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Reference : UMR5086-LUCMON-003
Workplace : LYON 07
Date of publication : Thursday, June 3, 2021
Type of Contract : FTC Technical / Administrative
Contract Period : 11 months
Expected date of employment : 1 September 2021
Proportion of work : Full time
Remuneration : about 1600€/month (gross salary)
Desired level of education : 5-year university degree
Experience required : Indifferent
The recruited ITA will be part of the bioinformatics team of MMSB (UMR 5086 ; équipe MOBI). He/she will have 2 main tasks: (1) to guarantee the development and maintenance of bioinformatics tools for simulation of proteins at the coarse-grained level (Martini 3 force field) ; (2) to contribute to the different tasks planned for the ANR project MixAndMove.
The recruited person will be responsible for:
• Contribute to the various tasks linked to the modeling of proteins involved in the intracellular transport of phosphatidilserine (PS), which is the main subject of the ANR MixAndMove project.
• Develop and implement algorithms for the preparation of CG simulations with the Martini 3 force field.
• Contribute to the development of the Martini 3 force field for proteins; in particular, the recruited ITA will take care of the optimization of the different elastic network models.
• Develop and implement new methodologies for the analysis of trajectories of molecular simulations, carried out by the MOBI team.
• Train newcomers to the MOBI team in good programming practices, the use of IT resources available in the MOBI team, and data storage.
• Maintain programs and libraries installed on the laboratory's computing cluster.
• Update the development environments of the workstations used by the non-permanent members of the MOBI team.
• General theoretical knowledge in the field of structural biology (biological membranes, membrane proteins).
• General knowledge of the principles of physical chemistry determining the structure of biological macromolecules (in particular proteins and lipid membranes) and their interactions.
• Theoretical and practical knowledge of the principles and algorithms of molecular dynamics, and in particular of the GROMACS software.
• Theoretical knowledge and desired experience with the Martini 3 force field.
• Practical knowledge of the Linux operating system (including the basics of systems administration), bash language and computer task schedulers for computation clusters.
• Working knowledge of Python language and its libraries of scientific calculations and data analysis.
MMSB has set up a scientific computing infrastructure (576 CPU, 2GPU) and an infrastructure dedicated to web services (96 CPU, 2 GPU). At MMSB, the MOBI team (bioinformatics and molecular modeling) is involved in the development of the Martini force field, a collaborative project that involves several research teams in different countries.
The recruitment of an ITA will allow the continuation of the work in progress related to the development of the Martini force field, and in particular the MixAndMove project.
Constraints and risks
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