# How do you organise scientific papers?

**URL:** <https://discourse.julialang.org/t/how-do-you-organise-scientific-papers/28364>\
**Category:** Community\
**Created:** [September 4, 2019, 9:19am UTC](https://discourse.julialang.org/t/how-do-you-organise-scientific-papers/28364 "2019-09-04T09:19:43Z")\
**Posts on this page:** 13\
**Page:** 2

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**Author:** ![tbeason](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/tbeason/32/15898_2.png) [@tbeason](https://discourse.julialang.org/u/tbeason)\
**Post date:** [September 4, 2019, 3:03pm UTC](https://discourse.julialang.org/t/how-do-you-organise-scientific-papers/28364/22 "2019-09-04T15:03:50Z")

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I save the pdfs in a folder and when I need the bibtex reference I grab it from Google Scholar… maybe I should check out Zotero haha

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**Author:** ![cscherrer](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/cscherrer/32/7631_2.png) [@cscherrer](https://discourse.julialang.org/u/cscherrer)\
**Post date:** [September 4, 2019, 4:24pm UTC](https://discourse.julialang.org/t/how-do-you-organise-scientific-papers/28364/23 "2019-09-04T16:24:58Z")

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I used to use Mendeley, tried switching to Zotero because Elsevier.

Look and feel seem much more native than with Mendeley, but other than that it’s been kind of a mess. Trying to import things left me with this weird hierarchy, with papers attached to the wrong citation. And the single feature I use most, full text search, doesn’t seem to work at all. It often tells me there’s no match, even in cases where I know that’s not right.

The whole thing has been really frustrating

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**Author:** ![mbaz](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/mbaz/32/17295_2.png) [@mbaz](https://discourse.julialang.org/u/mbaz)\
**Post date:** [September 4, 2019, 6:55pm UTC](https://discourse.julialang.org/t/how-do-you-organise-scientific-papers/28364/24 "2019-09-04T18:55:52Z")

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> [@cscherrer](#):
>
> full text search, doesn’t seem to work at all

For what it’s worth, I use Zotero and haven’t had problems with full-text search.

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**Author:** ![chakravala](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/chakravala/32/6832_2.png) [@chakravala](https://discourse.julialang.org/u/chakravala)\
**Post date:** [September 4, 2019, 6:59pm UTC](https://discourse.julialang.org/t/how-do-you-organise-scientific-papers/28364/25 "2019-09-04T18:59:02Z")

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I no longer digitally organize papers, I have a laser printer and print out whatever I find important. In the past I experimented with Jabref and other tools, but none of them satisfy me. Someday I want to make my own tool based on [VerTeX.jl](https://github.com/chakravala/VerTeX.jl) for references, as I discussed before

> [@Replacing CITATION.bib with a standard metadata format](https://discourse.julialang.org/t/replacing-citation-bib-with-a-standard-metadata-format/26871):
>
> Many Julia packages are starting to use a CITATION.bib file containing bibTeX citations for the package, as suggested on the [Julia Research](https://julialang.org/research/) page. I think it is a mistake to use a Julia-specific format here — providing code metadata is not a Julia-specific problem, and there is a huge community interested in promoting better metadata formats. BibTeX is very convenient for those of us in mathematical sciences where LaTeX is popular, but it is pretty inconvenient outside of a TeX environment (e.g…

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**Author:** ![Zach\_Christensen](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/zach_christensen/32/7220_2.png) [@Zach\_Christensen](https://discourse.julialang.org/u/Zach_Christensen)\
**Post date:** [September 4, 2019, 9:30pm UTC](https://discourse.julialang.org/t/how-do-you-organise-scientific-papers/28364/26 "2019-09-04T21:30:52Z")

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I’ve used refworks and recently tried endnote, all because of collaboration on papers. Can’t get over how much easier Zotero is.

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**Author:** ![cscherrer](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/cscherrer/32/7631_2.png) [@cscherrer](https://discourse.julialang.org/u/cscherrer)\
**Post date:** [September 4, 2019, 9:33pm UTC](https://discourse.julialang.org/t/how-do-you-organise-scientific-papers/28364/27 "2019-09-04T21:33:16Z")

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@mbaz did you have to do anything special to set things up? I had hoped to just point it at a directory of pdfs and let it work through them. But it seemed to require selecting a small subset at a time and dragging documents in manually. And I’m not sure why search isn’t working, but the whole thing is only a small benefit (for citations) without it.

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**Author:** ![mbaz](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/mbaz/32/17295_2.png) [@mbaz](https://discourse.julialang.org/u/mbaz)\
**Post date:** [September 4, 2019, 9:44pm UTC](https://discourse.julialang.org/t/how-do-you-organise-scientific-papers/28364/28 "2019-09-04T21:44:57Z")

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I don’t recall having to do anything. I just re-read the documentation ([searching [Zotero Documentation]](https://www.zotero.org/support/searching)) and I found that about half my PDF files were not indexed. I rebuilt the index and now most of the files are indexed. The ones that are missing might be scanned PDFs that don’t contain any actual text. I hope this helps – let me know if you want me to run any tests on my side.

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**Author:** ![mbeach42](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/mbeach42/32/5747_2.png) [@mbeach42](https://discourse.julialang.org/u/mbeach42)\
**Post date:** [September 4, 2019, 10:33pm UTC](https://discourse.julialang.org/t/how-do-you-organise-scientific-papers/28364/29 "2019-09-04T22:33:24Z")

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> [@tamasgal](#):
>
> it requires some lib-path adjustments on ArchLinux, I was not able to run. I then

the [AUR](https://aur.archlinux.org/packages/zotero/) version works great for me on Arch.

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**Author:** ![anon92994695](https://avatars.discourse-cdn.com/v4/letter/a/ce7236/32.png) [@anon92994695](https://discourse.julialang.org/u/anon92994695)\
**Post date:** [September 4, 2019, 10:44pm UTC](https://discourse.julialang.org/t/how-do-you-organise-scientific-papers/28364/30 "2019-09-04T22:44:54Z")

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I use my brain and a nesting of directories with \*.pdfs. Not the most satisfactory answer, but it’s honest.

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**Author:** ![mbaz](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/mbaz/32/17295_2.png) [@mbaz](https://discourse.julialang.org/u/mbaz)\
**Post date:** [September 4, 2019, 10:52pm UTC](https://discourse.julialang.org/t/how-do-you-organise-scientific-papers/28364/31 "2019-09-04T22:52:41Z")

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I used to do that, but my brain overflows pretty easily these days (and it’s only getting worse over time 🙂)

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**Author:** ![swt30](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/swt30/32/4667_2.png) [@swt30](https://discourse.julialang.org/u/swt30)\
**Post date:** [September 5, 2019, 10:37am UTC](https://discourse.julialang.org/t/how-do-you-organise-scientific-papers/28364/32 "2019-09-05T10:37:03Z")

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If you are using Zotero, don’t miss [ZotFile](http://zotfile.com/), which makes it easy to add PDF attachments to items, and also automatically renames/moves them into the location of your choice. I use this to put all my downloaded PDFs into a “papers” folder on Google Drive. It also promises to sync PDFs and annotations to/from iOS/Android.

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**Author:** ![Juan](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/juan/32/7657_2.png) [@Juan](https://discourse.julialang.org/u/Juan)\
**Post date:** [May 17, 2020, 11:51pm UTC](https://discourse.julialang.org/t/how-do-you-organise-scientific-papers/28364/33 "2020-05-17T23:51:15Z")

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I’m using Zotero and Jabref for bibliography, none is perfect but at least they work and are free. If you want to use it for Latex I think Jabref works better.  
I would like to use EndNote but it’s absurdly expensive.

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**Author:** ![dalanicolai](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/dalanicolai/32/13350_2.png) [@dalanicolai](https://discourse.julialang.org/u/dalanicolai)\
**Post date:** [June 4, 2020, 3:17am UTC](https://discourse.julialang.org/t/how-do-you-organise-scientific-papers/28364/34 "2020-06-04T03:17:57Z")

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You could try the Emacs solution using Spacemacs. It uses Evil, which is like VIM build in Emacs. You can still use VIM for everything else, although Emacs is a superb Latex editor itself (setup is a breeze with Spacemacs). You will also get the awesome org-mode, and generally very good support via Spacemacs gitter. If you will try, then switch to the develop branch immediately. I think it is really worth it to check it out. I switched myself from VIM to Spacemacs almost completely, but I still have VIM available.

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