Consultant - Bioinformatics Pipeline Automation Specialist

Overview

Support the Animal Production and Health Laboratory in modernizing bioinformatics infrastructure.

You have:

• Advanced university degree (masters) in Genomics/Bioinformatics or another related field.
• Minimum five years of experience in bioinformatics training and capacity building on data analysis pipelines, bacterial and viral genomics, and machine learning methods for disease prediction.
• Strong background in High-Performance Computing facility management.
• Good oral and written command of English. Knowledge of other official IAEA languages (Arabic, Chinese, French, Russian and Spanish) is an asset.

Organizational Setting

The Department of Nuclear Sciences and Applications implements the IAEA's Major Programme 2, "Nuclear Techniques for Development and Environmental Protection". This Major Programme comprises individual programmes on food and agriculture, human health, water resources, environment and radiation technologies. These programmes are supported by laboratories in Seibersdorf, Monaco and Vienna. The Major Programme's objective is to enhance the capacity of Member States to meet basic human needs and to assess and manage the marine and terrestrial environments through the use of nuclear and isotopic techniques in sustainable development programmes.

The Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture assists Member States of the Food and Agriculture Organization of the United Nations (FAO) and the IAEA in using nuclear techniques and related technologies to improve food security, alleviate poverty and promote sustainable agriculture. The Joint Centre consists of five Sections, each with an associated laboratory (located in Seibersdorf, 45 km south-east of Vienna), in the areas of: animal production and health; plant breeding and genetics; insect pest control; soil and water management and crop nutrition; and food and environmental protection.

The Animal Production and Health Section and Laboratory assist Member States in improving livestock productivity through the efficient use of locally available feed resources, reproduction and breeding practices, and disease diagnostic tools and control measures.

Main Purpose

The consultant will support the Animal Production and Health Laboratory (APHL) in modernizing its bioinformatics infrastructure. Key responsibilities include configuring research servers into a High-Performance Computing (HPC) cluster and deploying a local Galaxy instance to enhance pipeline accessibility.

The consultant will establish automated workflows for Whole Genome Sequencing (WGS), Shotgun Metagenomics, and Metatranscriptomics, utilizing Machine Learning (ML) and advanced bioinformatics. These pipelines must support multiple platforms, including Oxford Nanopore, Ion Torrent, PacBio, and ilium ina.

A major focus is capacity building for the November 2026 APHL course. The consultant will develop a dedicated Virtual Machine (VM) and syntax-highlighted instructional materials. These efforts strengthen APHL's role as a World Organisation for Animal Health (WOAH) Collaborating Centre and support the Food and Agriculture Organization of the United Nations (FAO) network, enabling high-quality genomic analysis and disease diagnosis for Member States.

Functions / Key Results Expected

• Provide technical expertise in establishing automated pipelines for the analysis and visualization of WGS, Shotgun Metagenomic, and Metatranscriptomic datasets.
• Carry out an analysis for Whole Genome Sequencing (WGS), Shotgun Metagenomic, and Metatranscriptomic data utilizing advanced bioinformatics and Machine Learning (ML) tools.
• Provide technical input to Configure research and training servers into a high-performance computer cluster optimized for large-scale data analysis.
• Provide expertise in deploying a local instance of Galaxy on research servers and migrate existing APHL pipelines into Galaxy Workflows to enhance accessibility for APHL staff.
• Contribute to the update of current APHL bioinformatics pipelines to support data analysis for Oxford Nanopore, Ion Torrent (S5), PacBio, and Iliumina platforms.
• Provide technical expertise in preparing comprehensive training materials for the APHL course scheduled for November 2026.
• Develop a dedicated Virtual Machine (VM) pre-loaded with necessary software and create syntax-highlighted instructional materials to ensure effective learning for trainees.

Knowledge, Skills and Abilities

• Animal Diseases

Qualifications and Experience

• Advanced university degree (masters) in Genomics/ Bioinformatics or another related field.
• Minimum five years of experience in bioinformatics training and capacity building on data analysis pipelines, bacterial and viral genomics, and machine learning methods for disease prediction.
• Strong background in High-Performance Computing facility management.
• Good oral and written command of English. Knowledge of other official IAEA languages (Arabic, Chinese, French, Russian and Spanish) is an asset.

Remuneration

The remuneration for this consultancy is a daily fee of up to a maximum of € 260, based on qualifications and experience. In case duty travel is required within the assignment, a daily subsistence allowance (DSA) and travel costs are provided. Health coverage and pension fund are the responsibility of the incumbent.

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Potential interview questions

Added 5 months ago - Updated 5 months ago - Source: iaea.org