IT Systems Specialist – Linux at KEMRI Wellcome Trust Research Programme (KWTRP)

Reference Number: IT-SSL02062021

Category: Epidemiology and Demography

Job Grade: 7.01

JOB PURPOSE: 

This will be a full-time job. The candidate will be responsible for providing a robust Linux System Administration support to our genomics and bioinformatics team and to work with the IT team in technical matters such as network integration and hardware selection. In addition, the holder will provide support in the development of custom bioinformatics tools, software, databases, and web interface and provide standard bioinformatics tools and software installation and maintenance supporting a range of genomics and machine learning projects aimed at understanding the COVID-19 transmission dynamics in Kenya and building viral genomics capacity across East Africa.

Description: 

REPORTS TO:

• Head of IT
• Infrastructure Manager

BUDGET AND RESOURCE RESPONSIBILITY:

Advice on the management of resources to plan, estimate and carry out Bioinformatics support. This should be within budget, meet quality specifications and targets in accordance with appropriate industry standards.

KEY RESPONSIBILITIES:

• Install, configure, tune, and troubleshoot a suite of Linux storage and compute servers including dedicated GPU servers (Tesla V100 and A100).
• Improve the current server architecture (e.g., setup and install GNU-Guix to support a consistent whole-system configuration mechanism and easily setup transactional server upgrades).
• Setup and deploy container-based solutions to end-users and clients.
• Organise and manage day-to-day Linux HPC operations that support the institute’s research activities including the production efforts of the bioinformatics team that generates and analyses next-generation sequencing data.
• Ensure that the computing equipment is maintained at peak performance by evaluating software and security updates.
• Participate and enhance automation of the Next Generation Sequencing (NGS) processes e.g., maintenance of NGS pipelines and server status for a nascent and evolving HPC environment.
• Work with the Bioinformatics lead, Head of IT to ensure HPC issues are resolved in a timely manner.
• Perform routine Linux system audits, system upgrades, reporting and carries out preventive maintenance of the systems.
• Installing and configuration of modules on the Linux environment.
• Responsible for articulating technical opinion on issues related to Linux infrastructure.
• Responsible for business continuity and disaster recovery for the Linux ecosystem.
• Overseeing and assisting in managing bioinformatics modules running through there lifecycle on the Linux servers.
• Building and evolving architectural diagrams for Bioinformatics environment and providing documentation for all processes.
• To carry out projects to implement new Linux system solutions.

QUALIFICATIONS:

Essential

• BSc in Computer Science, IT, Physics or Mathematics (Upper second class or higher); Masters Degree is an added advantage.
• Minimum 5 Years experience with 3 Years’ at Supervisory level
• Expert knowledge of Linux operating (e.g., RedHat or Centos, Debian etc.) and file systems (GlusterFS, Lustre, JuiceFS etc.)
• Experience working with multiple GPUs including the NVIDIA series.
• Demonstrated knowledge of system monitoring and strong scripting skills (Bash or Perl
• Working knowledge of ICT environments, equipment and devices and ability to install and maintain computer equipment.
• Ability to establish and maintain working relationships with managers and end-users or clients.
• Linux support and Management – shell scripting.
• Experience in installing and supporting Linux environment.

Desirable

• Undertaken and completed an advanced Certification in Linux System Administration e.g., GCUX, Linux+, LFCE (Linux Foundation certified Engineer)
• Experience with GPU virtualization, Docker, Kubernetes and Singularity
• Knowledge and capability in systems programming e.g., C, C++, or Rust,
• Knowledge and capability in scripting languages e.g., Python, Julia, R
• Experience is supporting a 20+ server environment.
• Experience working in a research establishment

SKILLS AND COMPETENCIES:

• Linux Certification, i.e., RHCE, (Must give evidence of the exam certificate done by an authorised testing body, i.e., Pearson VUE, Prometric, etc.)
• The ability to plan own workload and keep accurate scientific records in a changing work priorities environment.
• Excellent communication (Oral and written) and interpersonal skills

RELATIONSHIPS:

• Working in collaboration with members of the IT and the bioinformatics/genomics teams across the Kilifi and Nairobi hubs.