Harnessing digital tools in your research
DALL.E2 Francis Bacon-inspired woman scientist
How can we use digital tools to aid in our research?
Now is an exciting time for conducting research. We have access to amazing new tools, such as calcium imaging, to peer into the cellular and sub-cellular workings of the brain. We can even manipulate neuronal activity with methods such as optogenetics with impeccable temporal precision. But what may be even more exciting and make our “research life” a little easier is our access to digital tools such as advanced note-taking applications and reference managers, as well as machine-learning algorithms that are capable of answering simple questions, conducting literature searches, and generating pictures with specific prompts like the one you see above ^^ (DALL.E2 [Francis Bacon-inspired woman scientist]).
Currently, there is a massive boom of generated digital tools and AI algorithms to assist in a variety of our everyday activities. Here, i compile a short list of the digital tools that i use in my research every day. These tools are free as of the date this post was published.
Obsidian
Perhaps my most-used digital tool, and one that i swear has carried me through my graduate school studies, is Obsidian. Obsidian is a note-taking app like you’ve never seen. Imagine taking notes and, at the click of a button, being able to recall and link similar previous notes to your current notes…*chefs kiss*. Further, the notes that you link together can be viewed in graph form—think bubble map. This is incredibly helpful if you want to get ideas for over-arching themes that you have written about. Obsidian is a markdown-based note-taking tool, which writes and organizes your notes using plain text. This is nice because you get all of the simplicity of using any other plain text note-taking app (i.e. Apple’s Notes), but get the added bonus of adding structure and emphasis to your text without the complex formatting. Plus, Obsidian has a ton of different plugins that you could easily download to customize the application to your liking. Lastly, each individual Obsidian note is saved as an individual text file (.txt), as well as an individual markdown file (.md) on your computer’s local storage. In other words, your notes are not saved in a cloud of some application that could potentially be lost if the application is discontinued. Instead, Obsidian notes are saved straight to your computer and will remain there even if you uninstall the program. Overall, amazing application. It takes a while to fully start appreciating it. But as soon as you feel like you have endless notes that you can recall at the click of a button, all of the note-taking effort will become so worth it.
Zotero
A reference manager is a must for anyone that publishes work citing journal articles. There are many reference managers to choose from, including Mendeley and Paperpile. Mendeley, Paperpile, and Zotero can connect to Microsoft Word using plugins. However, during the first year of my Ph.D., i switched from Mendeley to Zotero due to Zotero’s capability to connect to Obsidian using a plugin (Obsidian: Community Plugin - Zotero Integration). This is a feature that Mendeley currently lacks. Like many reference managers, Zotero allows you to group your articles in many different ways, annotate and highlight the articles, and—of course—extract citations of many formats. Additionally, the Zotero browser integration is seamless—you can import articles from the web directly into a specified folder in Zotero. The Zotero plugin for Obsidian is incredible because it allows you to extract and seamlessly transfer all the necessary information from any article in Zotero directly into your notes in Obsidian. This makes note-taking worlds easier. A pro tip is to use Zotero citation keys when linking articles to Obsidian. In the end, any reference manager for a researcher will do. However, if you plan on using Obsidian, Zotero is the reference manager for you. Unfortunately, Obsidian does not currently integrate well with Mendeley and Paperpile.
Research Rabbit
Imagine you have a collection of articles in a Zotero folder all surrounding a particular topic, such as Chaos theory in neuroscience. By the nature of your topic, many of the articles in your collection were published before the 21st century. You are curious about new literature surrounding the same topic discussed in your collection, but Boolean searches are just not cutting it. Luckily, Research Rabbit has the potential to solve your problem! Research Rabbit is an online research tool that allows you to explore articles similar to the articles you feed it. In your case, Research Rabbit connects to your Zotero, imports an article collection of your choice, and lets you explore papers with similar work, earlier work, later work, explore the work of the authors within your collection, or explore like-authors. If you are a visual person, Research Rabbit has a cool feature that lets you see your collection, as well as the articles that it suggests, connecting in a network based on citations, or visualized in a timeline. Your literature exploration is saved online so that you can always return to it later, and can be shared with collaborators. Lastly,—because i love a seamless research streamline—the new articles you discover using Research Rabbit can easily be imported to your Zotero collection. So, thanks to Research Rabbit, you now find that there are some newer works about Chaos theory in neuroscience, unveiling fresh perspectives on how chaos can be used for biological information processing.
I am currently making a comprehensive guide that provides detailed, step-by-step instructions for utilizing these three tools, so you can incorporate them into your research(: stay tuned!
