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About

Biomolecule random walk analysis

I am in charge of developping the TRamWAy Python library for random walk analysis. The library features multiple tools to build processing chains/pipelines for the spatial or spatio-temporal resolution of physical properties of moving biomolecules such as observed using localization microscopy techniques. These tools include – but are not limited to – tracking biomolecules, segmenting space and time to sample from the identified displacements, and infer local parameters such as diffusivity and effective potential energy or force/drift. This latter inference step is based on a model that derives from the overdamped Langevin equation. In addition, these computation steps can be assembled into a pipeline and TRamWAy can dispatch the computations from a local Jupyter notebook onto a remote high-performance-computing cluster such as Maestro (at Institut Pasteur). I have also developed various analysis applications based on TRamWAy in the context of projects such as Mapping Receptor Dynamics in Synapses. I took part in collaborations that aimed at analyzing the dynamics of GlyB receptors in synapses, of Gag proteins at the membrane of CD4+ lymphocytes, and I still contribute to studies on the formation of Virus-Like Particles, with localization microscopy data for various molecules such as Tetherin, GT46 and CD59.

Modelling of the Drosophila larva behaviour

I have taken an increasingly active part in the main research axis of the G5 Decision and Bayesian Computation group: Deciding in Complex Environments. I first brought technical support to various collaborating groups with the deployment of the behaviour-tagging pipeline solution developed by Jean-Baptiste Masson. I did so at Tomoko Ohyama’s lab at McGill University, Montreal, Canada, and at Marta Zlatic’s lab at the Laboratory of Molecular Biology in Cambridge, UK. I also implemented extensive parts of the data management and data processing automated pipeline at Tihana Jovanic’s lab at NeuroPSI in Gif-sur-Yvette, France, from the experimental setup (acquisition station) to Institut Pasteur, and then back to NeuroPSI. Lately, I am working on building a dictionary of behavioural responses using string metrics on string-like representations of the responses.

Courses

Scientific Programming in Python

The ever growing usage of high throughput technologies in Biology is revolutionizing the life sciences and profoundly changing its practices. Scripting languages are used on a daily basis in life science labs in order […]

2017-03-06 09:30:00 2017-03-18 17:00:00 Europe/Paris Scientific Programming in Python The ever growing usage of high throughput technologies in Biology is revolutionizing the life sciences and profoundly changing its practices. Scripting languages are used on a daily basis in life science labs in order […] 25 Rue du Dr Roux, 75015 Paris, France

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