Date : 15/03/2012

Laboratory
Laboratoire de Biochimie Théorique
UPR 9080, CNRS, Univ Paris Diderot, Sorbonne Paris Cité
IBPC, 13 rue Pierre et Marie Curie
75005 Paris
Website
Main discipline : Biophysics
Lab director : Philippe Derremeaux

PhD Supervisors
Marc Baaden / Antoine Taly
email : This e-mail address is being protected from spam bots, you need JavaScript enabled to view it / This e-mail address is being protected from spam bots, you need JavaScript enabled to view it
phone: +33 0 6 09 84 32 17 / +33 1 58 41 51 66

Subjects
1.: Molecular visualization
2.: Structural biology
3.: Molecular properties and classification

Tools and Methodologies
1.: Unity3D game engine
2.: Prototyping platform
3.: BioBlender


This project has applied for a european funding (Marie Curie FP7 ITN IDP 2012)
within the "Wiser Games" Innovative Doctoral Program of the FdV School.

* Eligible candidates under ITN IDP regulations :

- Early Stage Researchers must be (at the time of recruitment by the host organization) : in the first four years (full-time equivalent) of their research careers and not yet have been awarded a doctoral degree. This is measured from the date when they obtained the degree which would formally entitle them to embark on a doctorate, either in the country in which the degree was obtained or in the country in which the research training is provided, irrespective of whether or not a doctorate is envisaged.

- At the time of recruitment by the host organization, researchers must not have resided or carried out their main activity (work, studies, etc) in the country of their host organization for more than 12 months in the 3 years immediately prior to the reference date.

Summary of lab's interests
Our lab has solid and internationally recognized expertise in computational modeling of biological systems. This includes the development of tools for interactive simulations and molecular visualization. We have started to port these developments to the Unity3D game engine, with our UnityMol project. Building up on this solid foundation, we now aim to expand on challenging scientific discovery games, promising a strong link and novel between citizens and research.

Summary of project
This project will extend our UnityMol application implemented with the Unity3D game engine towards a platform for prototyping scientific discovery games related to structural biology. As a validation of this development, we will simultaneously create a serious game aimed at the human classification of biological structures based on the visual analysis of a variety of properties (topology, shape, electrostatic profile, lipophilicity, etc.). Several levels of scientific applications are possible, e.g. small-scale to specific families of molecules, large-scale to structural databases or even extending to models of yet unsolved sequences. The aim is to deliver a prototype game for human classification of proteins. This work will be carried out in close collaboration with Monica Zoppe in Italy, an internationally recognized expert in the field, developing the BioBlender tool that we will use in preparing game assets. Research Objectives: - creation of a structural biology toolkit for scientific discovery games - educational tool with intuitive learning about the molecular properties of proteins

Interdisciplinarity of the project
In this project, several disciplines are united: structural biology and molecular modeling form the basis for the content of the game, computer science is required to build state-of-art molecular visualizations and handle the technical challenges imposed by a game engine programming environment. Perceptual and cognitive issues - a domain of expertise of our international partner - are also important to convey the properties of molecules, an entity that lay people have never before encountered.