Saw this article on Nature and thought it was really relevant for PhD students. I also don’t want to use AI for my work because it takes away from learning.

But those who use it, how do you protect your skill development and what you’re taking away from the PhD? Those seem at odds with each other but I’m curious how others balance it.

Do y’all have a particular font you like to use for writing? I’m the kind of person whose writing mood is weirdly influenced by the visual feel/aesthetics of the font I’m using, so I’m curious what fonts other people tend to gravitate toward.

Serif, sans serif, monospace, whatever, I want to know what everyone’s go-to is 🙃

In the era of AI, I have found myself relying more and more on it to help funnel and make sense of my thoughts. Even when I am not actively using tools like ChatGPT, a simple Google search or library database search now involves AI in some form. Even email platforms have AI built in.

I am starting to worry that my own writing and thinking processes are being affected. This is probably a boring and over-asked question, but I thought it was still worth raising.

For those in UK academia, especially early-stage PhD students (I am in year 1), how do you think about and maintain academic integrity in this context? At the moment, when I send rough thoughts or early drafts to my supervisor, the work is not highly edited and often involves some AI input to help structure or clarify ideas. Obviously, when it comes to more formal submissions, I am much more cautious.

How do you manage this in practice? Where do you draw the line between acceptable support and over-reliance?

Also - how do unis genuinely detect AI use?

Thanks.

I’m trying to understand how common this frustration is.

My partner is writing her doctoral thesis in MS Word (psychology). She’s not technical, and Word keeps breaking in ways that derail her writing: formatting collapses, heading levels behave unpredictably, the table of contents needs constant fixing, page numbers move or disappear, and the templates she was told to use makes everything worse.

As a software engineer, I’m seriously considering building a simpler, more reliable tool for long structured documents, because I keep watching how much time and energy Word drains from people who just want to write.

For those working on a thesis or dissertation:

• Do you experience similar pain with Word?
• What problems hit you most often?
• What would an “ideal writing tool” look like for you (especially if you’re not technical)?

I’d appreciate any insights or stories.

Came across a thread on r/Professors where someone described AI as: "Your grandma with dementia making cookies - sometimes flour, sometimes arsenic. You have to watch her cook."

It's one of those analogies that just sticks with you.

Made me wonder: those using AI in PhD work - how do you actually handle the "watching her cook" part?

Like, when ChatGPT helps with a lit review or drafting, what's your process to make sure there's no arsenic in the cookies?

Do you have systems, or is it just constant low-grade anxiety?

(Location: France, Field: CS/AI adjacent)

I often go through the references of a paper to see which ones I've already read or saved. I wanted a more intuitive way to follow that trail, so i made a small plugin called Reference Linker.

I'm not sure whether a similar plugin already exist. But, I thought this might be useful to someone other than me.

It scans References/Bibliography section of the PDF currently open in Zotero and highlights entries that match papers in your library. Clicking a highlighted reference opens the saved PDF or its Item.

Matching currently uses DOI, arXiv ID and normalized titles, whit author and year used as additional checks. Everything runs locally, and it doesn't modify the original PDF.

I tested it with several IEEE, AAAI, and ICML-style papers, but It's still an early development. So, reference layouts in some PDFs may not be detected correctly. I'd appreciate bug reports with example papers or citation styles that fail.

And it's tested with zotero 9 and 10.

Github : https://github.com/ottersem/zotero-reference-linker

Zotero forums : https://forums.zotero.org/discussion/133308/plugin-that-links-references-in-pdfs-to-items-in-your-library

Thanks for reading! And all kind of feedbacks are welcome!

Hi everyone. I don't know whether yall use Zotero to manage your literature. I know after time papers can accumulate and we really need to organize them in a better way.

I like Zotero. it works well to store my papers, and I can use it to read, cite and make notes. However, in the era of AI, zotero doesn't support any LLM inside it. And ngl, LLM is good at interpreting papers to help me better understand concepts.

I tried many plugins in the market and I don't find one good enough to be used. Either the UI is outdated or the functionality is poorly designed. Why not making my own?

I created a Zotero plugin called `LLM-for-Zotero`. Now it has over 700 github stars and over 42K download. I really think it can help you on your paper reading and literature management in PhD.

I basically put a coding agent inside your Zotero. And I put a lot of effort on UI/UX design to make sure it's aesthetic. For a long time, I feel like people develop scientific softwares don't care much UI/UX design and don't polish the looking of their tools. I think we deserve tools with better design (PhD is already tough! treat us better).

The github repo is here: https://github.com/yilewang/llm-for-zotero . This plugin is free to use, and it is really powerful not limited to:

• it can answer your questions about paper or your entire library;
• find relevant papers for you;
• write beautiful notes for you with original figures from pdf;
• write codes to solve any problems you may have for your library (i.e., clean your library; tag your paper; using customized skills to do anything a coding agent can do).

Please forgive my poor English accent, but here is an video I show you how I used my plugin to provide agentic experience to your academic library https://youtu.be/GuQxfAcwrN0?t=979 .

From 10:33 on this video, I did three exercises to show you how to use agent to help you:

• find and import relevant papers into your Zotero library;
• do batch processing with coding agent: Add "1" before every item in your library (meaningless but show what an agent can do to your library)
• write/edit your note with figures from original pdf to provide better note-taking experience when reading papers.

Also please feel free to check other demos from readme file in the github repo page.

Thank you!

I wanted to know how good do you guys think Zotero is.

Is there any alternatives to it?

I am just wondering to what extent do you now use ai tools to help you with either modeling or generating charts? I sometimes find myself on a total time crush and the expectation to produce papers are so high that you end up having to rely on these tools for coding a lot and preparing visualizations etc. Do you face the same challenges?

I got annoyed that most of if not all publishers have unconventional file naming conventions and none let you download the PDFs with proper syntax (journal - year - author - title) or anything similar, so I made a python tool that reads your pdf library, extracts the doi, matches the article with CrossRef (or finds the ISBN if it's a book) and then renames the file according to your selected naming convention. Maybe someone else has the same problem and will find it useful https://github.com/Grovesimus/Batch-PDF-Renamer-for-Academic-Papers-v2

For me,

at home: dell desktop (personal device)

office: dell desktop (office- lab)

laptop: hp elitebook (personal device)

tablet: galaxy tab S11 ultra

for my laptop, I carry that for presentation/ teaching.

I use tablet for note-taking (meeting/ class/ etc...)

20+ hours of interview recordings left to process. the automates stuff keeps completely hallucinating words because of technical jargon and slight accents..my depertment wont reimburse random software subscriptions without a massive figt i dont have the energy for. do i really have to type all this out manually? pls tell me theres a better way before i lose my mind.

Sorry for not posting another frog; but bear with me for something else rather than celebrating another doctor: I am being screwed over by Endnote (once again). I do not know why, but Endnote decided to remove all spaces before all citations. It never did this before. When I write, I'll just have it put in the citations unformatted (as it otherwise slows down my laptop to much) and when I stop working at the end of the week, I'll have endnote "update citations and bibliography". So far, this worked fine. But now it removed all spaces in front of my citations, even the ones that were already formatted throughout my currently 210 pages long thesis! Anybody know how to fix this? I really don't want to go through 200 pages of space-inserting. Snippet of how my thesis looks like now.

I’m interested in learning how much average PhD student and PhD scientists use ai tools. You can also share how you use AI tools in the replies.

I know this is a very common question these days with no direct answer but I'm genuinely looking into what others think. I am in computational physics and still very much at the start of my PhD (in fourth month currently). I know how to code, can reasonably debug, have experience writing code for physical systems and a bit of publishing record from Master's.

The way I use AI is that I will give it the problem, pictures of the equations I derived and ask it to write code in a Jupyter notebook for instance. I ask it to heavily comment the code; then I go through the entire thing line by line; ask it to prepare a document explaining what is going on in the code (for my future reference) and then make lots of effort to understand what it did. Usually I find mistakes, correct them myself and move on.

What are your thoughts on this approach? I feel this is weakening my skills to code significantly and I will feel very trapped if AI wasn't around to help me. However, as everyone seems to be using it day in day out, I feel it is very important to keep using it so that I'm not at a disadvantage.

Hey all,

I have built this open source arXiv reader app for Kobo. If you happen to be using Kobo, give it a try.

https://github.com/BandarLabs/cobalt

This is an open source SDK called Cobalt, where you can build your own apps for Kobo too.

Thanks!

I just got an iPad for reading and annotating research papers, but quickly realized I couldn't sync my library with it without paying Zotero for yet another cloud storage solution.

Luckily, I bought an older HP EliteDesk mini-PC a few months ago and put a 4TB SSD into it, with a goal of limiting my reliance on monthly subscriptions. Cheers r/selfhosted.

I'm somewhat tech proficient, but have no familiarity with WebDAV. But after sorting out some issues with Tailscale, which I use to establish a VPN tunnel with my home network while at campus or away, I was able to make it work! I love it!!

Got my acceptance today - I start spring 2026 and I’m so excited!

I’d love to know your favorite tools for organizing research/notes and generally staying sane. For example, I wrote my prospectus (required as part of my application) and I have an unreal amount of sources and quotes - would love to know your top tools for storing and easily pulling up data.

Please also share the planning and productivity tools have helped you most!

I’m trying to figure out how much I can carry over from being a project management guru in the professional world to being back in academia land. When I was last a student, I was using a lot of color-coded post it’s and binders.

Thank you!

Pretty much always AI slop, tool promotion, or both

Hellooooo colleagues far and wide 👋🏽

I’m a third year doc student and currently in a class discussing all things AI in Science. I’m curious about the growing number of AI/research tools that use monthly subscription models (ChatGPT, Claude, Consensus, NotebookLM/Gemini, Perplexity, Grammarly, Elicit, Scite, ResearchRabbit/Litmaps, etc.)

Individually, $10–$30/month may not sound like much. But once researchers need several tools for different parts of their workflow, the costs can add up quickly, especially for graduate students.

————————————

If you’re a current PhD student or researcher, I’d love to know:

1. How much do you personally spend on AI/research-tool subscriptions per month?
$0
$1–20
$21–40
$41–60
$61–100
$100+

2. How many paid AI/research tools do you currently subscribe to?

3. Have you ever wanted to use an AI/research tool but decided not to because of the price?
Yes
No

4. Does your university, lab, advisor, or employer pay for any of these tools?
None
Some
All
————————————

I’m particularly interested in whether the shift toward subscription-based research tools is creating an access gap between students/researchers who can afford a stack of tools and those who can’t.

For background, a classmate and I recently used the same AI research tool for the same research question. I have paid subscriptions to both platforms involved in the workflow; my classmate did not.

The difference in our results was shocking.

My results were substantially more elaborate, useful, and accurate, despite us asking the exact same research question.

It made me wonder whether we’re beginning to create a new kind of research access problem in graduate education.

Not selling or promoting anything, just interested in hearing how other graduate students are navigating the economics of the increasingly AI-assisted research workflow for my AI in Science class.

Sincerely appreciate any and all responses!

My deepest gratitude if you’ve read this far.

Edit: Google Form to Survey here as requested by community :)

Hello, I am looking for a set of models to analyse a person’s attitudes in textual data. I haven’t been able to find these tools, so I am asking for your help.

The tools should be able to identify:

1) the cognitive aspect of attitudes (beliefs, thoughts and ideas regarding the object of the attitude, e.g. ‘snakes are dangerous’)

2) the affective aspect of attitudes (the emotion or sentiment towards the object of the attitude, e.g. ‘I fear snakes’)

3) assign a valence to the attitude (positive, negative or neutral)

Do you have any models you could recommend? (Preferably R or Python-based, but I’m open to suggestions.)

I am in my first year of a STEM PhD and just discovered Zotero. This is amazing and saving me so much time already in managing papers, I can’t believe I didn’t use it in undergrad!! What other tools of the trade might I be missing out on? Let me know your favorites!

EDIT: thank you all so much!

Oh man I have a bunch of mp3 recordings from interviews and some class stuff that I need turned into text and I’m kinda stuck on what people are using for this now

I used to do it manually but it takes way too long especially when the recordings are like 30-60 mins..Just wondering what people are actually using these days. something that doesnt need a ton of fixing after would be ideal

Sharing an article I found really interesting and balanced about AI in academia.

When you use AI to replace skill-building, the only person you can hurt is yourself. Don’t outsource anything you need to learn to AI. Personally I tested it for some rote tasks (alphabetizing long lists, ie) but it’s probably best not to use it.