Community Models of Hippocampus
Accessing most of our resources requires an account on the Brain Simulation Platform (BSP). To obtain your free account on the BSP, please email firstname.lastname@example.org
To become familiar with the BSP you can start from the Guidebook
A suite of use cases and a model collab are available here.
Single cell building is available here.
An integrated workflow for single cell building and in silico experiments is available here.
You can discover the models we have built in the HBP Model Catalog.
The hippocampus (wikipedia, scholarpedia) is a brain region that is known to play a key role in memory and spatial navigation, and is also heavily involved in brain disorders such as Alzheimer’s disease and epilepsy. Yet, despite intensive experimental and theoretical study, the mechanisms through which the hippocampus contributes to these cognitive functions and dysfunctions are poorly understood.
What makes the hippocampus special?
The hippocampus is an evolutionarily conserved, old cortical region. Its structure is significantly simpler than that of neocortex, but it is also in many ways (e.g., in terms of its main cell types) similar to other cortical areas, which makes it a popular target for experimental studies. Functionally, it is a high-level multimodal associational area linking many different types of information, and it is indispensable for remembering personal events (“episodes”) and is important for learning new facts. It also contains neurons that explicitly encode location in space (the so-called “place cells”); these are critical ingredients in the brain system responsible for navigation.
What are the specific questions we want to address in the HBP?
Our primary goal is to develop and test strategies for fostering community convergence through data-driven reconstruction and simulation of the hippocampus. A taskforce of HBP partners works with the hippocampus community to develop community-driven models and tools. These include models of hippocampal neurons and synapses, cellular level models from the microcircuit to the whole hippocampus, simplified versions of models for use in in silico experimentation, and a validation suite for neurons, synapses and networks. In addition, we use the models we develop to address scientific questions regarding the operation and functions of hippocampal cells and networks (including, for instance, the origins and consequences of neuronal variability, and the mechanisms underlying the generation of different types of oscillations in the hippocampus).
What is our specific take?
Building upon existing tools and the HBP platforms, we wish to create a collaborative environment for building, sharing, running, testing, and comparing data-driven models of the hippocampus (and other brain regions). In doing so, we also aim to promote a new way of building models in neuroscience, which is based on unambiguous identification of all data sources, model components, and assumptions; generic model representations; reproducible workflows; and extensive, automatic validations.
Building a model of hippocampus from sparse, fragmented data, and improving our understanding of hippocampal function, requires a critical mass of people and expertise, and can only be achieved in a collaborative manner.
In March 2015, the HBP-sponsored workshop HippocampCA1 initiated a community effort to model the hippocampus in an integrative manner. In May 2017, we followed up with the Hippocamp2017 workshop and we plan to make these workshops a recurring event for the community.
At present, the project already involves several HBP partners (in experimental and theoretical neuroscience, neuroinformatics, brain simulation, high-performance computing, and neurorobotics), and several non-HBP groups have expressed their interest in contributing data, using the models, or participating in the modelling effort.
In March 2016, we released (internally) a first draft model of area CA1 of the rodent hippocampus. In June 2017, a new version was released; the single cell models and the 3D cell placement were made available via the Brain Simulation Platform. New releases are planned to occur approximately every 6 months (the next one is expected in April 2018). Several publications are in preparation, and our corresponding models will be publicly released at the time of publication. Optimized models of single neurons in area CA1, as well as the full model for the CA1 region are expected to be released in 2018. Models for the CA2, CA3 and DG regions, for both rat and mouse, are at the initial stages of the workflow. Simplified versions of the neuronal and circuit models will also be available.
Who is Involved?
Building and simulating a model of hippocampus requires a critical mass of people and expertise. The following people and their teams are currently the main contributors of this effort:
Audrey Mercer, University College London
Michele Migliore, , Institute of Biophysics, National Research Council
Eilif Muller, Blue Brain Project, École Polytechnique Fédérale de Lausanne
Armando Romani, Blue Brain Project, École Polytechnique Fédérale de Lausanne
Benefits to the Community
Model use: If you simply want to use some of the results of our work (e.g. take a CA1 pyramidal neuron for a spin, create your own variant thereof, analyse a CA1 network, etc.) you can go to the Brain Simulation Platform and launch one of the respective use cases. Alternatively, you can download data and models; they will be made available upon publication of the relevant paper(s).
Participate in community modelling: We would be happy to hear from you. If you would like to get involved and contribute to our community effort, please contact any of us to discuss our common interests. Email email@example.com