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Blue Brain BioExplorer

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Description

Exploration relies on building software that combines data integration, analysis and interactive visualization to build, modify and navigate through large scientific datasets. For this, Blue Brain built and open-sourced the Blue Brain BioExplorer. The Blue Brain BioExplorer (BBBE), which started as an internal project, is now open source. It was originally developed to answer key scientific questions related to the Coronavirus as a use case and to deliver a visualization tool. Today, the BBBE allows to reconstruct, visualize, explore and describe in detail the structure and function of highly-detailed biological structures such as molecular systems, neurons, astrocytes, blood vessels, and more. You can see the first application of the BBBE in 'A Machine-Generated View of the Role of Blood Glucose Levels in the Severity of COVID-19' study, and see the SARS-COV-2 coronavirus as you have never seen it before by clicking on the following image!

<div align="center"> <a href="https://youtu.be/Czn-YGLGfiA"/> <img src="https://github.com/BlueBrain/BioExplorer/blob/master/bioexplorer/pythonsdk/doc/source/images/covid19_movie_preview.png" style="width:50%;"> </a> </div>

On the third anniversary of the first lock-down, we look back at how #MachineLearning helped reveal the role of blood glucose levels in the severity of COVID-19. Imagine what else could be tackled with OpenScience.

<div align="center"> <a href="https://lnkd.in/e57vqgcq"/> <img src="https://github.com/BlueBrain/BioExplorer/blob/master/bioexplorer/pythonsdk/doc/source/images/covid19_documentary_preview.png" style="width:50%;"> </a> </div>

An extended and improved CCFv3 annotation

The Blue Brain Project presents the first comprehensive mouse brain atlas based on the Allen Institute’s Common Coordinate Framework version 3. This atlas includes anatomical Nissl reference data that has been precisely aligned within this reference space, providing the scientific community with a crucial tool for automated and accurate mapping of a wide range of histological slices or volumes of the mouse brain. We have also integrated additional layers, such as the spinal cord, barrel columns, as well as the granular and molecular layers in the cerebellum. This allowed us to create an enhanced version of our cell atlas, mapping every cell in the mouse brain by location, region, and type. From this data, properties such as neuron soma and morphology can be derived, paving the way for increasingly accurate simulation models.

<div align="center"> <a href="https://www.youtube.com/watch?v=upulBqczL0g"/> <img src="https://github.com/BlueBrain/BioExplorer/blob/master/bioexplorer/pythonsdk/doc/source/images/ccfv3_movie_preview.png" style="width:50%;"> </a> </div>

• An extended and improved CCFv3 annotation and Nissl atlas of the entire mouse brain

The Harvard Brain

Do you want want to know more about the full story? Read the Studies In Silico: An Interview With Cyrille Favreau On EPFL’s Blue Brain Project.

Social Media

• Blue Brain BioExplorer 1.6 goes RTX!
• On the third anniversary of the first lockdown, we look back at how Machine Learning helped reveal the role of blood glucose levels in the severity of COVID-19.
• If you’re traveling to Spain over the holiday break, don’t miss the amazing exhibition Brain(s) opening soon in Madrid featuring images from the EPFL Blue Brain Project. Join the more than 86'000 visitors who already enjoyed it while on its Barcelona stop!
• The BlueBrainBioExplorer 1.4 is now out and ready to explore additional bio assemblies from neurons and astrocytes to vasculatures and more!
• The EPFL Blue Brain Project will be featuring in the exciting Brain(s) exhibition at the Barcelona Centre of Contemporary Culture starting tomorrow!

BioExplorer at PASC 2023

<div align="center"> <img src="https://www.pasc-conference.org/wp-content/uploads/2022/07/PASC_23_2.jpg" width="25%" height="25%" alt="Image" /> </div> On the 27th of June 2023, the Blue Brain BioExplorer was presented at the PASC23 conference in Davos (Switzerland), as part of the *MS4E - Scientific Visualization of Big Data* minisymposium: [Visual Scientific Exploration at Blue Brain, and Beyond](https://pasc23.pasc-conference.org/presentation/?id=msa164&sess=sess168)

BioExplorer goes RTX!

BioExplorer now benefits from NVIDIA OptiX backend compatibility, allowing it to fully utilize the NVIDIA RTX acceleration hardware capabilities for fast and high-quality rendering of scientific datasets. This advanced feature, along with the new stereo perspective camera, enables virtual reality use-cases with pure ray-tracing. Additionally, an AI-powered denoiser has been incorporated to enhance the real-time rendering quality.

Simply add the OptiX engine command line argument when starting the BBBE.

service --engine optix6 --plugin BioExplorer

Note that, in order to offer the best experience on local desktops, the BBBE now also has a native viewer.

viewer --engine optix6 --plugin BioExplorer

At the museum

July 2022: The EPFL Blue Brain Project is featuring in the exciting Brain(s) exhibition at the Barcelona Centre of Contemporary Culture at the Fundación Telefónica Madrid.

<div align="center"> <img src="https://actu.epfl.ch/image/121700/1108x622.jpg" width="50%" height="50%" alt="Image" /> </div>

The Blue Brain images on show were created with the BBBE. Checkout the news article for more information.

Architecture

The BBBE application is built on top of a fork of Blue Brain Brayns 1.0.0 , the Blue Brain rendering platform. The BBBE uses the underlying technical capabilities of the rendering platform to create large scale and accurate 3D scenes from Jupyter notebooks.

More information can be found in the architecture documentation.

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 color 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. Individ