Research Software Engineer (FlowJo Alternatives)

Introduction

The Walter and Eliza Hall Institute (WEHI) Research Computing Platform (RCP) is seeking dedicated interns to research and evaluate alternatives to FlowJo, assessing both desktop and web-based software options. The ideal candidates will leverage their backgrounds in biology, R/Shiny, mathematics/statistics, or bioinformatics to contribute to a multi-disciplinary team.

FlowJo is a widely used software application designed for analyzing flow cytometry data, primarily from Fluorescence-Activated Cell Sorting (FACS) experiments. FACS is a sophisticated laboratory technique that uses laser-based technology to sort and analyze cells or particles in a fluid stream based on their fluorescent characteristics. FlowJo facilitates the interpretation of complex data generated by FACS, allowing researchers to visualize cell populations, quantify specific markers, and perform multi-parametric analysis.

Duties while on placement - The Research Software Engineer Intern role will:

• Conduct research to identify existing alternatives to FlowJo. This will involve evaluating open-source and commercial software solutions across platforms (Linux, Windows, and Mac).
• Investigate the feasibility of creating an R Shiny application to serve as an alternative or complement to existing software solutions.
• Since the internship will operate without direct input from researchers, interns will need to gather insights solely from online resources, employing a best-effort approach.
• Work with FACS files integrated with the Genomics Metadata Multiplexing intern project if appropriate, ensuring that any alternative solutions can manage these types of data effectively.
• Identify challenges encountered with current software options and propose potential solutions.
• Document the setup processes and usage of any prototype applications developed using synthetic data.
• Analyse and improve the user experience (UX) and user interface (UI) of alternative software by reviewing feedback and performance metrics.
• Collaborate within the intern team to brainstorm and prototype cost-effective solutions that reduce maintenance and improve usability.

Skills and Pre-requisites

We are aiming to build a multi-disciplinary team where each person would have at least one of these skill sets:

• basic knowledge or ability to learn quickly R/Shiny/Javascript/CSS and Linux command-line
• basic knowledge or ability to learn quickly high-level biology / bioinformatics
• basic knowledge or ability to learn quickly high level mathematics/statistics
• basic knowledge or ability to learn quickly organisational, project management, and communication skills

All people in this multi-disciplinary team should:

• have the ability to synthesise data, understand software usability, and critically analyse code to identify and address performance issues,
• be motivated to work alongside a diverse team, sharing ideas and tackling challenges collectively,
• be able to tolerate or learn to tolerate complexity, and
• be able to tolerate or learn to tolerate ambiguity.

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.

Benefits for students

The student will gain practical Research Software Engineering (RSE) experience with potential exposure to Flask, Virtual Machines, and how to improve business workflows.

The student will gain understanding of how real-world software is assessed, developed and how priorities and requirements are established within a research environment.

The student will have an opportunity to self-direct and be proactive in their approach to a new environment.