ELIXIR Software developer cloud data processing

Ghent VIB-UGent Center for Plant Systems Biology

15 Jul 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

The PLAZA platform for comparative, evolutionary, and functional genomics is a data resource that integrates gene and genome information (https://bioinformatics.psb.ugent.be/plaza). It offers a wide variety of tools to end-users through a web interface, in order to help speed up both small-scale and large-scale data analyses. Multiple independent instances of the platform exist, where each instance either focuses on a different phylogenetic clade, or uses improved gene annotations and genome assemblies compared to previous instances. In order to scale up the building of these instances, we are looking for a software developer to help with moving the PLAZA platform to cloud-based systems. As a software developer,

  • you will be responsible for the design and implementation of the necessary tool-chain for building PLAZA instances in the cloud (e.g. OpenStack, Amazon cloud, Azure, etc.),
  • you will assist with the building of new PLAZA instances, and help with the implementation of unit-tests to check the status and validity of newly build PLAZA instances,
  • you will implement configuration and administration utilities for end-users, to facilitate building PLAZA instances.

You will be integrated in a dynamic research group, under the supervision of the primary developers of the PLAZA platform. Furthermore, you will have regular contacts with academic and industrial collaborators to explore novel technologies and boost new developments.

Profile

Essential

  • Bachelor or Master in computer science, bioinformatics, (bio)engineering, biotechnology or equivalent
  • Proficiency in at least one programming language (e.g. Java, Python, …) and one scripting language (e.g. Perl, Python, …)
  • Hands-on experience with Linux/Unix environments and BASH scripting
  • Good working knowledge of relational databases and SQL
  • Fluent in English, with good communication skills
  • Willing and able to learn and implement new technologies
  • Able to work both independently as well as in a team 

Desirable but not required

  • Knowledge of web development technologies (PHP, HTML, JavaScript, CSS)
  • Experience in working with life-science data
  • Experience with virtualization technologies (e.g. Docker)
  • Experience with automated deployment tools (e.g. Puppet, Ansible, etc.)
  • Version control experience (e.g. GIT)

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 on the successful renewal of the national project.
  • 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.