Show HN: Stempad – Fast Online Scientific Writing | Hacker News Reader

Show HN: Stempad – Fast Online Scientific Writing

stempad.io

144 pointsralph_r45 comments

I'm building an online text-editor editor to write and save scientific documents fast. Here's a video of how it works: https://youtu.be/Hyk8CvCdEWE

As an engineering student, I hated that handwriting was the only viable way to do fast or impromptu scientific writing. It would be the only way to take quick notes in class or in a lab, write an assignment, or create a presentation. Here's a few things I witnessed in academia:

* Unsuitable editors: Students attempt to resort to text editors unoptimized for science, such as Notion or Word, to take notes and write assignments.

* Slow or expensive software: Students, teachers, and researchers using high-friction and high-cost tools for writing

* Messy class notes: Professors upload pictures of hastily handwritten class notes as supplementary material

The list could go on. I believe that the ability to quickly document scientific ideas with a keyboard would be a huge QOL improvement for anyone learning or doing science.

I recently launched the ability to export Stempad documents to LaTex. I tested it by rewriting part of a paper I found online (Metabolic scaling in small life forms by Marc E. Ritchie & Christopher P. Kempes) and exporting it. You can try the editor and export yourself using the post url. The export button is on the top right of the page. In case you want to see the result directly, this was it: https://www.overleaf.com/read/zjccqbjdyhtc#6e146c

Feedback is really appreciated! If anyone thinks they might find Stempad useful, let me know and I'd love to get in touch.

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Very nice work. I'll definitely play around with it. For the use case of a digital lab notebook, it would be nice to be able to annotate (superimpose drawings, highlight, etc.) images and pdfs directly in the editor. This would be even more powerful if such annotations could be grouped or locked, so that their position relative to the annotated image remains fixed. This is something that all other note taking apps either miss entirely or implement poorly (or maybe there's something else out there that does this well?). Is this possible in Stempad, or are you considering adding such functionality?

Glad to hear you're interesting in trying it. For your use case, I'm curious, are you referring to general use annotations (ex. highlighting, text boxes, commenting, drawing), or are you specifically interested in scientific annotations (ex. Adding an annotation with math or code in it)?

Regardless, it's definitely a realistic feature to have. I'm thinking of it as a block right now, perhaps a file block, that can be resized and annotated freely. Maybe annotations can be mini, floating, moveable and resizable editors. Would that make a big difference for you?

I'm mostly interested in general use annotations. Basically, I want the ability to quickly circle a feature in a plot and point to it with an arrow associated with a text box with some explanation. I think the mini, floating blocks as you described could work well as long as they can be grouped and "locked" in place so they don't accidently get pushed away. OneNote has the ability to add such general annotations very easily, but there's no ability to lock the positions, and so as a result notebooks can easily become a jumbled mess.

Sounds good, I'll work on adding comments and annotations (that can lock in place) and update you when that happens.

Nice work, the video looks terrific.

Just so you know, the vast majority (I'd say everything but molecules) of this is already possible with Org Mode, and can be done just as quickly with Evil (VIM keybindings). That said, I'm sure that people will love this.

I love and use org mode a lot. I wouldn't know how to do half of these things within it though.

Can you point me to good resources on how to do them?

Interesting project. It seems like your functionality, other than the browser-based editor and renderer, overlaps with Quarto (https://quarto.org/)

I use a tiled text editor/quarto preview browser pane with a lot of success for scientific notes.

Since you are keen on feedback:

A LaTeX using collegue I forwarded this to objected that you need to approve latex keywords (\alpha) and can't just keep on typing.

Not much of a LaTeX user myself, so just forwarding the feedback as is.

Fixed! Thanks for the suggestion

This is really cool, I gave it a try this morning at work. Unfortunately, as much as I like it, I can't see myself using this regularly precisely because it's a webapp. I'm sure there's a lot of folks out there that would love it though.

Perhaps it's just a personal preference, but I'm just reticent to fall into the habit of using something which requires an internet connection, you know?

This is a cool app, but I have one major criticism. It's really, really slow.

If I'm going to be using something for writing or notes, I needs to be snappy. You need to do some profiling and debug the lag. Other than that, great work!

Thanks for the feedback! Do you mind me asking what machine and browser you were using it with?

LG gram 17, Brave browser

Is it possible to embed the stempad editor in something like a react app?

Only with an iframe at the moment unless I open source the editor at some point.

In resulted pdf there're weird spacings all over the document. Figures are referenced by manually indexing them rather by name. No hyperlinks. Equations have no numbering. Some equations/formulas in text aren't using math mode. (For units better use the siunitx package.) Bibliography is basically simple text rather generated, making it hard to switch to other styles.

Regarding the editor, seems math and text cannot be written together. Copying math and pasting to text field results in pasting LaTeX code.

Now if just said made this because wanted to wouldn't have mentioned it, but as you provide a reasoning, LyX (LaTeX frontend) and TeXmacs (not frontend but can export to LaTeX) provide a way to get LaTeX documents without writing LaTeX.

Overall the site can function as cool math-enabled notepad but (for now at least) seems hard to use it as platform to author papers.

Hey! The LaTeX feature is still brand new and I'm looking on improving it, thanks for the feedback. The PDF export seems to be misinterpreting the code blocks, I'll have a fix out tonight! (Edit: done!)

I would describe it as more than a math-enabled notepad with support for 6 other scientific block types and the ability to run code. However, I agree that it's definitely not built to write full blown scientific papers at this stage :)

This could become useful for me in the short-term future, thabk you for sharing!

Glad you like it :)

Have you heard of pandoc?

I have not. At a glance, it seems really useful if someone needs to have plaintext documents be able to export to many different formats.

IMO it covers a different use case than this tool

Wonder if perfect SEO will dissuade new projects. If a Linus T was able to google "any unixes for i386?".

Is the Python code executing via Pyodide in the browser?

That's correct

My biggest frustration as an academic was reproducibility of papers I was reading. The pdf is such a useless medium for information transfer and the academic publishing industry is a complete racket where all the value is generated by the authors and reviewers who work for free and have to pay (in most cases) to have their work accessible freely to the public. I would love to see this turn into a default way to publish papers

If you're lucky, someone releases code+data associated with their published paper. If you're really lucky, that code and data is in the same state as it was in the published paper. If you're really really lucky, someone besides the author can get it to run.

If you can consistently locate and run academic publication code without direct help from the authors, you are The Chosen One.

[edit]

In seriousness, reproducibility is also my biggest concern. Scientific/academic publishing could do a lot better than rendering pretty static documents - we can provide the data, code, version control, and build processes which produced the paper so anyone can reproduce what they see in the paper. AND we could host them together so they're bidirectionally linked, to facilitate other scientists building on top of our work.

That could be our future, with the right incentive structures in place.

Isn't that the idea (or perhaps the promise) of languages like R or notebook tools like Jupyter or Collab, which provide a means to ingest, clean, analyse and present your data, then share the code you've used to do that.

I like notebooks, they are a useful tool. But they are just a slight adjustment to the programming model and an alternative type IDE. It does not do much in terms of helping reproducibility. Data, software and dependency versioning is much more important. And verification that the code indeed runs on another machine, and produces the correct results. Setting up CI for the project, and basic end2end tests is the minimum level I set for my research (in applied machine learning).

Notebooks aren't very git-friendly, so in practice you rarely know which version produced the paper.

The fact you can run notebook cells out-of-order exacerbates this problem. Not only do you not know what version the entire file was, you also don't know in what order or how many times each cell within the file executed in order to produce the plots you see in the paper.

This isn't to discount the improvement in UX that you get from notebooks compared to my preferred alternative (emacs with org-mode). Maybe I'm just bitter that the ipynb format exists at all. If notebooks were just a UX layered on top of emacs+org-mode, that would fix most of the core issues.

if you want this to go main stream, you have to at least make some parts of it open source

We don't need faster scientific writing

We need slower scientific writing.

Edit: While I understand policy involved, apologies, I'd contend 'shallow'. Not lengthy? Sure. But the point was made enough @kbk et al. got it

Ouch, straight to the point.

For reference http://slow-science.org/

> We are scientists. We don’t blog. We don’t twitter. We take our time.

It is good that the actual scientists aren’t going to do this task.

It is a shame that we’ve more or less given up on the idea of having science communicators to do that job.

IMO when journalism ended the worst side-effect was that people who would be otherwise employed actually doing things have had to start blogging about the fact that they were doing them, instead of actually doing them.

> having science communicators to do that jo

Were is Sagan, Clark, Asimov. Burke when one needs them? Maybe AI might help here

"Where is" ...

While the concept of slow work has merit, the ideas in this manifesto are deeply flawed and lack nuance. Also the application of this manifesto to the tool above is similarly flawed. The tool helps save time in non thinking work e.g faster representation of information. Slow works happens after the representation of notes. Rarely during the creation of notes, creation of notes being the goal of this Stempad.

The original idea of this notebook is a new system which can reduces bad time usage e.g. writing A x A x A x A x A. becomes A^5 The tool allows representation of ideas quicker. This means there's more time for important work, more time for slow work mentioned in the last paragraph of that manifesto.

Points in regards to the flaws of this manifesto:

To use the same framework of the initial statement to show flaws in thinking:

>We are scientists. We don't blog. We don't twitter. We take our time.

We are experts. We don't reflect online. We don't communicate online. We take our time.

If the quote said: We are scientists. We protect our time to focus on important work. We choose to not engage in shallow discourse. And value depth over speed even at the cost of time. We believe speed for speed's sake comes at a cost.

Then there is a leg to stand upon to protect "slow work".

>Slow science was pretty much the only science conceivable for hundreds of years; today, we argue, it deserves revival and needs protection. Society should give scientists the time they need, but more importantly, scientists must _take_ their time.

Slow science is not defined in any way, and so prevents discussion and debate. Something being the only conceivable option does not mean it was the best option. Nor does the time span it existed give the process extra value. For millennia humans used 2 legs for our primary mode of transport. There is no movement to protect the usage of slow transport -

"Walking was pretty much the only transported conceivable for hundreds of years; today, we argue, it deserves revival and needs protection. Society should give humans time to walk to destinations, but more importantly, humans must take their time"

I agree science does need time to think, explore and discuss, but it does not need time to express ideas using AxAxAxAxA when tools such as Stempad exist to write A^5.

"Please don't post shallow dismissals, especially of other people's work. A good critical comment teaches us something."

https://news.ycombinator.com/newsguidelines.html

https://news.ycombinator.com/showhn.html

I totally get where you're coming from, maybe I could have worded the title differently. In contexts such as publishing scientific papers and journals, patience and attention to detail are really important.

There are however many other contexts where I would argue speed and a simple UX makes a big difference.

* Notes that need to be taken on the fly: class notes, lab notes, field observations, general notes

* Prototyping, brainstorming, ideation sessions, especially collaborative ones

* Drafting outlines

* Creating presentations on work you've already completed

* Doing schoolwork, such as assignments or lab reports

* Creating teaching material on content material you're a subject matter expert in

That's a few examples but there are plenty more. The goal isn't to rush the scientific process. The goal is to have a tool that doesn't get in your way and enables speed-of-thought writing for science. This can be helpful in many ways, especially for students, but also for scientists.

I think you are very right. I have been missing a "simple" UI for digital scientific notes and your project looks great. Less for documentation or papers maybe, more as a tool of thought or impromptu communication. Or both, who knows.

During my Master's or PhD I would have agreed with the "slow science" sentiments here. These days I want to get things done and work with collaborators.

Another way to put this while avoiding the slow/fast argument is that the tools for note-taking should not hobble you.

That is, stempad is a blow against artificially slow writing, not against all slow writing.

It ideally doesn't keep you from thinking deeply and may help if it lets you avoid thinking about the tool instead of the content.

> against artificially slow writing, not against all slow writing.

This is really well put

Impediments not deliberate choice

Thanks. I could also have been less laconic. If you are the author accept sincere apology and honest best wishes

Speed is definitely a good thing sometimes.

Note: Maybe you could play it "both ways" and have a "flow", or focus or no distraction mode?

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