Genomics Metadata Multiplexing Student Intern Project

Introduction

Core sequencing facilities, such as WEHI Genomics, process hundreds of sequencing runs every year. They have to keep track of the how samples are merged (multiplexed) so that they can be uncoupled (demultiplexed) after the sample has been digitised (sequenced) through the sequencing machine. This is a type of metadata.

While this allows the sequencing facility to save money by processing samples in bulk, the ability to keep track of these multiplexes is complicated. This is especially significant because there is no resourcing to provide an assistant to be able to check the quality all the metadata at the time of multiplexing.

We will propose to do a proof-of-concept to help track multiplexing and other sample transformations as part of the WEHI Genomics facility.

Duties while on placement

The Research Software Engineer Intern role will:

• work closely with researchers to identify their needs around genomics metadata multiplexing
• Review the options available for building a proof-of-concept application based on maintainability and extensibility
• Implement, build, or trial applications to test fit-for-purpose

There is also a fair amount of flexibility with this project to allow the student to inject their own ideas and introduce new features and functionality.

Skills and Pre-requisites

Skills and Pre-requisites:

• Basic knowledge or ability to learn quickly Java/Javascript/CSS, databases and Linux command-line
• Ability to learn and understand high-level concepts quickly
• Ability to work independently and to report to a group and discuss theories and results
• Good analytical skills
• Working with git would be an advantage

Benefits for students

Benefits for students whilst undertaking the internship include:

• Each student will get hands on experience in working in an emerging research software environment within a highly regarded medical research institute.
• Gain understanding of how real-world software is assessed, developed and how priorities and requirements are established within a research environment.
• Gain understanding of the importance of maintainable, scalable and extensible code.
• Improving oral and written communication skills in a team environment.

Further reading

• Genomics Metadata Multiplexing