Timeline and Achievements


Blue Brain co-develops COVID-19 Diagnostic Implementation Simulator
With the EPFL Blue Brain Project’s determination to make our computing resources and expertise available for the fight against COVID-19, we brought our experience in software development to team up with the Foundation for Innovative New Diagnostics (FIND). FIND is a global non-profit organization focused on diagnostics, currently co-convening the Access to COVID-19 Tools (ACT) Accelerator Diagnostics Partnership alongside The Global Fund, as a key part of the global response to the pandemic. According to the World Health Organization (WHO), diagnostic testing for COVID-19 is critical to tracking SARS-CoV-2 (the virus responsible for COVID-19), understanding epidemiology, informing case management, and suppressing transmission. With diagnostics emerging as one of the most pressing issues in the COVID-19 crisis, Blue Brain has collaborated with FIND to develop a Diagnostic Implementation Simulator for SARS-CoV-2 diagnostics. 

Blue Brain Nexus Forge: Building and using Knowledge Graphs made easy
A deluge in digital data, the trend for cross-disciplinary and multi-modal scientific investigations along with the tremendous computing power now available, has led to team based, data-driven and data-intensive methods commonly used in science. These advances also come with a set of challenges summarized in the FAIR (1) guiding principles for research data management – make heterogeneous data generated from different contexts, Findable, Accessible, Interoperable and Reusable. Accordingly, Knowledge Graphs have become the go-to key solution across both research and industry to address these challenges.

EPFL and ETH Zurich deliver Academic Resources platform for COVID-19
With Switzerland starting to transition out of lockdown, testing for SARS-CoV-2, being a cornerstone of all response strategies, is more important than ever in order to contain the risk of a renewed increase in cases as public life slowly picks up again. Ensuring an adequate number of daily tests for this task requires precise and timely distribution of equipment, supplies and other resources. To support this endeavor, the EPFL Blue Brain Project and ETH Zurich, as part of the National COVID-19 Science Task Force, are collaborating with Spiez Laboratory on an online platform, Academic Resources for COVID-19 (ARC), to match critical support needed by Switzerland’s diagnostic laboratories with the support offered by the Swiss academic sector.

Blue Brain enable next generation brain simulations with performance modelling
Scientists at the Blue Brain Project have extended performance modelling techniques to the field of computational brain science resulting in findings that are useful for today and indispensable for the future. In a paper published in Neuroinformatics, we provide a quantitative appraisal of the performance landscape of brain tissue simulations, and analyze in detail the relationship between an in silico experiment, the underlying neuron and connectivity model, the simulation algorithm and the hardware platform being used. Thereby deriving the first analytical performance models of detailed brain tissue simulations, which is a concrete step to enable the next generation of brain tissue simulations.

Neuron_Reduce – a brand new tool to simplify complex neuron models.
Blue Brain collaboration with the Hebrew University of Jerusalem.
For the first time, Scientists at the Hebrew University of Jerusalem and the Blue Brain Project have formulated a unique analytical approach to the challenge of reducing the complexity of neuron models while retaining their key input/output functions and their computational capabilities. ‘Neuron_Reduce’ is a new computational tool that provides the scientific community with a straightforward capability to simplify complex neuron models of any cell type and still faithfully preserve its input-output properties while significantly reducing simulation run-time.


Blue Brain finds the secret to how neurons in the mouse neocortex form billions of synaptic connections
Researchers at Blue Brain have combined two high profile, large-scale datasets to produce something completely new – a first draft model of the rules guiding neuron-to-neuron connectivity of a whole mouse neocortex. Based on these rules, we were able to generate statistical instances of the micro-connectome of 10 million neurons, a model spanning five orders of magnitude and containing 88 billion synaptic connections that will serve as the basis of the world’s largest-scale simulations of detailed neural circuits.

Brain finds order amidst chaos
How does the brain find order amidst a sea of noise and chaos? Blue Brain found the answer to this long-standing question by using advanced simulation techniques to investigate the way neurons talk to each other while submerged in a sea of noise and chaos. In a paper published in Nature Communications, we found that by working as a team, cortical neurons can respond even to weak input against the backdrop of noise and chaos, allowing the brain to find order.

Blue Brain ion channel study beckons first whole-brain simulation
The Blue Brain Project’s ‘Channelpedia’ is open to brain modellers and pharmacologists everywhere. Pores at the surface of neurons and muscle cells control your every thought, movement; the very beating of your heart. The way the pores behave – that is open, close, or lock for a short time (inactivate) depending on voltage – shapes signals in the form of electrical charge (ions) moving across the cell surface. For the first time, we have mapped the behavior of the largest family of these voltage-gated ion channels: Kv channels. Published in Frontiers in Cellular Neuroscience, with freely available online data.

Blue Brain solves a century-old neuroscience problem
In a front-cover paper published in Cerebral Cortex, Blue Brain explains how the shapes of neurons can be classified using mathematical methods from the field of algebraic topology. Neuroscientists can now start building a formal catalogue for all the types of cells in the brain. Onto this catalogue of cells, they can systematically map the function and role in disease of each type of neuron in the brain.

Second NM2 Conference Concluded
After the launch in 2017 of our Neuromodulation of Neural Microcircuits NM² Conference series, we concluded a second stimulating, interactive and highly collaborative event. https://actu.epfl.ch/news/second-neuromodulation-of-neural-microcircuits-con/

Blue Brain builds the first next-generation models of thalamocortical neurons
In July 2019, Blue Brain announces it has built the first next-generation models of thalamocortical neurons. These digital models of thalamocortical neurons were built using state-of-the art optimization techniques, which directly constrain unknown parameter values with experimental data.


Blue Brain Nexus: an open-source knowledge graph for data-driven science
The Blue Brain Project creates and open sources Blue Brain Nexus, which allows the building of data integration platforms. Blue Brain Nexus enables data-driven science through searching, integrating and tracking large-scale data and models.

Blue Brain Project deploys HPE supercomputer for digital reconstruction and simulations of the mammalian brain to advance the understanding of the brain
In July, Hewlett Packard Enterprise (HPE) announced that the EPFL Blue Brain Project had selected HPE to build a next-generation supercomputer for modeling and simulation of the mammalian brain. The new supercomputer, called ‘Blue Brain 5’, will be dedicated to simulation neuroscience, in particular simulation-based research, analysis and visualization, to advance the understanding of the brain.

The Blue Brain Portal
– a knowledge space for simulation neuroscience is launched as a public resource
Released in August, the Blue Brain Portal brings together in one place open-sourced software, tools, models and data, both from us and our collaborators. The aim is for this knowledge to be utilized by both the neuroscientific and the wider scientific community to develop the field of simulation neuroscience.

Blue Brain Project releases first-ever digital 3D brain cell atlas
Like “going from hand-drawn maps to Google Earth,” the Blue Brain Cell Atlas allows anyone to visualize every region in the mouse brain, cell-by-cell – and freely download data for new analyses and modelling.

The first digital 3D atlas of every cell in the mouse brain provides neuroscientists with previously unavailable information on major cell types, numbers and positions in all 737 brain regions – which will potentially accelerate progress in brain science massively.


Blue Brain Team Discovers a Multi-Dimensional Universe in Brain Networks
A team of scientists led by the Blue Brain Project used a sophisticated type of mathematics in a way that it has never been used before in neuroscience. The team uncovered a universe of multi-dimensional geometrical structures and spaces within the networks of the brain.

This research, published in Frontiers in Computational Neuroscience, has significant implications for our understanding of the brain.

Blue Brain Project launches three-day conference to kick-start neuromodulation research – NM2
The NM2 Conference was conceived to address understanding the mechanisms by which neuromodulators operate which is both fundamental to Blue Brain’s pioneering work in simulating brain function and dysfunction, and for the global neuroscience community

Leading experts from around the world presented and took part in panel discussions across the three days. Additionally, the NM2 Conference provided a unique platform for students and junior researchers to interact with leaders in the field to collectively take part in shaping the future course of neuromodulatory research.


The Blue Brain Project releases the Blue Brain Python Optimization Library (BluePyOpt)an extensible open source framework for data-driven model parameter optimization that wraps and standardizes several existing open-source tools. The library includes methods for setting up small- and large-scale optimizations on a broad range of compute platforms – from laptops to large cloud-based compute infrastructures.


Blue Brain reaches a major milestone with the publication of a first draft of the digital reconstruction of neocortical microcircuitry (Markram et al, 2015). The study confirmed the feasibility of building and simulating a digital copy of a part of the brain and demonstrated that multidisciplinary Big Science in the field of neuroscience yields favorable results (82 scientists contributed to the study).

The paper, which appeared in the journal Cell, represents the most complete description of any neural microcircuit to date. It provides a complete digital map of all the cells and synapses in a block of neural tissue and describes simulation experiments replicating a range of previous in vivo experiments. In other words, our digital copy of a part of the brain behaves like a real part of the brain.

Most significantly, this study advances the case for simulation as a useful new method in neuroscience. It proves that we understand the basic properties of the components and interconnections of the brain well enough to be able to reconstruct and simulate certain physiological functions. This advance makes it feasible, in principle, to reconstruct the human brain even though we can never measure all its parts.

The Neocortical Microcircuit collaboration portal is an online public resource of the Blue Brain Project’s first release of a digital reconstruction of the microcircuitry of juvenile Rat somatosensory cortex. Click here to access to experimental data sets used in the reconstruction and the resulting models.


The Blue Brain Project Computing team continues to improve the efficiency and scope of Blue Brain computing tools and supercomputing infrastructure. A series of publications describe the new tools.

In June, the BBP replaces its previous supercomputer (the BlueGene/P) with a BlueGene/Q machine (Blue Brain 4) hosted at the Swiss National Computing Centre (CSCS) in Lugano. The new machine offers higher performance and expanded memory.

In the same month, Blue Brain, IBM Research and ETH Zürich announce a collaboration to develop a new hybrid memory strategy for supercomputers, matching the heavy memory requirements for reconstructions of large volumes of neural tissue (brain regions, whole brains).

The Blue Brain Project completes validated digital reconstructions of neural microcircuitry in the brain of young rats. Work begins on a major paper, presenting the reconstruction, and on online resources, making the results available to the broader community.


On January 28, the EU Commission announces that it has selected the Human Brain Project as one of its two FET Flagship projects. Work on the project begins in October 2013, with the Blue Brain team playing a leading role. EPFL hosts the project’s first “Summit Meeting”.

The Blue Brain Project is officially granted the status of a Swiss National Research Infrastructure, funded by the ETH Board.

Two important Blue Brain publications describe the use of Blue Brain Project models to identify and characterize “neuronal clusters” in neural microcircuits, and to predict local field potentials.


In April, the Human Brain Project consortium concludes its preparatory study and publishes a public report. In October the HBP consortium submits its formal application to become a FET Flagship project. The Blue Brain team coordinates the preparation of the proposal.

An important paper in PNAS describes Blue Brain-developed methods, making it possible to predict the connectivity of neocortical microcircuitry.

At the Neuroscience 2012 conference in New Orleans, the Blue Brain Project presents more than 20 posters, describing a first reconstruction of the rat cortical column.


In January, the European Commission informs the Human Brain Project consortium that it has been selected to perform a preparatory study. Work on the study begins in May, coordinated by members of the Blue Brain Project.

The project hires new engineers and scientists. In November, the enlarged team moves to new office space in the EPFL Innovation Park. The project publishes several high impact papers describing new methods to generate cell models and in silico studies of virtual brain tissue.


The Blue Brain Project drives the formation of a Consortium to participate in the European Commission’s newly launched FET Flagship Programme. In December, the new consortium applies to the Commission to fund a large scale research project – the Human Brain Project. The goal of the new project is to understand the human brain and its diseases and, ultimately, to emulate its computational capabilities. A key objective is to reconstruct and simulate the whole human brain. The approach described in the project proposal builds on the methods and tools developed in the Blue Brain Project.


In June, thanks to the CADMOS initiative, the Blue Brain Project’s BlueGene/L supercomputer is replaced by a BlueGene/P, with double the number of processors . The new machine represents a major increase in Blue Brain computing power.

“In silico” experimentation is in full swing, testing the behaviour of Blue Brain Project models against results from other research groups. The results provide new insights into the principles underlying the construction of neocortical microcircuitry.


The Blue Brain team tests the accuracy of its model-building against anatomical and physiological data from laboratory experiments. In June, an article in the HFSP Journal summarizes the on-going debate on the size and location of functional cortical columns


In January, Prof. Henry Markram presents the project to the Davos forum.

November 26 marks the end of the first phase of the project, which announces the completion of an initial model of the rat cortical column.


In February, the project takes shape. An article in Nature Reviews Neuroscience by Prof. Henry Markram describes the project’s goals and methods.

During the summer, the BBP team generates its first model of a cortical column, using a simplified neuron model.


In June, the EPFL and IBM sign an agreement to launch the Blue Brain Project (BBP). The agreement provides for the installation of a BlueGene supercomputer on the EPFL campus.