The Software and Tools I use as a Grad Student

When I started at uni back in 2014, I was doing my bibliography manually and writing my reports locally on my computer. As I transitioned to dry lab work, I just literally didn't keep any kind of "lab book" because it seemed way to clunky to copy code into Microsoft Word and type electronic notes. For my first conference, I did the whole thing up in Powerpoint, which is commonly done but I will most definitely not be doing again for my next conference.

Over the years, I have been adding more tools and software to my toolbox to improve my scientific practice. Here's a bit about what I use to keep my projects running smoothly!

Zotero (Reference Management)

When I started uni, I used to keep an actual physical notebook with reference details and notes... then I would manually write up my entire bibliography for my report. Respectfully, my former self was majorly wasting her time. Now, I use Zotero to digitally keep my references in one central place. With Zotero, I can import citations for any paper I find online (though it pays to check for formatting problems, like all-caps titles and given/first names being switched), then make notes about that paper, insert screenshots and images, attach files, add keywords, and link it to other citations. This way, I am able to easily link related papers, and tag papers according to what section of my report I think I will use it for. This makes life so much easier come writing time. Gone are the days where I think to myself: "I swear there was another paper that had a similar finding that I should cite here..." I make different libraries for all of my projects to keep everything neat and tidy. Zotero also integrates to Google Docs (though it can unlink which is a pain to fix). Other reference managers exist, like Mendeley and EndNote, but Zotero is pretty flawless and regularly updated, so I haven't had the need to look into these!

Free

Scite.ai (Literature Review)

Scite is a fancier version of websites like Connected Papers (also free) which allow you to easily see which papers have cited a paper. Scite goes a step further by categorising those cited papers as "supporting", "mentioning" and "contrasting" (using AI), so it allows me to get a quick overview of a paper and see if it has been criticised or contested within the scientific community, or substantially built upon, verified, or used in some interesting way, to make sure I'm citing the most up to date information. It actually pulls up the exact paragraph where your paper has been mentioned, so I can quickly check what the citing authors said about it. In the premium version, this can all be visualised using a massive colour-coded spiderweb graphic, scaled according to citation count, so I can be sure I won't miss any "big" papers in my literature review. It's a super time-efficient way of finding relevant papers for my project, allowing me to easily find papers that have addressed a similar research question or used a similar approach. I was upgraded to a Premium account last year for reviewing Scite on social media, and after a year of using it can vouch for the fact that I use it all the time and it's worth the price - I will be renewing my premium account for future projects for sure!

Free and Premium versions (charged annually)

Writing Science in Plain English by Anne E. Greene (Book)

This is a concise book with lots of exercises to practise correcting common writing mistakes in scientific writing. I was first introduced to it in a Biological Communication class in my undergrad. It has examples from real published scientific papers and immediately usable tips & tricks for making your writing more readable and interesting. I read this book over just a few evenings before I started writing my first Masters thesis, and found it very helpful! It recommends telling a story, using an active voice, using common words and consistent wording, ordering your information logically, varying your sentence length, and logically structuring your paragraphs (e.g. from old to new information). It's a really handy reference book to own, because it's hard to become a master of everything she recommends after just one read!

Borrow from library or purchase

The Internet Archive

You may be familiar with the Wayback Machine, a robotic internet trawler that takes regular snapshots of "the internet" and stores them as a record of the internet. Well, the same folks (The Internet Archive) also have an open public library with copies of a lot of cool books (38 million of them) to either borrow for an hour at a time with a free account or simply to read. The books are either out of copyright or digitised and for electronic loans. I used it when I needed access to a particular volume of the Handbook of the Birds of the World, which contains information on every single bird on Earth (yes, really). Each volume weighs about 4kg and there are 16 volumes. As you can imagine, it's sometimes difficult and clunky to access the volume you need. Through The Internet Archive, I made a free account, and was able to borrow the volume I needed for 1hr periods throughout my project. I've been using it again this semester, this time to find digital and searchable copies of obscure and niche books on fern allies published in the 1800s and 1900s.

Free

Google Docs (Writing)

I only switched to using Google Docs last year, and I haven't looked back. Microsoft Word has crashed on me too many times to count. With Google Docs, I can quickly add notes to a report if I have a brainwave on the bus because it's accessible across all of my devices. The auto-save feature is reliable, and nothing is stored locally so I'm nowhere near as worried about losing my work. For me, the formatting works fine. It's also super easy to get supervisors and collaborators to add comments online, rather than sending copies back and forth via email!

Free

Office 365 (Excel)

In contrast to Google Docs, which works a treat for me, I did not find that Sheets (Google's online answer to Excel) was reliable. The formatting got glitchy immediately, and so I moved over to Office 365, which is the online version of Microsoft's usual suite of programs. I have been using Office 365 for a massive data table for my current project, and it is working seamlessly. Again, I wouldn't work locally anymore for fear of losing my data via a crash. The auto-backup on OneDrive that is offered for local users just didn't work for me.

Marxico (Workbook)

Marxico is a markdown editor integrated with Evernote. As a markdown editor, it has reliable formatting even for code. It was recommended to me as a way of keeping a 'lab book' for bioinformatics/computational projects, but I have continued to use it for general project logs - thoughts, problems, solutions, questions, definitions, meeting notes, brainwaves... and most importantly, to do lists! I use Evernote to keep track of my day-to-day life and overall project foci, but for the nitty gritty of what needs to get done in my project, I leave it to Marxico. Downsides: it gets laggy when it gets too long or if you insert too many screenshots (this happened for me for a 6 month project, so you would need to make separate files for a PhD project, such as monthly or quarterly notebooks). Also, formatting large tables is a pain. I'm not 100% convinced this is the best solution for keeping track of "dry lab" projects out there, and it is pricey for a student budget, but it meets my needs for now. Please comment if you have a better alternative!

Paid (annual)

Jupyter Notebook/R Markdown etc.

The extent of my coding practices used to be just commenting out my code. I have since learned the value of creating proper markdown documents of my code, with the actual graphical outputs embedded, and code, annotations, and "human notes" all together in one document. I learned about R Markdown years after I started using R, and only recently learned about Jupyter Notebook. I'm sure there are many others. I recently used R Markdown to create a resume in R (will save the details for another blog!), which is something I never thought you could do in R! Anyway: I cannot stress enough how useful it is to have a neat, comprehensive, final copy of your code and output to look back over or send to supervisors and collaborators!

Toggl (Time Management)

I don't use Toggl constantly, but it's a great tool for getting an overview of my time. Instead of forward-based approaches like the Pomodoro technique (which don't work for me, sorry!), Toggl is a retrospective tool that allows me to track where I am spending my time (you label the task yourself, then tag it with a project) so I can identify where I'm investing your time. When I get to the end of the week and think: "where did the time go!?", I can actually look back and see. It's also helpful for juggling multiple projects/priorities, making sure you are allocating your time appropriately. Available in your browser & as an app, for easy tracking.

Free

Biorender

Two years ago I attended a free two-day virtual conference by Biorender, and it was seriously awesome. They did some really great sessions on poster design tips as well as live poster makeover sessions (recordings available in their resource library). But most importantly, they introduced me to their free Poster Templates! No more manually making posters in PowerPoint for me! The templates make it easy to follow basic poster design guidelines: lots of white space, natural organisation of information, minimal text, and appropriate font size. BioRender's main "thing" is making snazzy scientific figures with their in-house icons, so you can also create figures with BioRender and then use them in your poster!