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see r141. The nest2 module has a Connection class, which we could implement for the other modules as well.

Imported from Trac ticket:37

Opened: 2008-01-08 10:40:08
Last modified: 2010-01-26 17:07:24
Component: common
Priority: major
Owner: apdavison
Reporter: apdavison

In PyNN it's called AdaptiveExponentialIF_alpha

but I think we should change the name to

ExponentialIF_cond_alpha_adaptive

or better

ExpIF_cond_alpha_CubaSFA_SubthrAdap

Since neuron types are really:
ExpIF, IF, QuadIF (Izhikevich-type), HH, etc...

and cond_alpha, curr_exp, cond_exp are synapse types

_CubaSFA_SubthrAdap

CubaSFA describes the current based adaptation mechanisms

SubthrAdap decsripes the sub-threshold adaptation

CobaSFA then describes conductance based adaptation mechanisms

as in IF_cond_exp_sfa_rr

should be IF_cond_exp_CobaSFA_CobaSFA

since the sfa and rr mechanisms are the same actually, just different time constants. That model has no sub-threshold adaptation. (Romain reported in his paper it was not strictly necessary to get a good fit to data).

Mechanims such as CobaSFA, CobaSFA, SubthrAdap, CubaSFA strictly speaking should not be part of the neuron model, but should be something like NeuronDynamics which can be added to a Neuron. For NEST, at Neuron creation time, otherwise Raise error. But NEURON, and I recall CSIM, support adding such mechanisms after the fact ...

Synapses too ... cond_exp, curr_alpha ... etc.

ok this got longer than I expected ... so I better post it as a ticket...

So, may I change the name of AdaptiveExponentialIF_alpha to

ExpIF_cond_alpha_CubaSFA_SubthrAdap

and IF_cond_exp_sfa_rr to

IF_cond_exp_CobaSFA1_CobaSFA2

or something?

Imported from Trac ticket:41

Opened: 2008-01-25 16:07:12
Last modified: 2008-02-02 18:46:21
Component: common
Priority: minor
Owner: emuller
Reporter: emuller

Cell parameters can be accessed using the ID class, e.g. cell1.tau_m.
It might also be nice to access variables, such as the membrane potential, as cell1.v, etc.

Imported from Trac ticket:35

Opened: 2007-11-14 15:18:42
Last modified: 2010-11-04 11:05:52
Component: common
Priority: minor
Owner: apdavison
Reporter: apdavison

At !CodeJam, some work was done on unifying the output formats (for spikes, membrane potential) of the nest and neuron2 modules. This needs to be throughly tested, and the same done for the pcsim module.

Imported from Trac ticket:17

Opened: 2007-04-24 13:51:00
Last modified: 2007-05-16 13:54:21
Component: unspecified
Priority: critical
Owner: somebody
Reporter: apdavison

One of the design goals of PyNN is to minimise the number of required dependencies. At the moment, numpy is supposed to be the only dependency. Therefore, use of pytables in the pcsim module should be made optional if possible.

Imported from Trac ticket:16

Opened: 2007-04-24 13:48:34
Last modified: 2007-05-11 14:00:32
Component: pcsim
Priority: major
Owner: somebody
Reporter: apdavison

As a test of the adequacy of the connection/projection API, a test model that contains multi-compartmental neurons and multiple synaptic locations within the cells. An olfactory bulb model would be a particularly challenging example, as the bulb has both axo-dendritic and dendro-dendritic synapses

Imported from Trac ticket:18

Opened: 2007-04-24 13:54:29
Last modified: 2011-01-04 17:02:41
Component: unspecified
Priority: major
Owner: apdavison
Reporter: apdavison

see ticket:22

Imported from Trac ticket:33

Opened: 2007-10-05 16:32:30
Last modified: 2008-02-02 17:07:39
Component: common
Priority: major
Owner: apdavison
Reporter: apdavison

Currently, the positions of neurons in space can only be specified by iterating over the whole population in Python, and using the setPosition() method of the ID class.

We should add a new method or methods to the Population class that allows the positions to be specified from a numpy array or using some algorithm, e.g., 'random positioning within a cylindrical volume', 'hexagonal close packed with separation x', etc.

Might be worth looking at [http://www.neuroconstruct.org/ neuroConstruct] to see how Padraig Gleeson does it.

Imported from Trac ticket:26

Opened: 2007-05-16 19:35:22
Last modified: 2010-03-19 08:07:51
Component: common
Priority: major
Owner: apdavison
Reporter: apdavison

Simulations cannot run When an MPI-enabled NEURON version is used to compile the MODL files. HOC claims that mindelay is 0 or less than dt, although min and max delays are properly set in setup().

This behaviour has been observed with NEURON version 6.2.994. Find attached the console log of an example (problem.log) and the log from debug=True (neuron.log).

Imported from Trac ticket:44

Opened: 2008-03-12 18:32:21
Last modified: 2008-03-14 17:37:45
Component: oldneuron
Priority: major
Owner: apdavison
Reporter: mschmucker

Imported from Trac ticket:30

Opened: 2007-06-20 16:17:05
Last modified: 2009-03-27 16:50:10
Component: pcsim
Priority: major
Owner: pierre
Reporter: apdavison

A test model that uses STDP is needed.

Imported from Trac ticket:19

Opened: 2007-04-24 13:55:45
Last modified: 2008-03-18 14:39:46
Component: unspecified
Priority: major
Owner: somebody
Reporter: apdavison

Problem:
Membrane potential indicates some spikes, but "spikes.dat" is empty.

To reproduce execute:
==== SNIP ====
from pyNN.neuron import *

setup()
n = create(IF_facets_hardware1, n=1)
s = create(SpikeSourcePoisson,{'rate':10.},n=10)
connect(s,n,weight=0.002)
record(n,'spikes.dat')
record_v(n,'membrane.dat')
run(1000)
end()
==== SNIP ====

Imported from Trac ticket:39

Opened: 2008-01-13 12:27:54
Last modified: 2008-02-15 14:06:47
Component: oldneuron
Priority: major
Owner: apdavison
Reporter: mueller

Some simulators allow writing variables other than spike times and membrane potential to file. To support these, we should have a single function and a single Population method for writing variables to file.

Also, python tends to use write(), rather than print(), for this kind of thing.

This should be done in a separate branch until we've made a release with the current API.

Imported from Trac ticket:1

Opened: 2007-04-24 11:32:13
Last modified: 2010-12-10 10:20:37
Component: unspecified
Priority: minor
Owner: apdavison
Reporter: apdavison

e.g.
{{{
>>> nest.list_standard_models()
[IF_curr_exp, ...]
}}}
i.e., should return a list of classes that are available in that simulator.

Imported from Trac ticket:32

Opened: 2007-10-04 15:24:02
Last modified: 2007-10-05 17:08:56
Component: common
Priority: minor
Owner: apdavison
Reporter: apdavison

One of the design goals of PyNN is to minimise the number of required dependencies. At the moment, numpy is supposed to be the only dependency. Therefore, use of pytables in the pcsim module should be made optional if possible.

Imported from Trac ticket:16

Opened: 2007-04-24 13:48:34
Last modified: 2007-05-11 14:00:32
Component: pcsim
Priority: major
Owner: somebody
Reporter: apdavison

The neuron module was really designed to have setup() and end() run only once per script. It is currently possible to call setup() more than once, but only to change the timestep. The network time is not reinitialised to zero, for example. Calling end() destroys the ParallelContext instance and it is not recreated when calling setup() a second time.

It would be desirable to be able to reinitialise the network, so a redesign with this in mind is needed.

I am not sure whether these issues also apply to the nest2 and pcsim modules.

Imported from Trac ticket:45

Opened: 2008-03-13 10:35:34
Last modified: 2010-01-26 17:17:02
Component: all
Priority: major
Owner: None
Reporter: apdavison

I recorded my whole network twice, because I stupidly run my recording part of my network twice. PyNN connected thereby the same spike_detector twice to a neuron, which then printed each spikes twice, which gave my some hard time. PyNN should maybe check if a neuron is already recorded before recording it twice.

Imported from Trac ticket:36

Opened: 2007-11-29 16:34:07
Last modified: 2008-03-21 09:40:13
Component: common
Priority: minor
Owner: apdavison
Reporter: JensKremkow

The current setup.py script does not install the hoc directory, nor compile its contents.

Imported from Trac ticket:11

Opened: 2007-04-24 13:32:15
Last modified: 2008-03-19 17:06:35
Component: nmodl
Priority: major
Owner: apdavison
Reporter: apdavison

It would be nice to be able to inject a time varying current into any standard cell in a simulator-independent way. This could be done in two ways:

(1) Create a new standard cell, CurrentSource, and extend connect(), Projection to allow non-synaptic connections

(2) Create an Electrode class, then either
(a) allow the i_offset parameter of each standard cell to be an Electrode object rather than a float.

(b) create an `inject()` function in the low-level API and/or an `inject()` method for the `ID` object.

I don't much like (1), since it does not fit with the general principle of spike-based communication, although if we allow gap-junction connections in future, it would fit better.

Concerning (2), if we add RC-circuit properties to the Electrode class, it could also be used to extend record_v().

(2b) would probably be simpler to implement than (2a)

Imported from Trac ticket:38

Opened: 2008-01-08 11:25:44
Last modified: 2009-06-04 14:54:13
Component: common
Priority: minor
Owner: apdavison
Reporter: apdavison

Imported from Trac ticket:48

Opened: 2008-03-17 16:36:21
Last modified: 2008-03-17 18:10:26
Component: oldneuron
Priority: major
Owner: apdavison
Reporter: apdavison

The spike times passed to a SpikeSourceArray can have arbitrary positive values. If a simulation has a shorter duration than the maximum spike time in the array, there will be unused values. In nest2, only the spikes that actually occurred during the simulation are written by printSpikes(), whereas in neuron, all the spikes, including unused ones, are written.

The neuron behaviour should be changed to match the nest2 one.

Imported from Trac ticket:47

Opened: 2008-03-17 11:46:08
Last modified: 2008-03-17 11:55:42
Component: oldneuron
Priority: minor
Owner: apdavison
Reporter: apdavison

i.e. returning suitable error messages if a file is read-only, etc.

If the user tries to write to a non-writable file, the temporary file should not be deleted and a Warning should be raised, giving the location of the temporary file, so that the user can attempt to recover the data.

Imported from Trac ticket:51

Opened: 2008-03-19 17:25:01
Last modified: 2011-01-04 17:05:28
Component: common
Priority: minor
Owner: apdavison
Reporter: apdavison

The current STDP API only works for NEURON, not for NEST v2, and probably not for PCSIM. STDP should probably be set-up on creation of a Projection, although it should be possible to change parameters later.

Imported from Trac ticket:34

Opened: 2007-10-05 17:18:28
Last modified: 2008-03-18 14:42:19
Component: unspecified
Priority: major
Owner: apdavison
Reporter: apdavison

I might be completely wrong, but in Population() constructor, we create several cells of same type, so why doesn't it use the create() function of the Low Level API ?

Imported from Trac ticket:27

Opened: 2007-05-22 13:07:25
Last modified: 2008-11-22 11:38:04
Component: common
Priority: minor
Owner: apdavison
Reporter: debeissat

Imported from Trac ticket:50

Opened: 2008-03-19 17:11:57
Last modified: 2008-03-19 19:15:54
Component: unspecified
Priority: major
Owner: apdavison
Reporter: apdavison

It would be nice to have the Izhikevich model as a standard model. Need to find NEST, PCSIM and NEURON implementations (try ModelDB for the latter), then standardise parameter names.

Imported from Trac ticket:9

Opened: 2007-04-24 13:28:01
Last modified: 2012-12-22 20:27:51
Component: unspecified
Priority: minor
Owner: somebody
Reporter: apdavison

What was pynest in NEST v1 is nest in NEST v2.
The problem is that import nest within nest2.py imports pyNN.nest rather than nest, since the import mechanism looks within the package first.

Two possible solutions:

1. Require Python 2.5. Versions >= 2.5 support absolute imports (from __future__ import absolute_import).
2. Rename pyNN.nest to pyNN.nest1 or something similar.

I don't really like either solution, but overall I prefer (1). Comments?

Imported from Trac ticket:31

Opened: 2007-07-19 11:43:13
Last modified: 2007-10-05 16:24:20
Component: nest
Priority: major
Owner: apdavison
Reporter: apdavison

The ID class is supposed to have a get() method, which gets the values of cell parameters. For this, we will need to implement reverse translation in the common.StandardCellType class.

Imported from Trac ticket:22

Opened: 2007-05-15 14:14:03
Last modified: 2008-03-20 19:16:22
Component: common
Priority: major
Owner: apdavison
Reporter: apdavison

On Friday 01 June 2007 13:05, Jens Kremkow wrote:

Hi,

I guess it was implicitly assumed that the spike_times that one gives
to a SpikeSourceArray object are sorted, but I made the mistake and
gave an unsorted array, which I got from a random generator, and
wondered why some spikes were missing. So make sure that your spike
times are sorted.

Cheers,
Jens

Please vote:

(A) the SpikeSourceArray should automatically sort the spike_times array (which could be computationally intensive)

(B) we should leave things as they are, but add a note to the documentation stating that the array must be already sorted.

Imported from Trac ticket:28

Opened: 2007-06-04 09:46:59
Last modified: 2007-10-05 16:36:53
Component: common
Priority: minor
Owner: apdavison
Reporter: apdavison

Need to check that the API is consistent for all the simulator modules (including output formats/return values as well as input arguments - need to extend checkAPI.py), check all the tests run, then release version 0.3.0.

Imported from Trac ticket:12

Opened: 2007-04-24 13:35:12
Last modified: 2007-05-24 13:26:54
Component: unspecified
Priority: blocker
Owner: apdavison
Reporter: apdavison

also add a ChangeLog

Imported from Trac ticket:49

Opened: 2008-03-19 17:11:34
Last modified: 2008-06-06 09:36:02
Component: unspecified
Priority: blocker
Owner: apdavison
Reporter: apdavison

Currently, a standard model combines both a membrane mechanism and a synaptic mechanism. If there are n of the former and m of the latter, we have to create n x m standard models (even more if there could be more than one synapse type per neuron). It would be cleaner to have standard membrane models and standard synaptic models that could be combined in user code to build arbitrary models. Only n + m models then have to be created/maintained.

Imported from Trac ticket:2

Opened: 2007-04-24 11:38:37
Last modified: 2010-11-04 11:00:25
Component: unspecified
Priority: major
Owner: somebody
Reporter: apdavison

(found by dr-joe)

line
--> 529 os.system("cat %s > %s" % nest_filename, user_filename)

generates :

TypeError: not enough arguments for format string

workaround :

--> 529 system_line = 'cat %s >> %s' % (nest_filename, user_filename)
--> 530 os.system(system_line)

to reproduce:

[perrinet@master0 ~]$ ipython

Python 2.5 (r25:51908, Apr 5 2007, 14:58:28)
Type "copyright", "credits" or "license" for more information.

IPython 0.8.2.svn.r2750 -- An enhanced Interactive Python.

In [1]: import pyNN.nest2 as sim

          -- N E S T --
      Neural Simulation Tool

Copyright 1995-2007 The NEST Initiative
Version 1.9-6564 Nov 30 2007 17:35:01

This program is provided to you AS IS and comes with NO WARRANTY.
See the file LICENSE for details.

Type 'nest.sysinfo()' to see details on the system configuration.
Type 'nest.authors()' for information about the makers of NEST.

In [2]: n = sim.Population(1,'poisson_generator',{'rate':2000.})

In [3]: n.record()

In [4]: sim.run(10000)
Out[4]: 10000.0

In [7]: n.meanSpikeCount()
Out[7]: 20040.0

In [9]: n.printSpikes('/tmp/dummy.txt',compatible_output=False)

TypeError Traceback (most recent call last)

/home/perrinet/ in ()

/home/perrinet/python/site-packages/pyNN/nest2/init.py in printSpikes(self, filename, gather, compatible_output)
851 """
852 _print(filename, gather=gather, compatible_output=compatible_output,
--> 853 population=self, variable="spikes")
854
855 def getSpikes(self):

/home/perrinet/python/site-packages/pyNN/nest2/init.py in _print(user_filename, gather, compatible_output, population, variable)
527 population, get_time_step())
528 else:
--> 529 os.system("cat %s > %s" % nest_filename, user_filename)
530
531 os.remove(nest_filename)

TypeError: not enough arguments for format string

In [10]:

Imported from Trac ticket:46

Opened: 2008-03-14 18:27:20
Last modified: 2008-03-19 17:22:47
Component: nest
Priority: major
Owner: apdavison
Reporter: LaurentPerrinet

It would be useful to have some benchmarks which would allow the performance of the different modules to be tracked over time.

Imported from Trac ticket:20

Opened: 2007-04-24 13:57:19
Last modified: 2010-12-10 11:00:22
Component: unspecified
Priority: minor
Owner: somebody
Reporter: apdavison

The API docs are autogenerated by the wikidoc.py script. This should be extended to output the Trac wiki format, then the API documentation moved to the !NeuralEnsemble wiki

Imported from Trac ticket:7

Opened: 2007-04-24 13:23:39
Last modified: 2007-05-15 15:39:45
Component: unspecified
Priority: major
Owner: apdavison
Reporter: apdavison

Would be cool to have a Population.getitem that takes a list/array of coordinates and returns their addrs.
Could be speed up the connect routines, so far, for each synapse the routine has to ask the id of a given coordinate in a loop.

Imported from Trac ticket:21

Opened: 2007-05-04 13:34:51
Last modified: 2009-06-04 14:47:29
Component: common
Priority: minor
Owner: apdavison
Reporter: JensKremkow

Currently, the algorithm to use for connecting two Populations is specified as a string argument, method in the Projection.__init__() method. Each string corresponds to a private method of the Projection class. To make it easier to add new connection algorithms, method should probably be a class, which inherits from an abstract ConnectionMethod class. (Take a look at how this is done in PCSIM).

Imported from Trac ticket:3

Opened: 2007-04-24 13:11:30
Last modified: 2008-01-08 10:48:54
Component: unspecified
Priority: major
Owner: apdavison
Reporter: apdavison

• The method parameters accepted in pcsim are not d_expression and allow_self_connections.
• The PCSIM class EuclideanDistanceRandomConnections only implements C*exp(-d/lambda) or something like this, not arbitrary expressions.

Imported from Trac ticket:29

Opened: 2007-06-05 14:53:22
Last modified: 2009-06-04 10:52:58
Component: pcsim
Priority: major
Owner: apdavison
Reporter: apdavison

A general refactoring of connection book-keeping in nest2 is needed. We are storing too much information in the Projection class that is also stored within NEST. It might be slightly slower to have to look it up when needed, but there should be a large decrease in memory required.

Currently, we store 1D arrays _sources, _targets, and _targetPorts, so 3xNxM values, assuming all-to-all connectivity between a Population of size N and one of size M. If we assume that cell ids in a Population are consecutive (this is the case, but should be more strictly checked), then it is not necessary to store anything except the first id in a Population - we simply filter the connection dicts returned by nest.GetConnections() and keep only the connections that have target ids within the post-synaptic population. This might be complicated somewhat when running a distributed simulation.

Need to create some performance benchmarks to check that the performance hit of the lookups is not too great.

Imported from Trac ticket:42

Opened: 2008-02-19 11:13:36
Last modified: 2010-02-03 13:18:32
Component: nest
Priority: minor
Owner: apdavison
Reporter: apdavison

I added the Population method getSpikes to the nest2 backend for Monte-Carlo type simulations
where one can load the spikes from one of many simulations right away and delete the file.

Implementation for the other PyNN backends is pending, and the subject of this ticket.

Imported from Trac ticket:40

Opened: 2008-01-23 18:00:13
Last modified: 2008-03-20 10:47:17
Component: common
Priority: minor
Owner: apdavison
Reporter: emuller

File references are not completely cleared between simulations with pyNN.neuron and recording single cells, for example using NeuroTools.benchmark.

In more detail, stale file references seem to hang around in vfilelist and spikefilelist (defined in neuron.init.py). Upon calling end() NEURON is told to write to those files, which are already closed.

I have attached a code sample that should reproduce this behaviour. Inspecting vfilelist and spikefilelist during the execution reveals the entries that cause an error during the second run of the benchmark.

Imported from Trac ticket:43

Opened: 2008-03-12 18:14:39
Last modified: 2008-03-13 11:55:43
Component: oldneuron
Priority: major
Owner: apdavison
Reporter: mschmucker

The facetsml module does not work yet. Getting to the stage of producing valid NeuroML, even for a very simple network, would be a good start.

Imported from Trac ticket:14

Opened: 2007-04-24 13:42:42
Last modified: 2009-01-07 23:09:59
Component: unspecified
Priority: minor
Owner: [email protected]
Reporter: apdavison
Keywords: facetsML neuroML xml

This means modifying the tests/runtests.py script

Imported from Trac ticket:15

Opened: 2007-04-24 13:45:12
Last modified: 2007-05-16 13:34:44
Component: pcsim
Priority: critical
Owner: apdavison
Reporter: apdavison

To allow easy specification of neuronal diversity, we should allow specification of int/float parameters using a pyNN.random.RandomDistribution object. The value for an individual cell/connection would be picked from this distribution.

Imported from Trac ticket:4

Opened: 2007-04-24 13:15:54
Last modified: 2010-12-09 20:59:03
Component: unspecified
Priority: major
Owner: Pierre
Reporter: apdavison

The adapting I&F neuron should be a standard model. This exists in NEST, and I think it exists in PCSIM, so NEURON and Brian versions are needed.

Imported from Trac ticket:8

Opened: 2007-04-24 13:25:50
Last modified: 2011-01-04 17:09:49
Component: nmodl
Priority: minor
Owner: apdavison
Reporter: apdavison

More documentation is needed. We should start with a user's guide, in HTML (wiki) and PDF formats.

Imported from Trac ticket:6

Opened: 2007-04-24 13:21:23
Last modified: 2007-05-24 17:22:06
Component: unspecified
Priority: major
Owner: apdavison
Reporter: apdavison

Formats should be those used in [http://neuralensemble.kip.uni-heidelberg.de/trac/NeuroTools NeuroTools].

My preference would be to allow printX() functions/methods to accept an open file-like object instead of a filename, so the file could be opened in user code and passed as an argument.

The alternative is to explicitly support [http://hdf.ncsa.uiuc.edu/HDF5/ HDF5] in PyNN by importing !NeuroTools or [http://www.pytables.org/ PyTables]. I would prefer to avoid this to minimise the number of dependencies PyNN has. It should at least be a soft dependency (i.e., if you have !PyTables, you can have HDF5, if not, you can only have ASCII).

Imported from Trac ticket:23

Opened: 2007-05-16 13:48:19
Last modified: 2009-09-23 15:26:42
Component: common
Priority: major
Owner: somebody
Reporter: apdavison

The current implementation for NEURON of the IF_curr_alpha, IF_cond_exp, etc models is flexible but inefficient. It should be replaced by ARTIFICIAL_CELL-type implementations. One possibility is to adapt Michael Hines' code from the Vogels-Abbott benchmarks.

Imported from Trac ticket:10

Opened: 2007-04-24 13:30:37
Last modified: 2010-12-10 11:00:09
Component: nmodl
Priority: minor
Owner: apdavison
Reporter: apdavison

Model parameters should have dimensions, units, minimum and maximum allowable values, as well as a value. Currently, units are determined by convention, but it might reduce errors if units, etc, could be specified directly (it would also make it easier to auto-generate GUIs, etc). One possibility is the traits package: http://code.enthought.com/traits/

Imported from Trac ticket:5

Opened: 2007-04-24 13:19:56
Last modified: 2011-10-03 13:53:54
Component: unspecified
Priority: major
Owner: somebody
Reporter: apdavison

Extend checkAPI.py to check file formats, return values and default arguments as well as input argument type.

Imported from Trac ticket:13

Opened: 2007-04-24 13:37:27
Last modified: 2007-05-24 13:28:45
Component: unspecified
Priority: major
Owner: apdavison
Reporter: apdavison