Exploration

Exploration relies on building software
that combines data integration, analysis
and interactive visualization to build,
modify and navigate through large
scientific datasets.

Blue Brain BioExplorer

The Blue Brain BioExplorer (BBBE) is a tool for scientists to extract and analyze scientific data from interactive exploration. The BBBE application is built on top of Blue Brain Brayns, the The BBBE uses the underlying technical capabilities of the rendering platform to create large scale and accurate 3D scenes from Jupyter notebooks.

BBBE started as an internal project within the Blue Brain to reconstruct, visualize, explore and describe in detail the structure and function of SARS-C0V-2 with the aim to answer key scientific questions related to the virus. Read the Blue Brain paper “A machine-generated view of the role of Blood Glucose Levels in the severity of COVID-19 published by Frontiers in Public Health.

Watch BBBE show the main impacts of high glucose in Airway Surface Liquid on the primary step of coronavirus infections in the lung and explain the increased susceptibility to respiratory viruses in at-risk patients.

Architecture

How to create Biological Assemblies

The BBBE is a tool that provides a simple API (Application Programming Interface) via a Python SDK (Software Development Kit). The API allows scientists to easily create and modify biological assemblies. The BBBE programming language is meant to be simple, and as close as possible to the language used by the scientists to describe molecular systems. The BBBE currently handles a number of components such as proteins or sugars, as well as more complex systems such as viruses or cell membranes.

Below explains how you can create these biological assemblies with the general components involved.

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.

As an example, an advanced Python API, with default coronavirus parameters, is provided by the BBBE:

for programming details:

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.

Glycan trees models located in the python sdk test folder were generated with Glycam Builder.

RNA sequence (work in progress)

The BBBE is a tool that provides a simple API (Application Programming Interface) via a Python SDK (Software DeAn 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

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

Virus

A viral particle (= “virus”) is an assembly consisting of a membrane, an RNA sequence, and a given number of S, M and E proteins. The virus has a predefined spherical shape defined by its radius. The default parameters for the virus are a radius of 45 nanometers, 62 S proteins, 42 E proteins, and 50 M proteins. Dimensions and concentrations were retrieved from the literature.

Membrane

A membrane is an assembly of phospholipids. Phospholipids structures are created following the process described in the VMD Membrane Proteins tutorial. The assembly itself is generated by the BioExplorer, for a given shape, and a number of instances of phospholipids.