Brian is a simulator for spiking neural networks available on almost all platforms. This is a git clone of the subversion repository used for development.
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Latest commit 2ac30d7 Feb 16, 2016 @mstimberg mstimberg ****** BRIAN 1.4.3 ******


============ B R I A N =============================
A clock-driven simulator for spiking neural networks

Version: 1.4.3
	Romain Brette
	Dan Goodman
	Cyrille Rossant
	Bertrand Fontaine
	Victor Benichoux
	Marcel Stimberg
	Jonathan Laudanski

==== Installation ==========================================================

Requirements: Python (version 2.5-7), the following modules:

* numpy (version >=1.4.1)
* scipy (version >= 0.7)
* matplotlib (version >=0.90.1, optional, necessary for plotting )
* sympy (optional, necessary for the "event-based" feature in Synapses)

All operating systems: run 'python install' from the download folder.

Windows: You can run the installer exe file.

==== Extras ================================================================

Included in the extras download are:

	Documentation for Brian including tutorials.

	Examples of using Brian, these serve as supplementary documentation.

	Fully worked through tutorials on using Brian. These can be read
	through in the documentation too.

==== Usage and Documentation ===============================================

See the documentation in the extras download, or online:

==== Changes ===============================================================

Version 1.4.2 to 1.4.3
A minor bugfix release to fix incompatibilities with the upcoming numpy
release. Also prepares for the removal of the `scipy.weave` package (replaced
by the `weave` package).

Version 1.4.1 to 1.4.2
This is a bugfix release that does not add any major features. See the commit
log at for details. Note that our
development efforts are now entirely focused on Brian 2
(, this will most likely be the last
release in the 1.x series.

Version 1.4.0 to 1.4.1

Major features:
* C extensions are compiled by default during installation (with a fallback to
  the Python version if compilation fails) -- this might lead to a considerable
  speedup for users who did not compile those extensions manually before 

Minor features:
* Convenience methods for the Synapses class, allowing to save and load the
  connectivity and to convert the weights into a matrix
* A new openmp option to switch on the use of OpenMP pragmas in generated C code
* Brian hears: Two new models, MiddleEar (filtering by the middle ear) and 
  ZhangSynapse (model of the IHC-AN synapse) 
* Brian hears: New convenience functions to get reasonable axis ticks for
  logarithmic axes
* Brian's documentation is now also available under
* ProgressReporter has context manager support (i.e. can be used in "with"
* NeuronGroup and Synapses work with empty model specifications. 
* C version of SpikeContainer is now picklable
Bug fixes:
* Synaptic equations referring to variables in the pre- or postsynaptic group
  are never considered as being linear (fixes ticket #83)
* Fix issue with static equations in synaptic models (see )
* Make LinearStateUpdater pickable, even if array B is "NotImplemented".
* Fixed the bug in which the StateSpikeMonitor didn't record variables defined
  with a static equation.
* Important bug fixes for brian hears, all users are encouraged to update:
	* Make sure that LinearFilterbank copies it source and therefore not
	  changes it (when not using weave) (fixes ticket #73)
	* Fix some bugs in the TanCarney model
	* Fix shifting multi-channel sounds with fractional=True (fixes ticket #80)

Experimental features:
* A C version of SpikeQueue (used in the Synapses class), which can lead to a
  considerable speedup (see "Advanced concepts/Compiled code" for instructions
  how to use it).
* Delays can be specified as a parameters of the Synapses model and then be
  changed dynamically.

Version 1.3.1 to 1.4.0

Major features:

* New Synapses class (plasticity, gap junctions, nonlinear synapses, etc)

Minor features:

* New AERSpikeMonitor class
* Several updates to library.electrophysiology


* Units should work better with static code analysers now
* Added Network.remove
* SpikeMonitor has a new .it attribute (returns pair i, t of arrays of spike times)
* Many new examples

Bug fixes:

* Assigning to a static variable (equation) now raise an error
* Fixed issues for TimedArrays with explicitly set times (fixes ticket #81)
* Fixed bug, repr and str didn't work for Sound
* Fixed bug where tone(array_of_frequencies, ...)
* Fixed SparseConnectionMatrix bug suggested by Owen Mackwood
* Fixed bug in Parameters reported by Jimmy Bonaiuto
* Fixed bug with contained_objects reported by Oleg Sinyavskiy
* Units __repr__ and __str__ fixes
* Sound.spectrum, Sound.pinknoise, brownnoise
* t wasn't available in StringReset and PythonThreshold

Deprecated or removed features:

* MultipleSpikeGeneratorGroup
* experimental.coincidence_detection

Experimental features:

* Generating model documentation automatically (experimental.model_documentation) 

Version 1.3.0 to 1.3.1

Minor features:

* New PoissonInput class
* New auditory model: TanCarney (brian.hears)
* Many more examples from papers
* New electrode compensation module (in library.electrophysiology)
* New trace analysis module (in library.electrophysiology)
* Added new function to use multiple CPUs to
  perform multiple runs of a simulation and save results to a DataManager,
  with an optional GUI interface.
* Added FractionalDelay filterbank to brian.hears, fractional itds to
  HeadlessDatabase and fractional shifts to Sound.shifted.
* Added vowel function to brian.hears for creating artificial vowel sounds
* New spike_triggered_average function
* Added maxlevel and atmaxlevel to Sound
* New IRNS/IRNO noise functions


* SpikeGeneratorGroup is much faster.
* Added RemoteControlClient.set(var, name) to allow sending data to the server
  from the client (previously you could only receive data from the server but
  not send it, except in string form).
* Monitors do not process empty spike arrays when there have not been any 
  spikes, increases speed for monitored networks with sparse firing (#78) 
* Various speed optimisations

Bug fixes:

* Fixed bug with frozen equations and time variable in equations
* Fixed bug with loading sounds using Sound('filename.wav')
* SpikeMonitor now clears spiketimes correctly on reinit (#75)
* MultiConnection now propagates reinit (important for monitors) (#76)
* Fixed bug in realtime plotting
* Fixed various bugs in Sound
* Fixed bugs in STDP
* Bow propagates spikes only if spikes exist (#78)

Version 1.2.1 to 1.3.0

Major features:

* Added Brian.hears auditory library

Minor features:

* Added new, moved from brian.experimental
* reinit(states=False) will now not reset NeuronGroup state variables to 0.
* modelfitting now has support for refractoriness
* New examples in misc: after_potential, non_reliability, reliability,
  van_rossum_metric, remotecontrolserver, remotecontrolclient
* New experimental.neuromorphic package
* Van Rossum metric added


* SpikeGeneratorGroup is faster for large number of events ("gather" option).
* Speed improvement for pure Python version of sparse matrix preparation
* Speed improvements for spike propagation weave code (50-100% faster).
* Clocks have been changed and should now behave more predictably. In addition,
  you can now specify an order attribute for clocks.
* modelfitting is now based on playdoh 0.3
* modelfitting can now use euler/exp.euler or RK2 integration schemes
* Loading AER data is much faster
* Freezing now uses higher precision (used to only use 12sf now uses 17sf)

Bug fixes:

* Bug in STDP with small values for wmin/wmax fixed (ticket #63)
* Equations/aliases now work correctly in STDP (ticket #56)
* Bug in sparse matrices introduced in scipy 0.8.0 fixed
* Bug in TimedArray when dt keyword is used now fixed (thanks to Adrien
  Wohrer for pointing out the bug).
* Units now work correctly in STDP (ticket #60)
* STDP raises an error if operations are reordered (ticket #57)
* linked_var works with static vars (equations) (ticket #68)
* Changing clock.t during a run won't end the run
* Fixed ticket #66 (unit bug)
* Fixed ticket #64 (bug with freeze)
* Can now run a network with no group
* Exception handling now works properly for C version of circiular spike
* ccircular now builds correctly on linux and 64 bit

Internal changes:

* brian.connection deprecated and replaced by subpackage brian.connections,
  making the code structure much more straightforward and setting up for future
  work on code generation, etc.

Version 1.2.0 to 1.2.1

Major features:

* New remote controlling of running Brian scripts via RemoteControlServer
  and RemoteControlClient.
Minor features:

* New module
* weight and sparseness can now both be functions in connect_random
* New StateHistogramMonitor object
* clear now has a new keyword all which allows you to destroy all Brian
  objects regardless of whether or not they would be found by MagicNetwork.
  In addition, garbage collection is called after a clear.
* New method StateMonitor.insert_spikes to have spikes on voltage traces.


* The sparseness keyword in connect_random can be a function
* Added 'wmin' to STDP
* You can now access STDP internal variables, e.g. stdp.A_pre, and monitor
  them by doing e.g. StateMonitor(stdp.pre_group, 'A_pre')
* STDP now supports nonlinear equations and parameters
* refractory can now be a vector (see docstring for NeuronGroup) for constant
* modelfitting now uses playdoh library
* C++ compiled code is now much faster thanks to adding -ffast-math switch to
  gcc, and there is an option which allows you to set your own
  compiler switches, for example -march=native on gcc 4.2+.
* SpikeGeneratorGroup now has a spiketimes attribute to reset the list of
  spike times.
* StateMonitor now caches values in an array, improving speed for M[i] operation
  and resolving ticket #53

Bug fixes

* Sparse matrices with some versions of scipy
* Weave now works on 64 bit platforms with 64 bit Python
* Fixed bug introduced in 1.2.0 where dense DelayConnection structures would
  not propagate any spikes
* Fixed bug where connect* functions on DelayConnection didn't work with
  subgroups but only with the whole group.
* Fixed bug with linked_var from subgroups not working
* Fixed bug with adding Equations objects together using a shared base equation
  (ticket #9 on the trac)
* unit_checking=False now works (didn't do anything before)
* Fixed bug with using Equations object twice (for two different NeuronGroups)
* Fixed unit checking bug and ZeroDivisionError (ticket #38)
* Fixed rare problems with spikes being lost due to wrong size of SpikeContainer,
  it now dynamically adapts to the number of spikes.
* Fixed ticket #5, ionic_currents did not work with units off
* Fixed ticket #6, Current+MembraneEquation now works
* Fixed bug in modelfitting : the fitness was not computed right with CPUs.
* Fixed bug in modelfitting with random seeds on Unix systems. 
* brian.hears.filtering now works correctly on 64 bit systems

Removed features

* Model has now been removed from Brian (it was deprecated in 1.1).

Version 1.1.3 to 1.2.0

Major features:

* Model fitting toolbox (library.modelfitting)

Minor features:

* New real-time ``refresh=`` options added to plotting functions
* Gamma factor in utils.statistics
* New RegularClock object
* Added brian_sample_run function to test installation in place of nose tests


* Speed improvements to monitors and plotting functions
* Sparse matrix support improved, should work with scipy versions up to 0.7.1
* Various improvements to brian.hears (still experimental though)
* Parameters now picklable
* Made Equations picklable

Bug fixes:

* Fixed major bug with subgroups and connections (announced on webpage)
* Fixed major bug with multiple clocks (announced on webpage)
* No warnings with Python 2.6
* Minor bugfix to TimedArray caused by floating point comparisons
* Bugfix: refractory neurons could fire in very extreme circumstances
* Fixed bug with DelayConnection not setting max_delay
* Fixed bug with STP
* Fixed bug with weight=lambda i,j:rand()

New examples:

* New multiprocessing examples
* Added polychronisation example
* Added modelfitting examples
* Added examples of TimedArray and linked_var
* Added examples of using derived classes with Brian
* Realtime plotting example

Version 1.1.2 to 1.1.3

* STDP now works with DelayConnection
* Added EventClock
* Added RecentStateMonitor
* Added colormap option to StateMonitor.plot
* Added timed array module, see TimedArray class for details.
* Added optional progress reporting to run()
* New recall() function (converse to forget())
* Added progress reporting module (brian.utils.progressreporting)
* Added SpikeMonitor.spiketimes
* Added developer's guide to docs
* Early version of brian.hears subpackage for auditory modelling
* Various bug fixes

Version 1.1.1 to 1.1.2

* Standard functions rand() and randn() can now be used in string resets.
* New forget() function.
* Major bugfix for STP

Version 1.1.0 to 1.1.1

* New statistical function: vector_strength
* Bugfix for one line string thresholds/resets

Version 1.0.0 to 1.1.0

* Short-term plasticity (Tsodyks-Markram model)
* New DelayConnection for heterogeneous delays
* New code for Connections, including new 'dynamic' connection matrix type
* Reset and threshold can be specified with strings (Python expressions)
* Much improved documentation
* clear() function added for ipython users
* Simplified initialisation of Connection objects
* Optional unit checking in NeuronGroup
* Spike train statistics (utils.statistics)
* Miscellaneous optimisations
* New MultiStateMonitor class
* New Group, MultiGroup objects (for convenience of people writing extensions mostly)
* Improved contained_objects protocol with ObjectContainer class in brian.base
* UserComputed* classes removed for this version (they will return in another form).

Version 1.0.0 RC5 to version 1.0.0

* 2nd order Runge-Kutta method (use order=2)
* Quantity arrays are disabled (units only for scalars)
* brian_global_config added
* UserComputedConnectionMatrix and UserComputedSparseConnectionMatrix
* SimpleCustomRefractoriness, CustomRefractoriness

Version 1.0.0 RC4 to version 1.0.0 RC5

* Bugfix of sparse matrix problems
* Compiled version of spike propagation (much faster for
  networks with lots of spikes)
* Assorted small improvements

Version 1.0.0 RC3 to version 1.0.0 RC4

* Added StateSpikeMonitor
* Changed QuantityArray behaviour to work better with numpy, scipy and pylab

Version 1.0.0 RC2 to version 1.0.0 RC3

* Small bugfixes

Version 1.0.0 RC1 to version 1.0.0 RC2

* Documentation system now much better, using Sphinx, includes
  cross references, index, etc.
* Added VariableReset
* Added run_all_tests()
* numpywrappers module added, but not in global namespace
* Quantity comparison to zero doesn't check units (positivity/negativity)

Version 1.0.0 beta to version 1.0.0 RC1

* Connection: connect_full allows a functional weight argument (like connect_random)
* Short-term plasticity:
  In Connection: 'modulation' argument allows modulating weights by a state
  variable from the source group (see examples).
* HomogeneousCorrelatedSpikeTrains: input spike trains with exponential correlations.
* Network.stop(): stops the simulation (can be called by a user script)
* PopulationRateMonitor: smooth_rate method
* Optimisation of Euler code: use compile=True when initialising NeuronGroup
* More examples
* Pickling now works (saving and loading states)
* dot(a,b) now works correctly with qarray's with homogeneous units
* Parallel simulations using Parallel Python (independent simulations only)
* Example of html inferfaces to Brian scripts using CherryPy
* Time dependence in equations (see phase_locking example)
* SpikeCounter and PopulationSpikeCounter