Research Software Engineer

Ghent VIB-UGent Center for Plant Systems Biology

22 Dec 2020

Ghent

VIB-UGent Center for Plant Systems Biology

Bio IT

1

Context

ELIXIR is the European life-sciences infrastructure for biological information. ELIXIR brings together bioinformatics tools, resources, and experts into a distributed infrastructure that enables researchers across Europe to share and analyze their life-science research data.

One of the key objectives of the Belgian ELIXIR node is to build data management and data analysis infrastructure for life-sciences. As such, we aim to provide tailored solutions to enable life sciences researchers to focus on their research question, rather than technical details of data, interoperability, compute resources, …. We are building on the internationally used platform FAIRDOM-SEEK (https://fairdomhub.org) for data management, and Galaxy (https://www.usegalaxy.be and https://usegalaxy.eu) for data analysis.

The ELIXIR Belgium research data analysis team is working in close collaboration with international partners involved in ELIXIR, the Galaxy project, and the H2020 EOSC-Life project. Our activities are aligned with initiatives in life-sciences in the context of FAIR data and the European Open Science Cloud.

Job description

Modern (molecular) biology rests on the generation, sharing, and integrated analysis of digital data. As life-sciences datasets grow larger and increasingly multidimensional, the computational resources required to process and analyze these “big data” frequently outgrow the capabilities of researchers. A powerful and flexible data analysis platform is key to pursue competitive and collaborative research.

Galaxy is an open-source, web-based platform for data-intensive biomedical research. The workflow management system provides support for reproducible science, facilitates the sharing of data and results, and removes the need for users to compile and install tools. In collaboration with the Galaxy Core Team and the ELIXIR Galaxy Community, we developed the useGalaxy.be instance which has been released for public use in 2019. As a Research Software Engineer, you

  • will assist in the implementation of specific data analysis workflows in the framework of our national and international activities,
  • will be responsible for designing and implementing use cases to further optimize the use of the useGalaxy.be platform,
  • will assess the needs of our community and find the most efficient approach to tackle these, making use of our current services and/or implementing new features when needed,
  • will be in close contact with researchers to evaluate their user experiences on the useGalaxy.be platform,
  • will work closely with the ELIXIR Belgium team, more specifically with our Galaxy developers and data scientists, and with the global Galaxy community

Profile

Essential

  • Bachelor or Master in computer science, bioinformatics, (bio)engineering, biotechnology or equivalent
  • Demonstrated programming experience in Python   
  • Hands-on experience with Linux/Unix environments
  • Experience with code versioning systems e.g. git
  • Willing and able to learn and implement new technologies
  • Fluent in English, with good communication skills
  • User-oriented attitude with a focus on service delivery
  • Able to work both independently as well as in a team 

Desirable but not required

  • Demonstrated experience with (some of) the mentioned platforms or technologies is an asset
  • Experience with working on a compute cluster is an asset
  • Experience with cloud computing is a plus
  • Experience with containers is a plus
  • Demonstrated activity in Open Source development is considered a plus
  • Knowledge or background in life-sciences is considered an advantage

We offer

  • A full-time position for 2 years initially. This is part of the long-term strategy for funding research infrastructures in Flanders, therefore prolongation is envisaged pending the successful renewal of the national project
  • Participation in the building of a future-proof, user-friendly ecosystem of a platform for data analysis open to all researchers, at the forefront of the developments in the European Open Science Cloud
  • An exciting international environment, engaging with the large life-sciences network across Europe of ELIXIR and the global Galaxy community
  • The workplace is the VIB-UGent Center for Plant Systems Biology (Ghent, Belgium)

About the institute and research infrastructure

The ELIXIR consortium (https://www.elixir-europe.org) is a European research infrastructure that unites life-science research groups. It coordinates, integrates, and sustains bioinformatics resources from the different member states.

The VIB-UGent Center for Plant Systems Biology (PSB, https://www.psb.ugent.be) is a world-leading plant science institute with the mission to integrate genetics, genomics, phenotyping, and bio-computing to unravel the biology of plants and to further explore the potential of plants to build a sustainable world.

The bioinformatics research groups at PSB develop novel software and web tools for the integration of large-scale data sets in the area of genomics, transcriptomic, and phenomics for which an extensive computational infrastructure is available on site. PSB coordinates the Belgian ELIXIR Node, more information on https://www.elixir-belgium.org.

How to apply?

Motivated candidates are asked to apply online.