1()
- built-in function
exists() (SectionRef method)
exp()
- built-in function
exp() (Matrix method)
Exp2Syn (built-in class)
ExpSyn (built-in class)
extra_scatter_gather() (CVode method)
extra_scatter_gather_remove() (CVode method)
extracellular (mechanism)

F

f() (CVode method)
- (KSTrans method)
f_rate (rxd.Reaction property), [1]
fadvance()
- built-in function
False
- guide, [1], [2], [3], [4]
family() (Graph method)
fastflush() (Graph method)
- (PlotShape method)
fastpas (mechanism)
fclamp()
- built-in function
fclampi()
- built-in function
fclampv()
- built-in function
fcurrent()
- built-in function
feround() (GUIMath method)
fft() (Vector method)
FIinitializeHandler
- guide
File (built-in class)
file() (MechanismType method)
fill() (Glyph method)
- (Vector method)
filter() (Vector method)
finite_difference_step_variable() (in module neuron.nmodl.ode)
finitialize()
- built-in function
FInitializeHandler (built-in class)
fit() (Vector method)
fit_praxis()
- built-in function
fixed() (Graph method)
fixed_step() (CVode method)
Fixing funny axes
- guide

flip_to() (Deck method)
float_epsilon (built-in variable)
floor() (Vector method)
flush() (File method)
- (Graph method)
- (PlotShape method)
- (Shape method)
fmatrix()
- built-in function
forall (keyword)
forsec (keyword)
forwards_euler2c() (in module neuron.nmodl.ode)
fprint()
- built-in function
fprint() (Matrix method)
frac() (KSState method)
fread() (SaveState method)
- (Vector method)
frecord_init()
- built-in function
free_event_queues() (CVode method)
Frequently asked questions (FAQ)
- guide
from_double() (Vector method)
from_python() (Vector method)
from_vector() (Matrix method)
- (RangeVarPlot method)
fscan()
- built-in function
fstim()
- built-in function
fstimi()
- built-in function
ftype() (KSTrans method)
full_request() (VBox method)
fwrite() (SaveState method)
- (Vector method)

G

Guides
- guide
GUIMath (built-in class)

H

has_loc() (pnt method)
has_net_event() (MechanismType method)
has_parent() (SectionRef method)
has_trueparent() (SectionRef method)
HBox (built-in class)
head() (StringFunctions method)
Here's a couple of graphs that may suggest why enabling inhibition in this model prevented all spikes after the first one. In these graphs M_Cell[0].soma.v(0.5) and R_Cell[0].soma.v(0.5) are Vm at the soma of M1 and R2, respectively. First the response when inhibiton was OFF
- guide
hh (mechanism)
hide() (PWManager method)
hinton() (PlotShape method)
hist() (Vector method)
histogram() (Vector method)
hname() (Section method)
Hoc
- guide
HOC built-in function
- pt3dconst()

hoc_ac() (neuron.hoc method)
hoc_pointer_()
- built-in function
hoc_stdout()
- built-in function
Holding() (Electrode method)
How about ENa-Vm, i.e. the driving force for INa? Maybe normalize this with respect to the driving force at t = 0?
- guide
How to delete v(.5) from the graph
- guide
How to get started with NEURON
- guide, [1]
How to move the labels
- guide
How to translate the view
- guide
hypergeo() (Random method)

I

integ_time() (ParallelContext method)
integral() (Vector method)
integrate2c() (in module neuron.nmodl.ode)
intercept() (Deck method)
- (VBox method)
internal_type() (MechanismType method)
interpolate() (Vector method)
IntFire1 (built-in class)
IntFire2 (built-in class)
IntFire4 (built-in class)
Introduction to Network Construction
- guide
inverse() (Matrix method)
ion() (KSChan method)
ion_charge()
- built-in function
ion_register()
- built-in function
ion_style()
- built-in function
is_array() (MechanismStandard method)
is_artificial() (MechanismType method)
- (StringFunctions method)
is_cas() (SectionRef method)
is_mapped() (PWManager method)
is_name() (StringFunctions method)
is_netcon_target() (MechanismType method)
is_point_process() (StringFunctions method)
ismapped() (VBox method)
ismembrane()
- built-in function
isopen() (File method)
issection()
- built-in function
iv_type() (KSChan method)
ivoc_style()
- built-in function

J

jacobian() (CVode method)

K

L

List (built-in class)
list() (RangeVarPlot method)
list_examples() (in module neuron.nmodl.dsl)
load_example() (in module neuron.nmodl.dsl)
load_file()
- built-in function
load_func()
- built-in function
load_proc()
- built-in function
load_template()
- built-in function
loc() (Impedance method)
- (pnt method)
Location() (Electrode method)
log()
- built-in function
log() (Vector method)
log10()
- built-in function
log10() (Vector method)
lognormal() (Random method)
look() (ParallelContext method)
look_take() (ParallelContext method)

M

m() (Glyph method)
machine_name()
- built-in function
mag() (Vector method)
make() (MechanismType method)
make_mechanism()
- built-in function
make_pointprocess()
- built-in function
make_symbol() (in module neuron.nmodl.ode)
makeFamily
manager() (PWManager method)
Managing a model cell with complex anatomy
- guide
map() (Deck method)
- (PWManager method)
- (TextEditor method)
- (VBox method)
mark() (Graph method)
- (PlotShape method)
- (Shape method)
- (Vector method)
Matrix (built-in class)
Matrix.x (built-in variable)
max() (Vector method)
max_histogram() (ParallelContext method)
max_ind() (Vector method)
maxorder() (CVode method)
maxstep() (CVode method)
mcell_ran4()
- built-in function
mcell_ran4_init()
- built-in function
MCellRan4() (Random method)
mean() (Vector method)
meansqerr() (Vector method)
mech_time() (ParallelContext method)

N

n3d()
- built-in function
name (rxd.Region property)
- (rxd.Species property)
name() (KSChan method)
- (KSState method)
- (MechanismStandard method)
- (PWManager method)
- (Section method)
name_declared()
- built-in function
nc_append() (ParallelNetManager method)
nchild() (SectionRef method)
ncol() (Matrix method)
nearest() (PlotShape method)
- (Shape method)
needs_finite_differences() (in module neuron.nmodl.ode)
negexp() (Random method)
nernst()
- built-in function
NetCon (built-in class)
NetCon.delay (built-in variable)
NetCon.threshold (built-in variable)
NetCon.weight (built-in variable)
NetCon.x (built-in variable)
netconlist() (CVode method)
NetStim (built-in class)
Network Builder tutorials
- guide
neuron._NEURON_INTERFACE (built-in class)
neuron.n.Section (built-in class)
neuron.nmodl
- module
neuron.nmodl.ast
- module
neuron.nmodl.dsl
- module
neuron.nmodl.ode
- module
neuron.nmodl.symtab
- module
neuron.nmodl.visitor
- module
neuronhome()
- built-in function
ngate() (KSChan method)
nhost() (ParallelContext method)
nhost_bbs() (ParallelContext method)
nhost_world() (ParallelContext method)
nligand() (KSChan method)
NMODL's built-in functions
- guide
NmodlDriver (class in neuron.nmodl)
NMODLRandom (built-in class)
nodes (rxd.Species property)
normal() (Random method)
nrn_allsec (C function)
nrn_cas (C function)
nrn_class_name (C function)
nrn_digest()
- built-in function
nrn_distance (C function)
nrn_double_pop (C function)
nrn_double_ptr_pop (C function)
nrn_double_ptr_push (C function)
nrn_double_push (C function)
nrn_feenableexcept()
- built-in function
nrn_function_call (C function)
nrn_function_call_nothrow (C function)
nrn_gargstr (C function)
nrn_get_plotshape_high (C function)
nrn_get_plotshape_interface (C function)
nrn_get_plotshape_low (C function)
nrn_get_plotshape_section_list (C function)
nrn_get_plotshape_varname (C function)
nrn_getarg (C function)
nrn_global_symbol_table (C function)
nrn_hoc_call (C function)
nrn_hoc_ret (C function)
nrn_ifarg (C function)
nrn_init (C function)
nrn_int_pop (C function)
nrn_int_push (C function)
nrn_is_double_arg (C function)
nrn_is_object_arg (C function)
nrn_is_pdouble_arg (C function)
nrn_is_str_arg (C function)

O

P

prelist() (NetCon method)
preloc() (NetCon method)
prepend() (List method)
preseg() (NetCon method)
print_event_queue() (CVode method)
print_session()
- built-in function
printf()
- built-in function
printf() (File method)
- (Matrix method)
- (Vector method)
printfile() (Graph method)
- (PlotShape method)
- (PWManager method)
- (Shape method)
printnames() (SectionList method)
priority() (VBox method)
prmat()
- built-in function
prstat() (ParallelNetManager method)
prstim()
- built-in function
prun() (ParallelNetManager method)
psection()
- built-in function
pset() (PtrVector method)
psolve() (ParallelContext method)
- (ParallelNetManager method)
psth() (Vector method)
pt3dadd()
- built-in function
pt3dchange()
- built-in function
pt3dclear()
- built-in function
pt3dconst()
- built-in function
- HOC built-in function
pt3dinsert()
- built-in function
pt3dremove()
- built-in function
pt3dstyle()
- built-in function
ptr_update_callback() (PtrVector method)
PtrVector (built-in class)
push_section()
- built-in function
push_selected() (PlotShape method)
- (Shape method)
pval_praxis()
- built-in function
pwman_place()
- built-in function
PWManager (built-in class)
py_allgather() (ParallelContext method)
py_alltoall() (ParallelContext method)
py_broadcast() (ParallelContext method)
py_gather() (ParallelContext method)
py_scatter() (ParallelContext method)
pyret() (ParallelContext method)

Q

queue_mode() (CVode method)

quit()
- built-in function

R

rxd.Parameter (built-in class)
rxd.Rate (built-in class)
rxd.re_init()
- built-in function
rxd.Reaction (built-in class)
rxd.Region (built-in class)
rxd.RxDException (built-in class)
rxd.ScalableBorder (built-in class)
rxd.set_solve_type()
- built-in function
rxd.Shell (built-in class)
rxd.Species (built-in class)
rxd.State (built-in class)
rxdmath.acos()
- built-in function
rxdmath.acosh()
- built-in function
rxdmath.asin()
- built-in function
rxdmath.asinh()
- built-in function
rxdmath.atan()
- built-in function
rxdmath.atan2()
- built-in function
rxdmath.ceil()
- built-in function
rxdmath.copysign()
- built-in function
rxdmath.cos()
- built-in function
rxdmath.cosh()
- built-in function
rxdmath.degrees()
- built-in function
rxdmath.erf()
- built-in function
rxdmath.erfc()
- built-in function
rxdmath.exp()
- built-in function
rxdmath.expm1()
- built-in function
rxdmath.fabs()
- built-in function
rxdmath.factorial()
- built-in function
rxdmath.floor()
- built-in function
rxdmath.fmod()
- built-in function
rxdmath.gamma()
- built-in function
rxdmath.lgamma()
- built-in function
rxdmath.log()
- built-in function
rxdmath.log10()
- built-in function
rxdmath.log1p()
- built-in function
rxdmath.pow()
- built-in function
rxdmath.radians()
- built-in function
rxdmath.sin()
- built-in function
rxdmath.sinh()
- built-in function
rxdmath.sqrt()
- built-in function
rxdmath.tan()
- built-in function
rxdmath.tanh()
- built-in function
rxdmath.trunc()
- built-in function
rxdmath.vtrap()
- built-in function

S

size() (Graph method)
- (PlotShape method)
- (PtrVector method)
- (SectionList method)
- (Shape method)
- (VBox method)
- (Vector method)
smhist() (Vector method)
snap() (PWManager method)
solv() (Matrix method)
solve()
- built-in function
solve() (CVode method)
solve_lin_system() (in module neuron.nmodl.ode)
solve_non_lin_system() (in module neuron.nmodl.ode)
sort() (Vector method)
sortindex() (Vector method)
source_var() (ParallelContext method)
spctrm() (Vector method)
species (rxd.node.Node property)
- (rxd.nodelist.NodeList property)
Specifying parameterized variation of biophysical properties
- guide
spgetrowval() (Matrix method)
spike_compress() (ParallelContext method)
spike_record() (ParallelContext method)
- (ParallelNetManager method)
spike_stat() (CVode method)
spike_statistics() (ParallelContext method)
spikebin() (Vector method)
spine3d()
- built-in function
splitcell() (ParallelContext method)
- (ParallelNetManager method)
sprint()
- built-in function
sprowlen() (Matrix method)
sqrt()
- built-in function
sqrt() (Vector method)
src() (KSTrans method)
srcgid() (NetCon method)
sred()
- built-in function
sscanf()
- built-in function
startsw()
- built-in function
state() (KSChan method)
- (StateTransitionEvent method)
state_magnitudes() (CVode method)
statename() (CVode method)
states (rxd.Species property)
states() (CVode method)
StateTransitionEvent (built-in class)
statistics() (CVode method)
stderr() (Vector method)
stdev() (Vector method)
Step 1. Define the types of cells
- guide, [1]
Step 1. Set up a SubsetDomainIterator
- guide
Step 2. Create each cell in the network
- guide, [1]
Step 2. Specify the model parameter(s) to be varied
- guide
Step 3. Connect the cells
- guide, [1], [2], [3]
Step 3. Specify and verify the functions that govern the parameters
- guide
Step 4. Use the model specification
- guide
step_time() (ParallelContext method)
step_wait() (ParallelContext method)
stiff() (CVode method)
Still working on the M class . . .
- guide
stop_praxis()
- built-in function
stoprun (built-in variable)
stopsw()
- built-in function
store_events() (CVode method)
strcmp()
- built-in function
string_dialog()
- built-in function
StringFunctions (built-in class)
structure_change_count() (CVode method)
sub() (Vector method)
submit() (ParallelContext method)
substr() (StringFunctions method)
subtree() (Section method)
- (SectionList method)
subworlds() (ParallelContext method)
sum() (Vector method)
sumgauss() (Vector method)
sumsq() (Vector method)
surface_area (rxd.node.Node1D property)
- (rxd.node.Node3D property)
- (rxd.nodelist.NodeList property)
svd() (Matrix method)
symbols()
- built-in function
SymChooser (built-in class)
symmeig() (Matrix method)
syn() (NetCon method)
synlist() (NetCon method)
system()
- built-in function

T

t (built-in variable)
t() (ParallelContext method)
tail() (StringFunctions method)
take() (ParallelContext method)
tanh()
- built-in function
tanh() (Vector method)
target() (KSTrans method)
target_var() (ParallelContext method)
tell() (File method)
Testlevel() (Electrode method)
text() (SymChooser method)
- (TextEditor method)
TextEditor (built-in class)
The appearance of NEURON's graphical windows is controlled by definitions in the file ``$(NEURONHOME)/lib/nrn.defaults`` (under MSWindows it's ``c:\nrnxx\lib\nrn.def`` where ``xx`` is the version number). This is a plain ASCII file that you can edit with a text editor.
- guide
The Print & File Manager
- guide
this_node()
- built-in function
this_section()
- built-in function
thread_busywait() (ParallelContext method)
thread_ctime() (ParallelContext method)
thread_how_many_proc() (ParallelContext method)
thread_stat() (ParallelContext method)
Threads() (ParallelContext method)

threshold() (ParallelContext method)
time() (ParallelContext method)
timeout() (ParallelContext method)
to_json() (in module neuron.nmodl)
to_nmodl() (in module neuron.nmodl)
to_python() (Vector method)
to_vector() (Matrix method)
- (RangeVarPlot method)
topology()
- built-in function
trans() (KSChan method)
transfer() (Impedance method)
transfer_phase() (Impedance method)
transform_expression() (in module neuron.nmodl.ode)
transform_matrix_elements() (in module neuron.nmodl.ode)
transition() (StateTransitionEvent method)
transpose() (Matrix method)
trigavg() (Vector method)
Tutorial 1 : Fitting a function to data
- guide
Tutorial 1: Making Networks of Artificial Neurons
- guide
Tutorial 2 : Fitting a model to data
- guide
Tutorial 2 : Making Hybrid Nets
- guide
type() (KSTrans method)

U

uniform() (NMODLRandom method)
- (Random method)
unique() (SectionList method)
UNITS Tutorial
- guide
Units used in NEURON
- guide
units()
- built-in function
unix_mac_pc()
- built-in function
unlink() (File method)
unmap() (Deck method)
unpack() (ParallelContext method)
upkpyobj() (ParallelContext method)
upkscalar() (ParallelContext method)
upkstr() (ParallelContext method)
upkvec() (ParallelContext method)
use_daspk() (CVode method)

use_exp_pow_precision()
- built-in function
use_fast_imem() (CVode method)
use_local_dt() (CVode method)
use_long_double() (CVode method)
use_mcell_ran4()
- built-in function
use_mxb() (CVode method)
userid() (ParallelContext method)
Using "Plot what?" to Specify a Variable to be plotted
- guide
Using NEURON on the Mac
- guide
Using NEURON's Optimization Tools
- guide
Using Session Files for Saving and Retrieving Windows
- guide, [1]
Using the Cell Builder GUI
- guide
Using the d_lambda Rule
- guide
Using the Import3D GUI
- guide

V

W

WinExec()
- built-in function
wopen()
- built-in function
wopen() (File method)
Working with PostScript and idraw figures
- guide
working() (ParallelContext method)
Wrapping up the M class and defining the R class.
- guide
writehoc() (SaveState method)

X

x (rxd.node.Node1D property)
- (rxd.nodelist.NodeList property)
x3d (rxd.node.Node property)
x3d()
- built-in function
xaxis() (Graph method)
xbutton()
- built-in function
xcheckbox()
- built-in function
xexpr() (Graph method)
xfixedvalue()
- built-in function
xlabel()
- built-in function
xmenu()
- built-in function
xopen()
- built-in function

xopen() (File method)
xpanel()
- built-in function
xpvalue()
- built-in function
xradiobutton()
- built-in function
xred()
- built-in function
xslider()
- built-in function
xstatebutton()
- built-in function
xvalue()
- built-in function
xvarlabel()
- built-in function

Y

y3d (rxd.node.Node property)
y3d()
- built-in function

Z

z3d (rxd.node.Node property)
z3d()
- built-in function

zero() (Matrix method)