Web Content Display
Model Downloads
Below are instances of models from the reconstructed neocortical microcircuit. The models are made available in the native format in use at the BBP, based on the NEURON simulation package (http://www.neuron.yale.edu).
See the Tools page for instructions on the execution of simulations using NEURON based models.
Neurons
Models of individual neurons (in the NEURON simulation environment) can be obtained from the me-type fact sheets. A model package contains a morphology file, the ion channel descriptions, the synapse descriptions and templates to instantiate the cell. There is code to construct the model, distribute the ion channels and synapses on the morphology, generate a GUI, and inject current clamp and synaptic input into the model.
The morphology description is a formatted as a Neurolucide ASCII file. The ion channel and synapse description are available as NEURON MOD files. The code for the templates, GUI and simulations is written in the NEURON HOC language or Python. The files containing the synaptic parameters and m-type mappings are tab-separated files.
The complete set of neuron models is available here
You can select specific neuron models in the interface below or by browsing to the relevant me-type fact sheet.
A JSON file with some extra data about each neuron model, like the resting membrane potential, input resistance and membrane time constant, can be downloaded here
NeuroML2 version
Thanks to a collaboration with Padraig Gleeson of the Open Source Brain, the model packages can be converted to NeuroML2:
https://github.com/OpenSourceBrain/BlueBrainProjectShowcase/blob/master/NMC/NeuroML2/README.md
A file with the NeuroML2 versions of the model packages is available here
Web Content Display
Circuit
.JSON file containing information about the circuit can be downloaded here:
Units are the same as in the circuit factsheet.
Layers
.JSON files containing information about the layers can be downloaded here:
Units are the same as in the layers factsheets.
Pathways
.JSON files containing anatomical and physiological data for all the pathways can be downloaded here:
Units are the same as in the pathways factsheets.
Connectome
Connectivity of an instance of a modeled microcircuit is available as an HDF5 file.
Gal, E., London, M., Globerson, A., Ramaswamy, S., Reimann, M.W., Muller, E., Markram, H., and Segev, I. (2017).
Rich cell-type-specific network topology in neocortical microcircuitry. Nat. Neurosci.
https://www.nature.com/neuro/journal/vaop/ncurrent/full/nn.4576.html
Reimann, M.W., Horlemann, A.-L., Ramaswamy, S., Muller, E.B., and Markram, H. (2017).
Morphological Diversity Strongly Constrains Synaptic Connectivity and Plasticity. Cereb. Cortex 1-16.
To download click the file name
- pathways_stripped_prod
- AVERAGE: 7 stochastic instances of a model microcircuit based on averaged measurements of neuron densities, E/I balance and layer widths.
- average_full.tar
- CONTROLS: 35 stochastic instances of a CONTROL microcircuit where connectivity is based on the overlap of AVERAGE morphologies instead of individual morphologies. To be used as a CONTROL. Specifically, there are 5 random instances, each preserving the number of connections found in one of 7 stochastic instances of a reconstructed microcircuit.
- controls_full.tar
- INDIVIDUALS: 35 stochastic instances of model microcircuits based on individual measurements of neuron densities, E/I balance and layer widths. Specifically, 7 random instances for each of 5 such measurements.
- individuals_full.tar
TERMS OF USE
VISION
Welcome to the Blue Brain Project ("BBP"") Neocortical Microcircuit Collaboration Portal ("Portal"").
This Portal provides an online public resource of the BBP's first release of a digital reconstruction of the microcircuitry of juvenile Rat somatosensory cortex, access to experimental databases used in the reconstruction, and the resulting models (collectively "Databases and Models""). The following functionality is provided through this Portal to support community engagement to use and refine the reconstruction.
The BBP is committed to ensuring that the outputs of the its research are managed and used in ways that maximize public benefit. Making Data widely available to the research community in a timely and responsible manner ensures that these data can be verified, built upon and used to advance knowledge and its application to generate improvements.
By accessing and using the Portal, you agree to the following terms and conditions of use ("Terms"") and to any future revision. We may chance, suspend, discontinue, limit or remove any part of the Portal at any time, without prior notice or liability. Your continued use of the Portal following any changes is an agreement by you to the change in Terms.
LICENCE
Subject to the Citation section below, under these Terms BBP grants you a world-wide, non-commercial, non-exclusive, nonsublicensable, royalty-free license on the Databases and Models to:
i) use, copy, distribute, publicly perform, publicly display, republish the Databases and Models for non-commercial purposes only;
ii) create derivative works for non-commercial purposes only.
Non-commercial purpose means: purpose not primarily intended for or directed towards sale, commercial advantage or monetary compensation. Use of Databases and Models for research and academic publication, in scholarly journal, textbook or other professional, academic or journalist publications (with appropriate Citation) is not considered commercial use.
Except for the limited permissions expressly stated in these Terms, all rights not specifically granted in these Terms are reserved. BBP/EPFL shall remain the sole owner of all and any intellectual property rights on Databases and Models. Additionally, BBP/EPFL retain its rights, title and interest in any Databases and Models that is part or it is used by you to create derivative works.
These Terms prohibits you to offer or impose any additional or different terms, conditions or purposes on derivative works if doing so restricts exercise of the licensed Databases and Models by BBP and any recipient of the Databases and Models.
You may not post any Databases and Models on social media or other third-party websites that require you to acknowledge that you own the Data you post.
CITATION
While BBP is committed to ensure that its Data are used in ways that maximize public benefit, in all cases where Data are used publicly BBP requests to give credit to the original authors by acknowledging the scientists who have provided the Data with an appropriate citation as detailed below ("Citation"").
The Citation shall be as follows:
1. Markram H, et al. (2015). Reconstruction and Simulation of Neocortical Microcircuitry. Cell 163:2, 456 - 492. doi: 10.1016/j.cell.2015.09.029
2. Ramaswamy S, et al., (2015). The Neocortical Microcircuit Collaboration Portal: A Resource for Rat Somatosensory Cortex. Front. Neural Circuits 9:44. doi: 10.3389/fncir.2015.00044
3. Reimann MW, et al., (2015). An Algorithm to Predict the Connectome of Neural Microcircuits. Front. Comput Neurosci. 9:28. doi: 10.3389/fncom.2015.00120
BBP AND EPFL LOGO
The BBP/EPFL logo may not be used for any purpose without explicit permission. Inappropriate and/or unauthorized use of logos can lead to legal action.
PRIVACY
Protecting your privacy and, in particular, your personal data is very important to us. When we receive your data through the website and via email, we comply with Swiss data protection legislation.
We save various types of information when you visit our website. These are:
-
Your personal data (such as your name and contact details) which you enter yourself
-
IP addresses, but only anonymous data (operating system details, browser version, etc.).
We use your data to constantly adapt and improve the Portal, in order to optimize our services. We do not sell, trade, or otherwise transfer to outside parties your personally identifiable information. We may release your information when we believe release is appropriate to comply with the law, or protect ours or others rights, property, or safety. However, non-personally identifiable visitor information may be used by other parties providing services (Google Analytics) to our site for optimization and statistic uses.
Right to Information
If you would like information on data relating to your person that has been collected and processed, if you want such data to be corrected, destroyed, or blocked, please contact the following address: bbp.privacy@epfl.ch
Cookies
Cookies are small files that a site or its service provider transfers to your computer hard drive through your Web browser (if you allow) that enables the sites or service provider systems to recognize your browser and capture and remember certain information. The Portal website uses cookies to optimize its services and save your preferences for future visits. You may refuse the use of cookies by selecting the appropriate settings on your browser, however please note that if you do this you may not be able to use the full functionality of this website.
THIRD PARTIES WEBSITES
The Portal contains links to third-party websites provided as a convenience to you. We are not responsible for the content found on any linked third-party website and do not endorse any third-party website or their goods or services. If you choose to use a third-party website, you will be subject to the terms and conditions of use that apply to such third-party website.
DISCLAIMER
Data on this Portal are provided by BBP as-is and as-available, and BBP makes no representations or warranties of any kind, express or implied, about the completeness, accuracy, reliability, suitability or availability, non-infringement, fitness for a particular purpose, absence of latent of other defects of the Data. Any reliance you place on Data is therefore strictly at your own risk.
LIMITATION OF LIABILITY
You assume all responsibility for any use of the Data offered on the Portal. In no event shall BBP/EPFL, its directors, officers, employees, agents, licensees, licensors, contributors, founders or advisors, or any other person who has been involved in the creation or production of the Portal or Data be liable for any direct, indirect, special, incidental, or consequential damages, lost profits, lost sales, or loss of goodwill, loss of data.
GOVERNING LAW
The laws of Switzerland govern these Terms. The exclusive place of jurisdiction shall be Lausanne, Switzerland.
TERMINATION
We may suspend or terminate your access to the Data at any time, without notice, and for any reason. If you fail to comply with these Terms, you no longer have authorization to use the Data and the Portal, and any and all rights granted to you under the Terms are revoked. Your obligations under these Terms will continue upon termination of your rights.