Monday, May 3, 2021
Thursday, April 22, 2021
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.
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.
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 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 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.
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 create membranes based on 3D meshes. This allows the construction of complex membranes where mesh faces are filled with proteins.
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.
See here for detailed documentation of the source code.
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.
docker run -ti --rm -p 5000:8200 bluebrain/bioexplorer
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
Code is here :
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:
docker run -ti --rm -p 8080:8080 bluebrain/brayns-ui:1.0.0
Open a browser on: http://localhost:8080/?host=localhost:8200
Saturday, April 11, 2020
Data is fake for now, but working on it...
PS: Use Chrome, Firefox does not seem to like my webpage.
Wednesday, February 26, 2020
"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
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
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
Wednesday, August 7, 2019
Tuesday, May 21, 2019
Wednesday, January 30, 2019
Saturday, January 12, 2019
Your mission if you accept itThe 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.
Tuesday, October 2, 2018
Blue Brain Brayns, A platform for high fidelity large-scale and interactive visualization of scientific data and brain structuresThe 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.