The Benefits of an Open-Science Approach in Student Research Projects

Keywords: Open Science, Student Research, Collaboration, Methods

Abstract


Student projects can sometimes be overlooked when considering open science methods. This is perhaps because of the limited time available to complete the project, a lack of confidence in their open research skills by supervision staff or students, and lower expectations of publications resulting from student project work (particularly at undergraduate level). However, open science methods add value to student projects and provide benefits on several levels.

This talk describes from both the student and supervisor perspectives how open science can benefit student projects - from methods to management - using recent undergraduate projects as an example. We give a brief description of the concept of open science as we understand it and discuss the general benefits of an open science approach to research.

The Edward Wallace lab (School of Biological Sciences, University of Edinburgh) has run several student projects working with and extending the open source software tool 'riboviz' to process and analyse ribosome profiling sequencing datasets. This collaborative project worked with experts in the UK and USA and aimed to add new features and capabilities to riboviz, thoroughly documenting the software, and successfully using it to analyse a diverse range of datasets from organisms across the tree of life.

Student projects recreated existing published results using riboviz, developed new visualisation scripts, and added new optional features to the codebase to address specific research questions.

This talk discusses how both the student project and the riboviz project fit into open science research, covering how open science tools were used to plan, manage and carry out an open science project and the challenges these presented. For example, as this was a computer-based project, we discuss the tools and skills needed by the students to successfully complete the project, including programming skills (Unix command-line, R, Python) and version control (using Git and GitHub) and the open resources used to learn and develop these skills.

Open software tools such as version control are also explained in the context of student supervision and project management (for example how to use GitHub issue tickets for identifying and quickly solving project problems remotely), and for writing collaborative manuscripts (such as the recently published riboviz 2 paper and open science article).

Our experiences provide a strong case study for successful open science approaches in student projects and clear evidence of their long-term benefits to students, supervisors and wider lab groups. We highlight our "top takeaways" aimed at students, day-to-day supervisors, and PIs and demonstrate how others can take the same approach.

Author Biography

Felicity Anderson, University of Edinburgh

PhD Researcher looking at improving Research Software using Software Engineering techniques at EPCC (School of Informatics) at the University of Edinburgh, formerly Research Assistant in Bioinformatics at Wallace Lab (School of Biology), University of Edinburgh.

Published
26-Jul-2022
Section
Presentations