Mots-Clés
Glycogenomics
database
web interface
Description
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Enhancements of fsec-DB : a database/web interface for fungal secretomics data
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Filamentous fungi degrade plant cell wall polymers using secreted enzymes to acquire nutrients. They hence play pivotal roles in the carbon cycle via the degradation of dead organic matter, and constitute invaluable resources for the biotechnological production of chemicals from renewable biomass, as an alternative to fossil reserves. Depending on the type of glycans and environments, fungi are exposed to constraints affecting their growth and degradation capabilities, and hence their secretomes.
The candidate will integrate the OxyMist project which aims to decipher the role of O2 in the degradation ability of the microbial communities. This collaborative project involves teams from Copenhagen, Cambridge and Marseille. In Marseille, the OxyMist project is piloted by the INRAE laboratory BBF which has a long-standing collaboration with the Glycogenomics group in AFMB laboratory. The Glycogenomics group, who will host the internship, maintains and develops since >20 years the CAZy database, the worlwide reference classification of enzyme families involved in glycan assembly and breakdown. Both laboratories are located on the Luminy campus in the middle of the Calanques National Park.
The missions of the candidate will be to improve several aspects of an existing database/web interface, fsec-DB that allow the exploration of secretomics data. This encompasses : (i) evaluating the database structure; (ii) adding a user management system; (iii) developping scripts to automatize both future insertion of novel secretomes and the regular updates of a part of the data (CAZy and Interpro annotations); (iv) integrate statistical analysis of this omics data and visualisation of these, to help in interpreting the data and building research hypotheses.
Expected skills:
Programming (Python, PHP, and/or corresponding frameworks)
Database management (SQL, phpmyadmin)
Bioinformatics of sequence analysis (Interproscan, blast, hmmer)
Statistics and visualisation (R and Rshiny)
Communication (oral, written and electronic)
Additional knowledge in biotechnology, glycobiology, fungal analysis, integration of -omics data could be an added value.
A personnal computer will be provided in the office and an access to to an in-house computing cluster is possible
References
https://pubmed.ncbi.nlm.nih.gov/30976326
https://pubmed.ncbi.nlm.nih.gov/34850161