Société Française de Bioinformatique

Mots-Clés

Cell Painting Morphological profiling Computational toxicology Web server development

Description

This internship is part of the CellMorphTox project, which aims to develop innovative computational methods for chemical risk assessment using high-content imaging data. Recent advances in Cell Painting technology [1] have enabled the extraction of morphological profiles from cells exposed to a wide variety of chemicals, offering a promising alternative to animal testing in toxicology. Building upon this resource, we plan to create a user-friendly web server that allows the scientific community to mine Cell Painting data and predict potential toxicity risks.

The student will contribute to the design and implementation of the CellMorphTox web platform. The project will involve developing a relational database (MySQL) to store chemical structures, morphological signatures, and associated toxicity annotations. The intern will implement the server architecture using the Django framework. Key functionalities will include interactive visualization of chemical distributions in morphological space using dimensionality reduction methods (e.g., UMAP), radar plots for feature perturbations, and tools to compare new user-submitted profiles against reference data.
The project will be performed at the Profilage Pharmacologique In Silico (IsPP) team (U1133, INSERM), member of the Biological and Functional Adaptive unit (CNRS UMR 8251), Université Paris Cité under the supervision of Pr. Olivier Taboureau.

References:
[1] Bray, M. A., et al. (2016). Nature Protocols, https://doi.org/10.1038/nprot.2016.105

Skills: It is required to have some skills in bioinformatics, programming in Python and web development (preferably with Django). Familiarity with relational databases (MySQL) and data visualization libraries. Knowledge in toxicology and high content imaging and, web development (preferably with Django) are suitable but not mandatory.