ELIXIR Software developer data management tools

Ghent VIB-UGent Center for Plant Systems Biology

15 Jan 2019

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 bioinformatic tools, resources and experts into a distributed infrastructure that enables researchers across Europe to share and analyze their life-science research data.

The Belgian ELIXIR node has been awarded a grant from the Flemish government to build a data management and data analysis infrastructure for life-sciences. The overall aim of this project is to build an interoperable data infrastructure that provides tailored solutions to enable researchers in life-sciences to focus on their research question, rather than technical details of data, interoperability, compute resources, …. We will build on, and further develop, existing internationally used frameworks and technologies such as FAIRDOMHub (https://fairdomhub.org) for data management, and Galaxy (https://www.usegalaxy.be and https://usegalaxy.eu) and containers (http://biocontainers.pro) for data analysis. To extend the ELIXIR team, we have 5 vacancies available within VIB.

This project is in close collaboration with international partners involved in ELIXIR and aligned with initiatives in life-sciences in the context of FAIR data and the European Open Science Cloud.  In short, if you’re interested in contributing to building the data research infrastructure for the future for life-sciences, these positions should be of interest to you. We are building a multidisciplinary team, therefore we are looking for talented people with complimentary expertise. 

Job description

Modern (molecular) biology rests on the generation, sharing and integrated analysis of digital data. Connecting the large amounts of digital life-science data fosters innovation, allowing to address major societal challenges. For this to succeed, research data and digital services need to be Findable, Accessible, Interoperable, and Reusable (FAIR). With ELIXIR Belgium, we will provide tools and guidance for researchers to facilitate the process of making their data FAIR.  This will be pursued by a hands-on approach in which we provide actionable best practices for commonly used data types and software development. As a Software developer for data management tools, you

  • will be responsible to set up, maintain and further develop the FAIRDOM open source platform that will be deployed as a tool for research data management,
  • will leverage FAIRDOM’s Application Programming Interfaces (APIs) to integrate existing systems or specialized platforms as the data management planning tool dmponline.be, the data analysis platform Galaxy, and the PSB Interface for Plant Phenotype Analysis platform (PIPPA),
  • will collaborate closely with the Data Steward and the developers of the respective platforms.

Profile

Essential

  • Bachelor or Master in computer science, bioinformatics, (bio)engineering, biotechnology or equivalent
  • Demonstrated programming experience e.g. in Python, Ruby, PHP
  • Knowledgeable of W3C standards, technologies and best practices in web development
  • Willing and able to learn and implement new technologies
  • Fluent in English, with good communication skills
  • Able to work both independently as well as in a team 

Desirable but not required

  • Experience in working with life-science data is an advantage
  • Experience with (some of) the mentioned platforms or technologies is an asset
  • Experience with virtualization technologies (e.g. Docker) is a plus
  • Experience with automated deployment tools (Puppet, Ansible, etc.) is a plus
  • Version control experience, GIT knowledge is a plus
  • Experience with Linux/Unix environments and BASH scripting 

We offer

  • A fulltime 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 user-friendly ecosystem of platforms for data management
  • A challenging and stimulating work environment with opportunities for personal input, at the edge of developments in this area in Europe
  • Engaging with the large life-sciences network across Europe of ELIXIR
  • Work place 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 which 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, transcriptomics 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.