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diff --git a/2025/talks/reference.md b/2025/talks/reference.md index b0264088..fae77439 100644 --- a/2025/talks/reference.md +++ b/2025/talks/reference.md @@ -59,6 +59,131 @@ being able to remove external reference managers from my workflow, something I have wanted for years, but that I haven't managed to do before this. +## Discussion / notes + +- Check out the ebib manual for an explanation of the features I + showed and more! + [https://joostkremers.github.io/ebib/ebib-manual.html](https://joostkremers.github.io/ebib/ebib-manual.html){rel="noreferrer noopener"}. + - Also my ebib config for the custom things + [https://github.com/Vidianos-Giannitsis/Dotfiles/blob/master/emacs/.emacs.d/libs/zettelkasten.org#ebib](https://github.com/Vidianos-Giannitsis/Dotfiles/blob/master/emacs/.emacs.d/libs/zettelkasten.org#ebib){rel="noreferrer noopener"} +- My 2022 talk if you're interested in the rest of my workflow + regarding scientific literature + [https://emacsconf.org/2022/talks/science/](https://emacsconf.org/2022/talks/science/){rel="noreferrer noopener"} +- Use link to directly download bib info to the library is cool. I + always did that manually. +- The reading list, for me every download item will directly inside a + manuscript. + +- Q: Which version of \`org-ref\` you are using? I am so dependent on + org-ref and org-mode, so that I had huge resistant to update + \`org-mode\`, \`org-ref\`, \`ivy-bibtex.el\`, etc + - A: I'm not sure how recently I updated, so it may not be + master, but I generally try to keep up to date with the packages + I use. I generally haven't had many problems, unless when there + is a new major version, which may need an afternoon to confirm + everything works. + - Thanks for sharing this. +- Q: Have you try ivy-bibtex/bibtex-completion.el, how it compares to + ebib? + - A: I think they are not mutually exclusive. I typically use + ivy-bibtex to find an article quickly, to initialize a + literature note (integration with org-roam-bibtex) or to add a + pdf to the entry, where it will automatically rename it as it + should. ebib is more of a tool to manage the .bib file more, + find an entry with full text search (instead of just + Author/Title search) and reading list management. There may be + some overlap, but I use both a lot. + - Got it, quick check with ivy-bibtex etc. + - ebib is for heavy lifting for academics +- Q: Do you find showing abstract on your navigation panel helpful? I + always delete all the abstract info in my bib to make things little + concise. Just want to know you thoughts on this. + - A: I like showing the abstract. It can be long and reduce + visibility, but the whole point of searching with the navigation + panel inside ebib is that I cannot easily find it through an + Author/Title search. Therefore, the abstract is often the next + line of search where you will find what you were looking for, so + for me it is helpful. I sometimes also use the small comments I + leave on the annote entry for this purpose. + - Try to find relevent info using search. Abstract helps you + search better. + - annotation entry also help +- Q: it seems that there's a meta problem here: too much + information. Do your tools reduce cognitive load? + - A: There is definitely too much information, but that is an + innate problem of handling a lot of literature. I think these + tools can reduce cognitive load, because things don't stay in + my mind. They can be moved to the computer, which can handle + more overload than my brain. So it is to a large extent the + externalization that reduces the load, because too much + information is a reality with literature. + - thanks. Sounds like externalizing the problem is the point. +- Q: When you download a new article, how do you integrate its file to + your database? For example, do you move and rename the file + manually? + - A:Find the file in ivy-bibtex, run M-o, select l (add PDF to + library), find from file (f), find where you saved it and it + will be renamed automatically. It is not moved automatically, + but the rest of my packages know to find it in the folder I save + initially. You may look at the README of the package for more + details, it is one of the more well written ones in my opinion + ([https://github.com/tmalsburg/helm-bibtex](https://github.com/tmalsburg/helm-bibtex){rel="noreferrer noopener"}). + - Ok, I see, Ivy-bibtex has a function for this, thanks! +- Q: What about annotations with ereaders. veiwng and taking on emacs + or erader touchscreen highlighting and notes, org-noter I think + would be an alternative out of ebook anotation alternative? + - A: I do not use an ereader. For touchscreen, I have a tablet, + which runs Emacs natively and I can work with org-noter with + touch, but in that case, nothing in the general workflow + changes. For books, I know org-noter also works with epub files, + so you can also directly take the notes there. If you use an + ereader for annotating that doesn't run Emacs, this is + obviously more complex. +- Q: How well do you feel about making notes an web sites, pdf, + videos, I know pdf is ussaly good but others I am less sure about? + - (Not the author) i always try to convert it to pdf, so only one + file format to worry about. Video is another story. + - I agree with the above comment. PDF is just the easiest to deal + with in general, so I try to go for it. For taking notes on web + sites, there is org-roam-protocol + ([https://www.orgroam.com/manual.html#org_002droam_002dprotocol](https://www.orgroam.com/manual.html#org_002droam_002dprotocol){rel="noreferrer noopener"}) + although I personally don't use it a lot. Video is much more + complex, but in practice, I tend to not annotate videos + directly, with a timestamp, but rather to take crude notes on + paper during the video and organize them online at a later + point. +- Q: how do you add a new article from scratch, a pdf that you did not + have in your bib file? How do you generate the 'bib' entry with + metadata and abstract? + - (Not the author) He mentioned he uses Zotra, which does that. + [https://github.com/mpedramfar/zotra](https://github.com/mpedramfar/zotra){rel="noreferrer noopener"} + - Yes, this is my approach. Specifically the function + zotra-add-entry. +- Q: When you fact check every details for a bib entry? The author + names, published journal, doi stuff. Always painful for me when I + need to upload a final version of a manuscript. Tons of work. Maybe + I can do it at the download step. + - A: I haven't worried about that, because I think automatically added + bib entries work well. But Org-ref has a tool to automatically check + it. I generally think it is best to do it directly when you add + them. + - [https://github.com/jkitchin/org-ref/blob/master/org-ref-bibtex.el#L119](https://github.com/jkitchin/org-ref/blob/master/org-ref-bibtex.el#L119){rel="noreferrer noopener"} + - Yes, i did it manully, so some time I have issues. + +- Comment: I just use Org headings for all the metadata. Why bother with bib files. https://0x0.st/Kvbi.txt + With Org, you can search through notes and title and metadata together. I use org-ql, but you can use anything that can search Org headings. And use attachments. can also directly export to .bib from org. with headings, reading list is just natural - assign todo to heading + - A: You can move this all to org, yes, but I think .bib is very ubiquitous and a lot of tools work well with it, so I haven't really felt the need to move away from it. It is an interesting approach though. I have seen some others use it as well + - A: Making a reading list is easy indeed. The primary goal of my additions were to be able to manipulate it without ever worrying about the file itself. I find it works better/faster for me if I can always access the content I want without opening the file. Which is mostly what the code I wrote for this does. +- I noticed that his command searches are automatically prefixed with "^" to prevent more generalized matching (e.g. all comands that have "copy") + - A: I believe that is done automatically by counsel-M-x. It served for something, but I don't remember exactly why. +- Q: for viewing pdfs, do you use pdf-tools? I always found it clunky imo. + - A: Yes, its pdf-tools With org-noter to take notes side by side. And I haven't had any problems with it. It generally works well. + - (audience): I tend to always call out to the external PDF viewers. + - (audience): maybe I didn't try it well enough, but I just prefer external viewers. pdf-tools feels like an image viewer to me + - A: Some external viewers can have more features, but again, the problem comes down to it not being Emacs :D Being in Emacs is better than not being in Emacs. + - A: Are you sure you are talking about pdf-tools and not doc-view? Because those problems are very much in doc-view, but I wouldn't say for pdf-tools. +- It's always interesting to watch other people work in their emacs environment. +- Thanks for the talk! There was a lot to digest, I'll have to rewatch it. [[!inline pages="internal(2025/info/reference-after)" raw="yes"]] |