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SIB Swiss Institute of Bioinformatics
Type of contract
Bioinformatics research in the Proteome Informatics Group is centered on molecular interactions taking place at the cell surface. This involves in particular, the development of integrated tools and databases to query knowledge of carbohydrates (glycans) attached to proteins, carbohydrate structures and protein-carbohydrate interactions.
In this overall picture, the present project focuses on bulky surface molecules called proteoglycans known as pathogen targets. However, solving their structure with precision is experimentally challenging. Sparse and scattered efforts to produce structural data can nonetheless be channeled into a pipeline to standardise description and collect relevant information. This work was manually initiated in a resource called MatrixDB (http://matrixdb.univ-lyon1.fr/) that describes and characterises interactions involving proteoglycans.
MatrixDB requires substantial updates both in content and implementation. In particular, it currently does not include data on host-pathogen interactions. It also needs to be modified to fit in the glycoinformatics ecosystem that we develop.
The associated tasks are:
- migration to classical database system such as PostGreSQL
- definition and implementation of RDF model
- definition and implementation of data analysis pipeline
- definition and implementation of interactome mapping tools These have to be completed in close collaboration with the team currently hosting MatrixDB and content curators.
The contract is for 1-year renewable once.
The successful applicant will be:
- experienced in using semantic web technologies
- experienced in data management systems
- knowledgeable in other programming languages such as Python
- cooperative and comfortable with interdisciplinary exchanges
Basic knowledge of molecular biology is a plus, especially in protein science.
The work will be conducted in both French and English. Fluent English is mandatory. Knowledge of French appreciated.
Start date: 01 Aug 2022
Application deadline: 01 Jul 2022