SIB Swiss Institute of Bioinformatics is a non-profit organization federating 70 Swiss research and service groups of experts in bioinformatics. SIB's 800 scientists join forces to empower advances in life sciences and health by providing life scientists and clinicians with state-of-the-art bioinformatics resources, services, expertise, and Training.

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To reinforce our team in Geneva, Switzerland, we are seeking a Bioinformatician.
Bioinformatician

Employer

SIB Swiss Institute of Bioinformatics


Work Location

Geneva, Switzerland


Employment fraction

100%


Type of contract

temporary

Job description

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.

Profile requirements

The successful applicant will be:

  • proficient in java and javascript, with some experience in using d3.js
  • 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 

How to apply
SIB is committed to ensuring and fostering diversity and equal opportunities in the workplace as well as in the scientific ecosystem.

If you are interested in this challenging and highly interesting position, please submit your application including CV and letter of motivation through our online portal by clicking the "Apply" button.