CARLsim5 Released!

Introduction

CARLsim5 is an efficient, easy-to-use, GPU-accelerated library for simulating large-scale spiking neural network (SNN) models with a high degree of biological detail. It allows execution of networks of Izhikevich spiking neurons with realistic synaptic dynamics using multiple off-the-shelf GPUs and x86 CPUs. The simulator provides a PyNN-like programming interface in C/C++, which allows for details and parameters to be specified at the synapse, neuron, and network level.

The present release, CARLsim 5, builds on the efficiency and scalability of earlier releases (Nageswaran et al., 2009; Richert et al., 2011, and Beyeler et al., 2015; Chou et al., 2018). The functionality of the simulator has been greatly expanded by the addition of a number of features that enable and simplify the creation, tuning, and simulation of complex networks with spatial structure.

New Features

1. PyNN Compatibility

pyCARL is a interface between the simulator-independent language PyNN and a CARLsim5 based back-end. In other words, you can write the code for a SNN model once, using the PyNN API and the Python programming language, and then run it without modification on the CARLsim5 simulator that PyNN supports.

Principal APIs supported:

• Neuron Models: pyCARL currently supports Izhikevich spiking neurons with either current-based or conductance-based synapses. Support for LIF neurons is planned for the future. Different groups of neurons can be created from a one-dimensional array to a three-dimensional grid.
• Synapse: pyCARL supports the following synapse models
• Static Synapse - A fixed weight and delay synapse.
• Spike-timing-dependent plasticity - STDP mechanisms can be constructed using weight-dependence and timing-dependent models.
• Connector Types: The pyCARL interface currently supports the following connectors:
• AllToAllConnector - Each neuron in the pre-synaptic population is connected to every neuron in the post-synaptic population.
• OneToOneConnector - The neuron with index i in the pre-synaptic population is then connected to the neuron with index i in the post-synaptic population.
• FixedProbabilityConnector - Each possible connection between all pre-synaptic neurons and all post-synaptic neurons is created with probability p.
• Spike sources: pyCARL currently supports a poisson source (SpikeSourcePoisson) and array-based spike source (SpikeSourceArray).
• Monitoring: Currently, pyCARL support spike and connection monitoring. CARLsim SpikeMonitors and ConnectionMonitors are internally defined for every group (Population) and connection (projection) in an application.
• Homeostasis: Homeostatic synaptic scaling has been observed experimentally and may serve to stabilize plasticity mechanisms that can otherwise undergo run-away behaviors. CARLsim implements a version of homeostatic synaptic scaling that helps stabilize STDP.

pyCARL is a work in progress and newer APIs and features will continue to be supported via the interface. Its sources and installation instructions are now available as a part of CARLsim5’s software release. Please refer to the CARLsim5 documentation https://uci-carl.github.io/CARLsim5/ch14_pyCARL.html for the pyCARL installation instructions.

2. Neuron monitor

Neuron monitor now supports observing the voltage and current traces of individual neurons. This provides a useful tool for users to analyze the network dynamics during the simulation. 

3. Docker images for Windows users and computer cluster users

It was not convenient for windows users to use CARLsim for the requirement of installing of Microsoft Visual Studio 2015 and the update of Visual Studio. As a result, we release docker images in which CARLsim5 has been installed in an ubuntu system and ready for use immediately.

4. Saving and Loading

CARLsim5 now supports saving the network during the run time. The saved network could be loaded again via reading the saved file when setting up the network in a new simulation. All information regarding to the connections including weights, delays, source and target neurons will be saved. For more information, see https://uci-carl.github.io/CARLsim5/ch8_saving_loading.html

5. Improved ECJ Interface (Coming soon)

CARLsim5 supports ECJ-23 for evolutionary parameter tuning for now. The new ECJ-28 will released and integrated into CARLsim5 soon.

NeuroML2/LEMS is moving into Neural Mass Models and whole brain networks

In the last months, as part of the Google Summer of Code 2018, I have been working on a project that aimed to implement neuronal models which represent averaged population activity on NeuroML2/LEMS. The project was supported by the INCF organisation and my mentor, Padraig Gleeson, and I had 3 months to shape and bring to life all the ideas that we had in our heads. This blog post summarises the core motivation of the project, the technical challenges, what I have done, and future steps.

Background
NeuroML version 2 and LEMS were introduced in order to standardise the description of neuroscience computational models and facilitate the shareability of results among different research groups1. However, so far, NeuroML2/LEMS have focused on modelling spiking neurons and how information is exchanged between them in networks. With the introduction of neural mass models, NeuroML2/LEMS can be extended to study interactions between large-scale systems such as cortical regions and indeed whole brain dynamics. To achieve this, my project consisted of implementing the basic structures needed in NeuroML2/LEMS to simulate Neural Mass Models and compare the results with previously published papers.

What I did
During the project I focused on the implementation of three previously described Neural Mass Models into NeuroML2/LEMS:

1. del Molino et al., 20172: This study analyses the dynamics and interaction between excitatory neurons and three types of interneurons (parvalbumin (PV), somatostatin (SST) and vasoactive intestinal peptide (VIP) expressing).  It first looks at the interactions between single units representing each population and then it scales up to analyse the interaction between a network with multiple interacting units in each population. A detailed description of the model that I have implemented in NeuroML and an illustrative Jupyter notebook that reproduces the main findings from the paper can be found at this git repository.

Overview of the del Molino et al., 2017 model implemented in NeuroML2/LEMS. The scheme on the left illustrate how the different populations are connected and the entry point of the top-down modulatory input. Once the dynamics of the interaction between single units have been analysed, we scale up to look at the interaction of a network of multiple interacting units in each population. The network population is illustrated on the right

2. Wilson and Cowan, 19723: This classic model describes the interaction between populations of excitatory and inhibitory neurons.  In this project, I have implemented a NEURON interpretation of the Wilson and Cowan model into NeuroML and compared the dynamics of the model by looking at the dynamics of the generated results. The repository with the Wilson and Cowan simulations can be found here.

Illustration of the population modelled with Wilson and Cowan simulation and how the dynamics over time change with (Drive) and without (No Drive) an additional external input current  

3. Mejias et al., 20164: analyses the dynamics across multiple scales of the primate cortex (intralaminar, interlaminar, interareal and whole cortex). This git repo so far implements the intralaminar and interlaminar simulations of the cortex in Python and provides the methods needed for analysing the results from the NeuroML2/LEMS simulation.  It also contains a first model of the interlaminar simulation using NeuroML2/LEMS that will be further extended to simulate the firing rate at interlaminar, interareal and whole cortex level.

Illustration of the Mejias et al., 2016 models implemented so far: While at the intralaminar level analyses the dynamics of the excitatory (in red) and inhibitory population (in blue) for each layer are considered independent, in the interlaminar the interaction between supra- (Layer 2/3) and infragranular (Layer 5/6) layers are taken into account

The technical challenges 

In order to be able to simulate Neural Mass Models, we had to extend previously defined  NeuroML2 components used to simulate spiking models. To this end we defined two new core components:

• baseRateUnit: which extends the baseCellMembPot but instead of exposing the membrane potential it exposes the population’s firing rate.
• rateSynapse: In the spiking models a change in current is only triggered if the cell membrane exceeds a specific threshold. In a rate base model, however, there is a continuous transmission of currents between the populations. Therefore we extended the baseSynapse component so that it allows the continuous transmission of currents between the population using continuous connections.

The detailed implementation of the two components can be found here.

The future

The projects I have worked on during these 3 months were a proof of concept to explore how NeuroML2/LEMS can be extended to simulate Neural Mass Models. They provided valuable insight into the necessary components to extend NeuroML2/LEMS to large-scale dynamics and a proof of concept that the generated signal is comparable to those generated with other tools.

These are, however, just the first steps into a very interesting direction: just imagine how incredible it would be to extend this data to a whole brain simulation. One possible candidate would be to use mouse data for the simulation (e.g. from the Allen Institute mouse connectivity datasets). So stay tuned for future updates!

The experience
Working on this project was not only a great way of getting to learn the intricacies of NeuroML, get a better understanding of Neural Mass Models but it was also a great opportunity to get my hands dirty with the code. It was also very satisfying to produce in a short time something from the beginning to the end. In addition to all these, it was also my first contact with the open source community. Thank you very much Padraig, for the help and the guidance during these months!

References

1 Cannon, R. C., Gleeson, P., Crook, S., Ganapathy, G., Marin, B., Piasini, E., & Silver, R. A. (2014). LEMS: a language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2. Frontiers in neuroinformatics, 8, 79 https://doi.org/10.3389/fninf.2014.00079 .

2 Garcia Del Molino, Luis Carlos, Guangyu Robert Yang, Jorge F. Mejias, and Xiao-Jing Wang. 2017a. “Paradoxical Response Reversal of Top-down Modulation in Cortical Circuits with Three Interneuron Types.” eLife 6 (December). https://doi.org/10.7554/eLife.29742 .

3 Wilson, H. R., & Cowan, J. D. (1972). Excitatory and inhibitory interactions in localized populations of model neurons. Biophysical journal, 12(1), 1-24 http://dx.doi.org/0.1016/S0006-3495(72)86068-5 .

4 Mejias, Jorge F., John D. Murray, Henry Kennedy, and Xiao-Jing Wang. 2016a. “Feedforward and Feedback Frequency-Dependent Interactions in a Large-Scale Laminar Network of the Primate Cortex.” https://doi.org/10.1101/065854 .  

PyNN 0.9.0 released

I'm happy to announce the release of PyNN 0.9.0!

This version of PyNN adopts the new, simplified Neo object model, first released as Neo 0.5.0, for the data structures returned by Population.get_data(). For more information on the new Neo API, see the Neo release notes

The main difference for a PyNN user is that the AnalogSignalArray class has been renamed to AnalogSignal, and similarly the Segment.analogsignalarrays attribute is now called Segment.analogsignals

What is PyNN?

PyNN (pronounced 'pine') is a simulator-independent language for building neuronal network models.

In other words, 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 and Brian as well as the SpiNNaker and BrainScaleS neuromorphic hardware systems).

Even if you don't wish to run simulations on multiple simulators, you may benefit from writing your simulation code using PyNN's powerful, high-level interface. In this case, you can use any neuron or synapse model supported by your simulator, and are not restricted to the standard models.

The code is released under the CeCILL licence (GPL-compatible).

Neo 0.5.0-alpha1 released

We are pleased to announce the first alpha release of Neo 0.5.0.

Neo is a Python library which provides data structures for working with electrophysiology data, whether from biological experiments or from simulations, together with a large library of input-output modules to allow reading from a large number of different electrophysiology file formats (and to write to a somewhat smaller subset, including HDF5 and Matlab).

For Neo 0.5, we have taken the opportunity to simplify the Neo object model. Although this will require an initial time investment for anyone who has written code with an earlier version of Neo, the benefits will be greater simplicity, both in your own code and within the Neo code base, which should allow us to move more quickly in fixing bugs, improving performance and adding new features. For details of what has changed and what has been added, see the Release notes.

If you are already using Neo for your data analysis, we encourage you to give the alpha release a try. The more feedback we get about the alpha release, the quicker we can find and fix bugs. If you do find a bug, please create a ticket. If you have questions, please post them on the mailing list or in the comments below.

Documentation:

http://neo.readthedocs.io/en/neo-0.5.0alpha1/

Licence:

Modified BSD

Source code:

https://github.com/NeuralEnsemble/python-neo

Updated Docker images for biological neuronal network simulations with Python

The NeuralEnsemble Docker images for biological neuronal network simulations with Python have been updated to contain NEST 2.10, NEURON 7.4, Brian 2.0rc1 and PyNN 0.8.1.

In addition, the default images (which are based on NeuroDebian Jessie) now use Python 3.4. Images with Python 2.7 and Brian 1.4 are also available (using the "py2" tag). There is also an image with older versions (NEST 2.2 and PyNN 0.7.5).

The images are intended as a quick way to get simulation projects up-and-running on Linux, OS X and Windows. They can be used for teaching or as the basis for reproducible research projects that can easily be shared with others.

The images are available on Docker Hub.

To quickly get started, once you have Docker installed, run

docker pull neuralensemble/simulation
docker run -i -t neuralensemble/simulation /bin/bash

For Python 2.7:

docker pull neuralensemble/simulation:py2

For older versions:

docker pull neuralensemble/pynn07

For ssh/X11 support, use the "simulationx" image instead of "simulation". Full instructions are available here.

If anyone would like to help out, or suggest other tools that should be installed, please contact me, or open a ticket on Github.

PyNN 0.8.1 released

Having forgotten to blog about the release of PyNN 0.8.0, here is an announcement of PyNN 0.8.1!

For all the API changes between PyNN 0.7 and 0.8 see the release notes for 0.8.0. The main change with PyNN 0.8.1 is support for NEST 2.10.

PyNN 0.8.1 can be installed with pip from PyPI.

What is PyNN?

PyNN (pronounced 'pine' ) is a simulator-independent language for building neuronal network models.

In other words, 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 and Brian as well as the SpiNNaker and BrainScaleS neuromorphic hardware systems).

Even if you don't wish to run simulations on multiple simulators, you may benefit from writing your simulation code using PyNN's powerful, high-level interface. In this case, you can use any neuron or synapse model supported by your simulator, and are not restricted to the standard models.

The code is released under the CeCILL licence (GPL-compatible).

EU Human Brain Project Releases Platforms to the Public

"Geneva, 30 March 2016 — The Human Brain Project (HBP) is pleased to announce the release of initial versions of its six Information and Communications Technology (ICT) Platforms to users outside the Project. These Platforms are designed to help the scientific community to accelerate progress in neuroscience, medicine, and computing.

[...]


The six HBP Platforms are:

• The Neuroinformatics Platform: registration, search, analysis of neuroscience data.
• The Brain Simulation Platform: reconstruction and simulation of the brain.
• The High Performance Computing Platform: computing and storage facilities to run complex simulations and analyse large data sets.
• The Medical Informatics Platform: searching of real patient data to understand similarities and differences among brain diseases.
• The Neuromorphic Computing Platform: access to computer systems that emulate brain microcircuits and apply principles similar to the way the brain learns.
• The Neurorobotics Platform: testing of virtual models of the brain by connecting them to simulated robot bodies and environments.

All the Platforms can be accessed via the HBP Collaboratory, a web portal where users can also find guidelines, tutorials and information on training seminars. Please note that users will need to register to access the Platforms and that some of the Platform resources have capacity limits."

   ... More in the official press release here.

 The HBP held an online release event on 30 March:

Prof. Felix Schürmann (EPFL-BBP, Geneva), Dr. Eilif Muller (EPFL-BBP, Geneva), and Prof. Idan Segev (HUJI, Jerusalem) present an overview of the mission, tools, capabilities and science of the EU Human Brain Project (HBP) Brain Simulation Platform:

A publicly accessible forum for the BSP is here:
https://forum.humanbrainproject.eu/c/bsp
and for community models
https://forum.humanbrainproject.eu/c/community-models
and for community models of hippocampus in particular
https://forum.humanbrainproject.eu/c/community-models/hippocampus