Scientific programmer supporting COVID-19 WikiPathways project

Scientific programmer supporting COVID-19 WikiPathways project

Published Deadline Location
21 Aug 6 Sep Maastricht

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Maastricht University is looking for a scientific programmer to join our COVID-19 project focused on improving our pathway curation tools and developing automated analysis workflows.

Job description

We are looking for a scientific programmer interested in joining the fight against COVID-19 and supporting us within the project “WikiPathways as a platform for COVID-19 pathway models” recently granted by the Dutch ZonMw funds. We focus on identifying underlying mechanisms explaining the differences in host immune response, disease severity and detection of mechanisms for targeted (drug) treatment”.

Within this project your main tasks are:

  1. Contributing to the COVID-19 Disease Map project, especially the conversion tools between our own GPML format and formats from other resources.
  2. Adding required new features to our pathway curation and analysis software PathVisio.
  3. Updating WikiPathways with new additional COVID-19 specific pathway information.
  4. Developing automated data analysis workflows in R and/or Python.
  5. Writing technical and user documentation.

Specifications

Maastricht University (UM)

Requirements

Function requirements

  • Bachelor or higher degree in computer science/bioinformatics or another relevant field
  • Good knowledge and programming experience in Java, Python and/or R
  • Experience with data analysis workflows is an advantage (Juypter notebooks, Galaxy)
  • Experience with computing platforms (cloud solutions, docker, etc.) is an advantage
  • Prior experience with WikiPathways and/or PathVisio is welcome
  • Experience in an agile environment is preferred
  • Technology-minded and willing to learn about new tools and technologies
  • English proficiency
  • Promote FAIR data and Open Science

Conditions of employment

Fixed-term contract: 2 years.

The terms of employment of Maastricht University are set out in the Collective Labour Agreement of Dutch Universities (CAO). Furthermore, local UM provisions also apply. For more information look at the website www.maastrichtuniversity.nl > Support > UM employees.

The position is temporary for the duration of 24 months, staring as soon as possible. Depending on experience and qualification, the gross monthly salary is scale 8 or 9 (max. € 4.012,-), based on a full-time appointment.

Department

The Department of Bioinformatics

The Department of Bioinformatics (https://www.maastrichtuniversity.nl/research/bioinformatics) has a dedicated, young, interdisciplinary team working in close collaboration with other scientists and institutions. Founded by Prof. dr. Chris Evelo in 2001, the research group is part of the NUTRIM School of Nutrition and Translational Research in Metabolism at the Faculty of Health, Medicine and Life Sciences at Maastricht University.

The department is involved in (inter)national initiatives to analyze, collect, share and integrate biological data. It uses a range of new methods and tools. These include:

  • high-throughput data analysis workflows
  • bioinformatics and cheminformatics software
  • structuring and collecting biological processes in WikiPathways
  • pathway analysis in PathVisio
  • network analysis in Cytoscape
  • semantic web tools using RDF, ontologies and SPARQL
  • FAIR data solutions
  • web services for all the above

Specifications

  • Research, development, innovation; IT
  • Natural sciences; Health
  • max. 38 hours per week
  • €2656—€4012 per month
  • University graduate
  • AT2020.248

Employer

Maastricht University (UM)

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Location

Universiteitssingel 50, 6229 ER, Maastricht

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