4 Lab Resources

This chapter provides useful links to software and associated resources for conducting research in the PALM Lab. The following is not a strict list; lab members are encouraged to explore what tools and resources are out there, especially open source software, to keep current with research.

4.1 Required

The following resources will likely be needed for conducting research in the PALM Lab.

MATLAB (or Python)

The code for conducting the experiments and data analysis will mostly be written in MATLAB. The University of Adelaide provides access to download and use the licensed software.

If a lab member is an experienced programmer (i.e. requiring not as much coding supervision from William), they can opt to write their experimental and analysis code in Python, an open source software with numerous well-maintained packages for scientific research.

PsychToolbox (or PsychoPy)

PsychToolbox is the software package we use for building psychology experiments (i.e. displaying stimuli and collecting responses) in MATLAB. A useful set of demos can be found on Peter Scarfe’s lab website. The Python alternative is PsychoPy.

EEGLAB

EEGLAB is the software we use for analysing electroencephalography (EEG) data within the MATLAB environment. EEGLAB provides a point-and-click interface to conduct most EEG analyses (such as calculating event-related potentials), as well as the base functions for custom analysis scripts. Our artifact rejection pipeline can be found on Github.

An introduction to the event-related potential by Steve Luck is a good starting point for learning about EEG and various event-related potentials.

R and RStudio

To run some statistical analyses, we may use R and RStudio.

R for Data Science by Hadley Wickham is a free book that is a great introduction into using R for data analysis and visualization.

Github and Github Desktop

For code management and version control, the lab uses Git and Github. The PALM Lab’s Github will contain all code repositories for our lab, including shared packages for our common processing or analyses (such as artifact rejection of EEG).

Github’s own start-up guide is a good place to learn how to use Github. For those less experienced with programming, Github Desktop is an easy-to-use interface for maintaining code between your local computer and Github.

4.2 Recommended

Zotero

Zotero is a desktop software app for organizing scientific papers and managing references. It has an in-built PDF reader with tools for annotations and note-taking, and plug-ins for inserting references and bibliographies into manuscripts.

Zotero Connector is a very useful Google Chrome extension for adding journal articles directly into Zotero from Google Scholar or journal webpages. This plug-in will also connect Zotero to Google Docs, enabling adding citations and bibliographies into any working manuscript (which can be ported to Microsoft Word at any time). An additional extension is needed to connect Zotero to Microsoft Word.

Jamovi or JASP

JASP and Jamovi are free, open-source statistical software programs that provide a point-and-click interface for conducting both frequentist and Bayesian statistical analyses.

Tenzing

Tenzing is an easy-to-use web app for quickly generating the author list, their affiliations and their contributions according to the Contributor Roles Taxonomy (CRediT). The PALM Lab uses a policy of contributorship to credit researchers. Use tenzing to generate the CRediT roles prior to the submission of a research manuscript for publication.

The app was created by Alex Holcombe, Marton Kovacs, Frederik Aust and Balazs Aczel. See Holcombe, A. O., Kovacs, M., Aust, F., & Aczel, B. (2020). Documenting contributions to scholarly articles using CRediT and tenzing. PLoS ONE, 15(12), e0244611..

4.3 Optional

Obsidian

Obsidian is a note-taking and knowledge management software that is designed to be a ‘second brain’ for the user. Notes are written and saved as Markdown files, and with the use of tags, links and community-built plugins, Obsidian can provide a powerful organization and navigation of the notes. Obsidian does have a steep learning curve and requires some setting up (including thought about structure and organization) before it can work well.

Adobe Illustrator

Adobe Illustrator is part of the Adobe Creative Cloud, and is useful for editing and cleaning up scientific figures for publication (for example, generating vector graphics to the appropriate sizes), and for creating well-designed conference posters.

Additional resources (mostly educational in nature) can be found in Chapter 6.