Ludovic Autin

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Increasingly complex research has made it more difficult to prepare data for publication, education, and outreach. Many scientists must also wade through black-box code to interface computational algorithms from diverse sources to supplement their bench work. To reduce these barriers we have developed an open-source plug-in, embedded Python Molecular Viewer(More)
As knowledge of individual biological processes grows, it becomes increasingly useful to frame new findings within their larger biological contexts in order to generate new systems-scale hypotheses. This report highlights two major iterations of a whole virus model of HIV-1, generated with the cellPACK software. cellPACK integrates structural and systems(More)
cellPACK assembles computational models of the biological mesoscale, an intermediate scale (10-100 nm) between molecular and cellular biology scales. cellPACK's modular architecture unites existing and novel packing algorithms to generate, visualize and analyze comprehensive three-dimensional models of complex biological environments that integrate data(More)
Proteins take on their function in the cell by interacting with other proteins or biomolecular complexes. To study this process, computational methods, collectively named protein docking, are used to predict the position and orientation of a protein ligand when it is bound to a protein receptor or enzyme, taking into account chemical or physical criteria.(More)
The Protein Movie Generator (PMG) is an online service able to generate high-quality pictures and animations for which one can then define simple storyboards. The PMG can therefore efficiently illustrate concepts such as molecular motion or formation/dissociation of complexes. Emphasis is put on the simplicity of animation generation. Rendering is achieved(More)
In this article we introduce cellVIEW, a new system to interactively visualize large biomolecular datasets on the atomic level. Our tool is unique and has been specifically designed to match the ambitions of our domain experts to model and interactively visualize structures comprised of several billions atom. The cellVIEW system integrates acceleration(More)
The uPy Python extension module provides a uniform abstraction of the APIs of several 3D computer graphics programs (called hosts), including Blender, Maya, Cinema 4D, and DejaVu. A plug-in written with uPy can run in all uPy-supported hosts. Using uPy, researchers have created complex plug-ins for molecular and cellular modeling and visualization. uPy can(More)
HIV-1 is rare among viruses for having a low number of envelope glycoprotein (Env) spikes per virion, i.e., ∼7 to 14. This exceptional feature has been associated with avoidance of humoral immunity, i.e., B cell activation and antibody neutralization. Virus-like particles (VLPs) with increased density of Env are being pursued for vaccine development;(More)
Protein docking studies how proteins combine with each other in 3d, in order to better understand their biological functions. The basic hypothesis of the french research projet CoRSAIRe is that Virtual Reality (VR) multimodal interactions can increase efficiency in reaching docking solutions. To this end, we have conducted an ergonomic analysis of the(More)
In scientific illustrations and visualization, cutaway views are often employed as an effective technique for occlusion management in densely packed scenes. We propose a novel method for authoring cutaway illustrations of mesoscopic biological models. In contrast to the existing cutaway algorithms, we take advantage of the specific nature of the biological(More)