Data & Software Infrastructure Manager | GenomeWeb

Data & Software Infrastructure Manager

Job Location
Wellcome Genome Campus
near Cambridge
CB10 1SD
United Kingdom

EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation. The remuneration package comprises a competitive salary, a comprehensive pension scheme and health insurance, educational and other family related benefits where applicable, as well as financial support for relocation and installation. We provide a dynamic, international working environment and have close ties with both the University of Cambridge and the Wellcome Trust Sanger Institute.

EMBL-EBI staff also enjoy excellent sports facilities, a free shuttle bus to Cambridge and other nearby centres, an active sports and social club and an attractive working environment set in 55 acres of parkland.

The initial contract is for a period of 3 years with the possibility of a fixed-term extension.

Job Description

We are seeking to recruit a Data and Software Infrastructure Manager to join the Protein Data Bank in Europe team at the European Bioinformatics Institute (EMBL-EBI) located on the Wellcome Genome Campus near Cambridge in the UK.

Protein Data Bank in Europe (PDBe; is a world leader in the archiving and dissemination of 3D biomacromolecular structure data. Together with our international partners, PDBe accepts and curate depositions of structural data for the two global archives, the Protein Data Bank (PDB) and the Electton Microscopy Data Bank (EMDB).  PDBe also maintains a number of databases that support advanced search services for the structural biologists and the wider scientific community. The PDBe team consists of an international and inter-disciplinary mix of professionals. The post holder will have two roles: Data management: you will be involved in the development of the PDBe relational database infrastructure (including Oracle, MySQL and Postgres), working closely with the EBI database group DBA support.  Your main responsibilities will include maintenance and development of database resources and supporting the other team members in the database environment.  You will liaise with the EBI Technical Services team to maintain and further develop PDBe infrastructure and to keep abreast of and evaluate new technologies that could benefit the team.  You will also interact with other EBI team to benefit from their experience in setting up and managing similar systems.  Tasks include:

  • Further development of the PDBe database loading processes to capture new forms of data as they become available;
  • Helping other members of the team develop new databases;
  • Further development and maintenance of processes for data transfer (rsyncs, snap mirrors and ftp) pertaining to both data desposition and data delivery services;
  • Investigating new technologies and their use by other teams at EBI, and suggesting possible improvements to PDBe data-management practices.

Software infrastructure management:  this will involve monitoring, maintenance and further development of the PDBe weekly release process, and general upkeep of the PDBe compute infrastructure in liaison with the EBI Technical Services team (for example rebooting Tomcats or helping set up web servers).  The software infrastructure management role will be shared with another member of the PDBe team to ensure continuous support and prompt action.  You will interact with other EBI teams to understand practices and benefit from the experience in developing PDBe infrastructure.  Tasks include:

  • Monitoring and rebooting servers;
  • Advising other members of the team on systems-related issues and helping them with requisitioning resources from the Technical Services team;
  • Ensuring that the weekly release process runs smoothly.

This is a unique opportunity for the right candidate to make an impact on the exciting future of structural biology where access to integrated information across a range of length scales and from a variety of biological data resources will enable exciting new knowledge discovery. 


You will have a degree in a software engineering-related field with a minimum of 2 years work experience in developing and maintaining software. You will be fluent in Java, scripting languages (esp. Python), and in SQL.  You should be conversant in database concepts and in working on Linux-based platforms. Excellent written and oral communication skills are essential including fluency in English, ability to work in a team and with international collaborators, and attention to detail.  The position may require occasional travel, mainly in the UK.

About Our Organization

The EBI is part of the European Molecular Biology Laboratory (EMBL) and it is a world-leading bioinformatics centre providing biological data to the scientific community with expertise in data storage, analysis and representation. EMBL-EBI provides freely available data from life science experiments, performs basic research in computational biology and offers an extensive user training programme, supporting researchers in academic and industry.

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