We recently found and fixed a bug which may silently cause spikes to be lost or extra spikes to be generated in certain circumstances. At the moment, the only known example of a problem is when using SpikeGeneratorGroup in a simulation with multiple clocks as in this message on the support group, but the problem may also appear in rare situations with other simulations with multiple clocks. We advise users to upgrade to Brian 1.1.4 when it is released next week.
We recently found a bug that may silently cause problems with many simulations. The bug causes problems in the following situation:
- You create a NeuronGroup
- You create a subgroup of that group
- You create a Connection from that subgroup
- The Connection has delays
If you have code running on an older version and think your code might be affected, please get in contact on the firstname.lastname@example.org list.
The Brian SVN has moved from SourceForge to neuralensemble.org. The current release (1.1.3) is still available at the SourceForge and PyPI pages, but future releases will be at the new page. The current development version will only be available on the new page from now on.
We have just produced a new release of Brian, version 1.1.3, with the following changes:
- 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
You will also notice that the manual now includes a developer’s guide. If you are interested in contributing, we suggest you to subscribe to the Brian development mailing list.
We will be at NeuroComp 2009 in Bordeaux on 16 September. We will give a tutorial at 4.30 pm. Try to install Brian before the tutorial, and we will help you if you have any problem with it. You will need to bring your laptop (no machine in the room). If there is anything special you would like us to address during the tutorial, please don’t hesitate to contact us.
Examples of the tutorial.
We will be at the Computational Neuroscience (CNS) meeting next week, at the Python in Neuroscience workshop. Romain Brette will give a talk on Brian in the morning session of the first day, and Dan Goodman will give a tutorial in afternoon/evening session on using Python for neuroscience, covering NumPy, SciPy, PyLab and Brian. Hope to see you there!
Brian is now part of the PyNN API since version 0.5. PyNN is a simulator-independent language for building neuronal network models. You can write the code for a model once, using the PyNN API and the Python programming language, and then run it without modification on any simulator that PyNN supports (currently NEURON, NEST, PCSIM and Brian).
At the moment, we’re working on these features for Brian 1.1.3 which should be coming very soon:
- STDP working with connections with heterogeneous delays.
- A new RecentStateMonitor for storing only the most recent values of a variable.
- A new TimedArray class to make it easier to set the values of a variable in an equation from a precomputed array.
- Progress reporting for simulation runs, with estimates of how long the computation will take.
- Support for parallel processing with a GPU - the work in progress on this is already available in the experimental subpackage in Brian.
- Support for automatic generation and compilation of C code for nonlinear differential equation solvers.
- A subpackage, “Brian hears”, for auditory system modelling, including efficient GPU based filterbank operations.
Brian has a new website! It’s now running on Wordpress and will feature blogs for Brian related news, announcements of new releases, and a development blog.