NMSAT is a python package that provides a set of tools to build, simulate and analyse neuronal microcircuit models with any degree of complexity, as well as to probe the circuits with arbitrarily complex input stimuli / signals and to analyse the relevant functional aspects of single neuron, population and network dynamics. It provides a high-level wrapper for PyNEST (which is used as the core simulation engine). As such, the complexity of the microcircuits analysed and their building blocks (neuron and synapse models, circuit topology and connectivity, etc.), are determined by the models available in NEST. The use of NEST allows efficient and highly scalable simulations of very large and complex circuits, constrained only by the computational resources available to the user.
The modular design allows the user to specify numerical experiments with varying degrees of complexity depending on concrete research objectives. The generality of some of these experiments allows the same types of measurements to be performed on a variety of different circuits, which can be useful for benchmarking and comparison purposes. Additionally, the code was designed to allow an effortless migration across computing systems, i.e. the same simulations can be executed in a local machine, in a computer cluster or a supercomputer, with straightforward resource allocation (see kernel parameters).
The code is licensed under GPLv2 and available on GitHub.
The code was developed primarily for personal use, as part of a PhD thesis due to the need to perform similar experiments and analyses on very diverse systems. The goal was to use the same code to run diverse numerical experiments, covering a broad range of complexity, in a fully transparent and reproducible manner, while making efficient use of computing resources. Due to the inherent time pressures of a PhD project and the very broad scope, the code is imperfect and under active use / development. Despite our best efforts, it is prone to errors and often difficult to understand, particularly due to the strict specificities on the structure of the parameters dictionaries and how they are used.
For a detailed description of the framework and to make the most out of it, please read the documentation.
- Python 2.7
- NEST version 2.8.0 or higher
- numpy version 1.7.0 or higher
- scipy version 0.12.0 or higher
- scikit-learn version 0.18.0 or higher
- matplotlib version 1.2.0 or higher
Optional (for additional functionality):
- PySpike version 0.5.1
- h5py version 2.2.1 or higher
- mayavi
- networkx
The code is currently available only in this GitHub repository. To use it, simply download the source or fork and clone the repository. To configure your system, source the configuration file
source /{path}/nmsat/configure.shThis last step requires the user to manually specify all the paths for his system, by editing the paths dictionary in
/defaults/paths.py, as:
paths = {
'system_label': {
'data_path': NMSAT_HOME + '/data/',
'jdf_template': NMSAT_HOME + '/defaults/cluster_templates/Blaustein_jdf.sh',
'matplotlib_rc': NMSAT_HOME + '/defaults/matplotlib_rc',
'remote_directory': NMSAT_HOME + '/export/',
'queueing_system': 'slurm'}
}The system_label specifies the name of the system. If running simulations on a local machine, the name must be set as 'local' (which is the default), otherwise, it can be any arbitrary name, as long as it is used consistently throughout (see examples). The remaining entries in this dictionary refer to:
data_path- specify where to store the output data generated by an experimentjdf_template- path to a system-specific job description file (see example in /defaults/cluster_templates); if running locally set to Nonematplotlibrc- in case the user wants to customize matplotlibremote_directory- folder where the job submission files will be written (only applicable if not running locally, but must be specified anyway)queueing_system- type of job schedulling system used (current options include 'slurm' and 'sge')..
A numerical experiment in this framework consists of 2 or 3 main files (see examples):
- parameters_file - specifying all the complex parameter sets and dictionaries required to set up the experiment.
- experiment_script - mostly used during development, for testing and debugging purposes. These scripts parse the parameters_file and run the complete experiment
- computation_file - after the development and testing phase is completed, the experiment can be copied to a computation_file, which can be used from the main... (*)
These files should be stored within a project folder, and in the parameters, scripts and computations
folders, respectively.
You can run experiments both locally and on a remote cluster. To run an experiment on your local computer,
just go to the main nmsat directory and execute the experiment as:
python main.py -f {parameters_file} -c {computation_function} --extra {extra_parameters}where parameters_file refers to the (full or relative) path to the parameters file for the experiment,
computation_function is the name of the computation function to be executed on that parameter
set (must match the name of a file in the project’s ’computations’ folder) and extra_parameters are
parameter=value pairs for different, extra parameters (specific to each computation).
To run experiments on a cluster, please check out the documentation.
After a simulation is completed, all the relevant output data is stored in the pre-specified data_path, within a folder named after the project label. The output data structure is organized as follows:
data
├── experiment_label
│ ├── Figures
│ ├── Results
│ ├── Parameters
│ ├── Activity
│ ├── Input
│ ├── Output
Analysis and plotting can be (and usually is) done within the main computation, so as to extract and store only the information that is relevant for the specific experiment. Multiple, standard analysis and plotting routines are implemented for various complex experiments, with specific objectives. Naturally, this is highly mutable as new experiments always require specific analyses methods.
Alternatively, as all the relevant data is stored in the results dictionaries, you can read it and process it offline, applying the same or novel visualization routines.
The Results folder stores all the simulation results for the given experiment, as pickle dictionaries. Within each project, as mentioned earlier, a read_data folder should be included, which contains files to parse and extract the stored results (see examples).
project = 'project_name'
data_path = '/path/label/'
data_label = 'example1'
results_path = data_path + data_label + '/Results/'
# set defaults and paths
set_project_paths(project)
set_global_rcParams(paths['local']['matplotlib_rc'])
# re-create ParameterSpace
pars_file = data_path + data_label + '_ParameterSpace.py'
pars = ParameterSpace(pars_file)
# print the full nested structure of the results dictionaries
pars.print_stored_keys(results_path)
# harvest a specific result based on the results structure
data_array = pars.harvest(results_path, key_set='dict_key1/dict_key1.1/dict_key1.1.1')Complete examples can be found in the nmsat/projects/examples folder. Currently there are 4 examples that you
can try out:
- Single neuron fI curve
- Single neuron with patterned synaptic input
- Balanced random network
- Stimulus processing
For more details about each example read the Examples section in the documentation.
If you find NMSAT useful and use it in your research, please cite it as:
Renato Duarte, Barna Zajzon, & Abigail Morrison. (2017). Neural Microcircuit Simulation and Analysis Toolkit [Data set].
Zenodo.
Copyright (C) 2017 Renato Duarte, Barna Zajzon
Uses parts from NeuroTools for which Copyright (C) 2008 Daniel Bruederle, Andrew Davison, Jens Kremkow Laurent Perrinet, Michael Schmuker, Eilif Muller, Eric Mueller, Pierre Yger
Neural Mircocircuit Simulation and Analysis Toolkit is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
The GNU General Public License does not permit this software to be redistributed in proprietary programs.
See the LICENSE file for details.
This work was done in the Functional Neural Circuits group, at the Institute for Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6), Jülich Research Centre, Jülich, Germany. We would like to thank Professor Abigail Morrison for her continued patience, advice and support and the Neurobiology of Language group, at the Max-Planck for Psycholinguistics, for valuable discussions and contributions.
We acknowledge partial support by the Erasmus Mundus Joint Doctoral Program EuroSPIN, the German Ministry for Education and Research (Bundesministerium für Bildung und Forschung) BMBF Grant 01GQ0420 to BCCN Freiburg, the Helmholtz Alliance on Systems Biology (Germany), the Initiative and Networking Fund of the Helmholtz Association, the Helmholtz Portfolio theme ‘Supercomputing and Modeling for the Human Brain’. We additionally acknowledge the computing time granted by the JARA-HPC Vergabegremium on the supercomputer JURECA at Forschungszentrum Jülich, used during development.