Monday, May 3, 2021

Elevated blood glucose levels as a primary risk factor for the severity of COVID-19

The paper is out (pre-print for now)!

Abstract

SARS-CoV-2 started spreading towards the end of 2019 causing COVID-19, a disease that reached pandemic proportions among the human population within months. The reasons for the spectrum of differences in the severity of the disease across the population, and in particular why the disease affects more severely the aging population and those with specific preconditions are unclear. We developed machine learning models to mine 240,000 scientific papers openly accessible in the CORD-19 database, and constructed knowledge graphs to synthesize the extracted information and navigate the collective knowledge in an attempt to search for a potential common underlying reason for disease severity. The literature repeatedly pointed to elevated blood glucose as a key facilitator in the progression of COVID-19. Indeed, when we retraced the steps of the SARS-CoV-2 infection we found evidence linking elevated glucose to each step of the life-cycle of the virus, progression of the disease, and presentation of symptoms. Specifically, elevations of glucose provide ideal conditions for the virus to evade and weaken the first level of the immune defense system in the lungs, gain access to deep alveolar cells, bind to the ACE2 receptor and enter the pulmonary cells, accelerate replication of the virus within cells increasing cell death and inducing an pulmonary inflammatory response, which overwhelms an already weakened innate immune system to trigger an avalanche of systemic infections, inflammation and cell damage, a cytokine storm and thrombotic events. We tested the feasibility of the hypothesis by analyzing data across papers, reconstructing atomistically the virus at the surface of the pulmonary airways, and performing quantitative computational modeling of the effects of glucose levels on the infection process. We conclude that elevation in glucose levels can facilitate the progression of the disease through multiple mechanisms and can explain much of the variance in disease severity seen across the population. The study proposes diagnostic recommendations, new areas of research and potential treatments, and cautions on treatment strategies and critical care conditions that induce elevations in blood glucose levels.

English commentaries
 
French commentaries

Thursday, April 22, 2021

Blue Brain BioExplorer

I have just released the Blue Brain BioExplorer, a tool for scientists to extract and analyse scientific data from visualization. BBBE is built on top of Blue Brain Brayns, the Blue Brain rendering platform.

 

 

Architecture

The BBBE application is built on top of Brayns, the Blue Brain rendering platform. The role of the application is to use the underlying technical capabilities of the rendering platform to create large scale and accurate 3D scenes from Jupyter notebooks.

General components

Assemblies

Assemblies are groups of biological elements, such as proteins, membranes, glycans, etc. As an example, a virion is made of a lipid membrane, spikes proteins, an RNA sequence, etc, and all those elements belong to the same object. That’s why they need to belong to the same container, the assembly. Assemblies can have different shapes: Sphere, Cube, etc, that are automatically generated according to the parameters of individual components.

Proteins

Proteins are loaded from PDB files. Atoms, non-polymer chemicals and bonds can be loaded and displayed in various colour schemes: chain id, atom, residue, etc. Proteins also contain the amino acid sequences of the individual chains. Sequences that can be used to query glycosylation sites, or functional regions of the protein.

Glycans

Glycans are small proteins that are attached to an existing protein of the assembly. Individual glycan trees are loaded from PDB files and attached to the glycosylation sites of the specified protein. By default, glycans are attached to all available glycosylation sites, but a set of specific sites can be specified.

RNA sequence

An RNA sequence can be loaded from a text sequence of codons. Various shapes can be selected to represent the RNA sequence: Trefoil knot, torus, star, etc. This allows the sequence to be efficiently packed into a given volume. A different color is assigned per type of codon.

Mesh-based membranes

Mesh-based membranes create membranes based on 3D meshes. This allows the construction of complex membranes where mesh faces are filled with proteins.

Python SDK

A simple API if exposed via the BBBE python library. The API allows scientists to easily create and modify assemblies, according the biological parameters. The BBBE programming language is not necessarily reflecting the underlying implementation, but is meant to be as simple as close as possible to the language used by the scientists to describe biological assemblies.

Documentation

See here for detailed documentation of the source code.

Deployment

BBBE binaries are publicaly available as docker images. BBE is designed to run in distributed mode, and is composed of 3 modules: A server, a python SDK, and a web user interface. This means that there are 3 docker images to be downloaded on run. Those images can of course run on different machines.

In this example, we will expose the server on port 5000, the python SDK jupyter notebooks on port 5001, and the user inferface on port 5002. One is free to change those ports at will.

Server

docker run -ti --rm -p 5000:8200 bluebrain/bioexplorer

Python SDK

docker run -ti --rm -p 5001:8888 bluebrain/bioexplorer-python-sdk

Web User Interface

docker run -ti --rm -p 5002:8080 bluebrain/bioexplorer-ui

Friday, December 25, 2020

Black Holes Suck!

 
 
I recently needed to explain my young 10 years old nephew what a black hole was, so I ported the Black hole with accretion disk shader toy to Brayns.

Code is here :

https://github.com/favreau/Brayns-UC-BlackHole


A docker image is available:

Run Black Hole plugin back-end using:

docker run -ti --rm -p 8200:8200 favreau/blackhole:0.1.0

Use the Blue Brain UI to visualize the Black Hole in your browser:  

https://hub.docker.com/r/bluebrain/brayns-ui

docker run -ti --rm -p 8080:8080 bluebrain/brayns-ui:1.0.0

Open a browser on: http://localhost:8080/?host=localhost:8200

Wednesday, February 26, 2020

Neurones, les intelligences simulées (Centre Pompidou)

Incredibly happy and proud to have created the Blue Brain Project movie that is currently being displayed at the Centre Pompidou. A world class modern art museum located in Paris.

"Alors que l’intelligence artificielle semble avoir envahi tous les domaines industriels du monde contemporain, de la finance au domaine médical, des jeux aux objets à comportement, de l’architecture au militaire, cette situation n’a jamais été véritablement mise en relation avec l’histoire des neurosciences et de la neuro-computation. L’exposition « Neurones, les intelligences simulées » souligne la continuité des recherches d’artistes, d’architectes, de designers et de musiciens avec celle développées par les grands laboratoires scientifiques ou ceux du monde industriel. Dans le cadre de « Mutations/Créations ».


Avec « Mutations/Créations », le Centre Pompidou se transforme en laboratoire de la création et de l’innovation à la frontière des arts, de la science, et de l’ingénierie. Chaque année, le programme réunit des artistes, des ingénieurs, des scientifiques et des entrepreneurs. En 2020, « Mutations/Créations » poursuit sa recherche prospective au travers de deux expositions, « Neurones, les intelligences simulées » et « Jeremy Shaw », après trois éditions successivement consacrées à l’impression 3D (« Imprimer le monde » et « Ross Lovegrove » en 2017), aux langages informatiques (« Coder le monde » et « Ryoji Ikeda » en 2018) et à la création mêlant artificiel et vivant (« La Fabrique du vivant » et « Erika Verzutti » en 2019)."



          More information available here.


Tuesday, January 28, 2020

Biggest and Most Detailed Map of the Fly Brain

Thanks to the amazing dataset provided by HHMI Janelia, I had to to see it by myself, and decided to create the few renders below





Dataset is downloadable from here: https://www.janelia.org/news/unveiling-the-biggest-and-most-detailed-map-of-the-fly-brain-yet





Saturday, December 7, 2019

Hemispheres of the Mind

Hemispheres of the Mind is a collaboration between the EPFL Laboratory of Experimental Museology and the EPFL Blue Brain Project for the ArtLab Infinity Room II 2019. 

A collaboration between Cyrille Favreau (Blue Brain Project),  Sarah Kenderdine (eM+ EPFL) and Peter Morse for ArtLab Infinity Room II 2019 celebrating 50 years of Ecole polytechnique fédérale de Lausanne.

Special thanks to Grigori Chevtchenko for the fisheye camera implementation, and Paweł Podhajski for allowing the deployment of Brayns on the Blue Brain Supercomputer.


Audio Production by Peter Morse and Cathie Travers.
Music by Kai Engel & Cathie Travers

#epfl #project #laboratory #bluebrainproject #brain #sciart




Tuesday, May 21, 2019

Journal for Neuroscience cover published!

Making an image of the brain always is a challenge. The idea behind the cover image is to pay tribute to the amazing work initiated by Camillo Golgi back in the late 19th century. His discovery of a staining technique called black reaction changed the way one could visualize brain structures. Recent studies have shown that the aesthetic of images representing data visualization in neuro-science plays a significant role in the way those image are understood. In the last years, computer technologies have improved dramatically, together with the field of computational neuro-science. Thanks to advanced computer graphics techniques, it is now possible to reconstruct realistic shapes of neurons from a set of points and radii describing the structure of the cell. Many of those data sets for single neurons can be found on the web. Combining them together and placing them in space makes it a simple way to imagine what regions of the brain could look like if they were to be seen using Golgi’s technique. In the near future, it seems clear that realistic, physically based rendering of in-silico data will become a necessary tool to understand how the brain functions. But if those new tools are very promising, one should not forget the work of the pioneers, and this is what this cover image is all about.

Wednesday, January 30, 2019

Celebrating the beauty of the brain






So... I played, and I won :) I somehow became the winner of the NeuroArt contest for December 2018, which is great

I am extremely happy to be one the winners of the NeuroArt contest for December 2018.

Making an image of the brain always is a challenge. The idea behind the cover image is to pay tribute to the amazing work initiated by Camillo Golgi back in the late 19th century. His discovery of a staining technique called black reaction changed the way one could visualize brain structures. Recent studies have shown that the aesthetic of images representing data visualization in neuroscience plays a significant role in the way those image are understood.

In the last years, computer technologies have improved dramatically, together with the field of computational neuroscience. Thanks to advanced computer graphics techniques, it is now possible to reconstruct realistic shapes of neurons from a set of points and radii describing the structure of the cell. Many of those datasets for single neurons can be found on the web. Combining them together and placing them in space makes it a simple way to imagine what regions of the brain could look like if they were to be seen using Golgi’s technique.

In the near future, it seems clear that realistic, physically based rendering of in-silico data will become a necessary tool to understand how the brain functions.
But if those new tools are very promising, one should not forget the work of the pioneers, and this is what this cover image is all about.


Saturday, January 12, 2019

Full stack/frontend software engineer wanted!

Your mission if you accept it

The EPFL Blue Brain Project (BBP), situated on the Campus Biotech in Geneva, Switzerland, applies advanced neuroinformatics, data analytics, high-performance computing and simulation-based approaches to the challenge of understanding the structure and function of the mammalian brain in health and disease. The BBP provides the community with regular releases of data, models and tools to accelerate neuroscience discovery and clinical translation through open science and global collaboration.

We are looking for a self motivated full stack/frontend software engineer (W/M) to join our team and help us with the development of our visualization tools.

You will be working in a dynamic team with highly skilled software engineers and our goal is to aid scientists in visualizing and understanding their (neuroscientific) data.

Main duties and responsibilities include :

Your responsibility will be to develop new features for our current interactive 3D viewer Brayns (on the frontend) and maintain existing ones, and to drive the development of our new hub application where the scientists can manage their data visualizations.
 
More information available here.


Tuesday, October 2, 2018

Talk at EPFL - Visual Computing Seminar

Super excited to visit Wenzel Jacob and give the following talk in the context of the Visual Computing Seminars.

Blue Brain Brayns, A platform for high fidelity large-scale and interactive visualization of scientific data and brain structures

The Blue Brain Project has made major efforts to create morphologically accurate neurons to simulate sub-cellular and electrical activities, for example, molecular simulations of neuron biochemistry or multi-scale simulations of neuronal function.

One of the keys towards understanding how the brain works as a whole, is visualization of how the individual cells function. In particular, the more morphologically accurate the visualization can be, the easier it is for experts in the biological field to validate cell structures; photo-realistic rendering is therefore important. Brayns is a visualization platform that can interactively perform high-quality and high-fidelity rendering of neuroscience large data sets. Thanks to its client/server architecture, Brayns can be run in the cloud as well as on a supercomputer, and stream the rendering to any browser, either in a web UI or a Jupyter notebook.

At the Blue Brain project, the Visualization team makes intensive use of Blue Brain Brayns to produce ultra-high resolution movies (8K) and high-fidelity images for scientific publications. Brayns is also used to serve immersive visualization on the large displays, as well as unique devices such as the curved OpenDeck located at the Blue Brain office.

Brayns is also designed to accelerate scientific visualization, and to adapt to the large number of environments. Thanks to its modular architecture, Brayns makes it easy to use various rendering back-ends such as Intel's OSPRay (CPU) or NVIDIA's OptiX for example. Every scientific use-case such as DICOM, DTI, Blue Brain research, etc, is a standalone plug-in that runs on top of Brayns, allowing scientists and researchers to benefit from a high performance/fidelity/quality rendering system, without having to deal with the technical complexity of it.

Brayns currently implements a number of basic primitives such as meshes, volumes, point clouds, parametric geometries, and pioneers new rendering modalities for scientific visualization, like signed distance fields.

During this talk, I will explain the motivations behind the creation of the Brayns platform, give some technical insight about the architecture of the system and the various techniques that we already use to render datasets. I will also describe how new datasets, as well as rendering components (engines, shaders, materials, etc), can be added to the platform.

Links:
https://github.com/BlueBrain/Brayns
http://rgl.epfl.ch/courses/VCS18f