We are seeking a highly motivated candidate to design and implement a next generation visualization platform for analysis of large-scale molecular simulations. In particular, we target two grand challenge applications: modeling a complete influenza virus and analyzing extensive simulations of the GLIC receptor that we recently published in Nature and PNAS, two leading journals. Project foundations were previously established, providing a well defined framework to get started (FvNano). Using visual analytics approaches and high performance interactive graphics, you will implement readily usable state-of-art tools scaling up to the next generation of simulations. This position is a unique training opportunity in a multi-disciplinary environment in collaboration with four leading teams in France and two international partners in the U.K. and in Germany.

PDF-page of this job offer and general background: http://exaviz.simlab.ibpc.fr
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Balises : Visualization, InEnglish, jobs

The FvNano project officially ended on 31 december 2011. We are currently updating the webpages because the project still produces output in the form of publications, posters, websites and code that can be downloaded and tested. Have a look at the FvNano webpage for the latest details.
FVNano-related research will continue in the ExaViz project about exa-scalable visual analysis for life & materials sciences. ExaViz already has its own website with a job section and several offers. An overall description of the project and the teams involved is also provided.

Balises : research, Visualization, InEnglish

I have added two talks on visualization to the teaching resources.

1. The first document explains some of the background related to molecular visualization on GPUs. It relates to a talk given at "Journée visu 2010" on 5-Oct-2010 at EDF Clamart: Visualizing Molecules on GPUs talk (PDF). You can also find related example code and extensive discussion at the HyperBalls website. A second, more detailed document is available, with some bits in French, some in English.
2. Ce document "La chimie fait son cinéma en visualisation moléculaire" explique quelques fondements de la visualisation sur cartes graphiques (GPU). Cette conférence a été présentée en mai 2011 aux MIEC-JIREC 2011. Vous pouvez télécharger le document ici: La chimie fait son cinéma en visualisation moléculaire (PDF, French+English).

Balises : InEnglish, EnFrançais, research, Visualization

The article "GPU-accelerated atom and dynamic bond visualization using hyperballs: A unified algorithm for balls, sticks, and hyperboloids" is now online at the Journal of Computational Chemistry website (see abstract below). There is a dedicated website about all things HyperBall, comprising some background information, a picture and movie gallery and download links: http://hyperballs.sourceforge.net.Read more...

Balises : research, InEnglish, Visualization, HotStuff

La représentation visuelle de la structure d’une molécule et de ses propriétés est centrale
dans l'enseignement de la chimie. Dans les années 60 par exemple, Kendrew fabriquait des
modèles en fil de fer comme outil pédagogique. L’utilisation des ordinateurs remonte à 1964,
quand Cyrus Levinthal et ses collègues du MIT ont animé sur un oscilloscope des modèles de
macromolécules, en « fil de fer » également. De nos jours, les illustrations de molécules
abondent, et tout le monde peut aisément créer de telles représentations, même sur des machines
de configuration modeste.

Néanmoins, ces dernières années marquent un tournant dans les possibilités de visualisation
offertes, et ce, notamment grâce aux progrès matériels et logiciels (cartes graphiques,
réalité augmentée, 3D,..). Un aspect concerne la visualisation interactive
d’édifices moléculaires de taille croissante, un autre les représentations de plus en plus
recherchées prenant en compte des effets d’ombre et de lumière à l'instar des productions
hollywoodiennes.

Le but de cet exposé sera d’illustrer l’évolution récente en visualisation scientifique de
systèmes moléculaires, que ce soit avec des dispositifs très courants ou par les technologies
immersives de la réalité virtuelle.

Le support de cette présentation est maintenant disponible sous forme de fichier PDF.

Balises : Visualization, EnFrançais, research

The visualization of field lines of the membrane-inserted BLT2 GPCR is implemented as WebGL-page using SpiderGL. There is an animation at my Youtube channel, a video that can be downloaded and a web-browser capable page at http://www.baaden.ibpc.fr/pub/blt2/jbn11.html. This visualization is supplementary material to the article Electrostatically-driven fast association and perdeuteration allow transferred cross-relaxation detection for G protein-coupled receptor ligands with equilibrium dissociation constants in the high-to-low nanomolar range by Catoire et al., Journal of Biomolecular NMR 2011.

Such molecular visualization applications of SpiderGL are described in more detail in M. Callieri et al., Visualization methods for molecular studies on the web platform, The Web3D 2010 Conference, 22-24 July 2010, Los Angeles, California

Balises : research, InEnglish, Visualization

In our paper "GPU-powered tools boost molecular visualization" we have an overview table with molecular visualization tools and methods that benefit from current GPU technology. You can now access an enhanced electronic version of this table with illustrations, software download links and videos to watch describing the methods. Check it out at http://www.baaden.ibpc.fr/projects/fvnano/gputools/.

Balises : research, InEnglish, HotStuff, Visualization