Brian 1.2.1

We have just released Brian 1.2.1.

This is mostly a bug fixing release, and minor new features. One highlight is the new remote control system which allows you to interact with a Brian script as it is running - e.g. changing parameter values, plotting intermediate results, etc. Also, GPU support on 64 bit and Linux machines is now much better.

Major features:

  • New remote controlling of running Brian scripts via RemoteControlServer and RemoteControlClient.

Minor features:

  • New module tools.io
  • 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.

Improvements

  • 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 resets.
  • 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).