Apps for doing Research in Linux [CLOSED]

On the topic of research and apps that help document research and write research papers in Linux (Fedora Workstation 31) this is my experience and opinion:

LibreOffice is most compatible with the all formats for research conferences and journal paper publication, it even supports LaTex format. https://www.libreoffice.org/download/download/

Gnome Latex works great and is one of the best apps for Latex format. https://github.com/GNOME/gnome-latex

Zotero is a great application for research for references and bibliographies organization, supports Open ID login by OpenID Foundation https://www.zotero.org

Atom is one of the best text editors for code writing, you can "hack it" (legally and supported by FOSS licence) and make it your own to best suite you + post it on github https://atom.io

(I hope Microsoft will not change that and give priority to their VSCode text editor)

DataHub (Guthub for datasets) CLI tool works in Linux, website works fine, they should have a graphical tool soon (not sure if CLI works in other Operating Systems) https://datahub.io

(Get Archive https://github.com/datopian/data-cli/releases/download/v0.9.5/data-linux.gz

unzip archive, make file executable "chmod +rwx data-linux" or "chmod 777 data linux" and start from terminal.)

Joplin is great note taking to do list app, supporting markdown format https://joplinapp.org
syncing with NextCloud https://nextcloud.com (other sync options supported).

Firefox one of the best browsers that respect privacy and is not chromium based. https://www.mozilla.org/en-US/firefox/new/

My Recommended Linux Operating system is Fedora Workstation with software from https://labs.fedoraproject.org or just use Fedora Labs from start.
My Recommendation based on experience for doing research in Linux (Fedora Workstation) is:
LibreOffice + Gnome Latex + Zotero + Atom (and github) + datahub CLI + Joplin + Firefox

Any comments or advice are welcome here, I am always happy to learn about new FOSS (free and open source software) applications that are used in research today.

All the above apps are tested in Linux Mint 19.3 Cinnamon and Manjaro with Cinnamon (also Fedora Workstation 31 using Cinnamon desktop) they all work great under Manjaro.

Regards, Alex

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FreeOffice reads latex files such as any other text files. But does it have any editing features (from the latex/syntax and compiling point of view)?

Also, if you're using FreeOffice and gnome-latex, I can only presume you intend to write text documents graphically. But FreeOffice, AFAIK, doesn't integrate with Zotero, so you loose a big deal by not using LibreOffice instead. Trust me, when you need to reference dozens of sources several times, change citations along the way and then write a bibliographic reference in the end it helps a lot (eventhough zotero gets slow - in MS Word).

Finally, FreeOffice LibreOffice has a plugin which allows to convert between latex and OpenDocument formats. I never used it, but I can see the advantage here, for someone who prefers latex but has to write in a different format or vice-versa.

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Are you talking about FreeOffice or LibreOffice? I'm not aware FreeOffice has a conversion plugin. Can you point me to it? Or you meant LibreOffice instead?

Oh! You're right, I was specifically talking about my master thesis, since that's where I've working on lately. The only papers I know with dozens of references are review papers, but those aren't that common.

:+1:

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Oops! I think the error came from my first reply. I presume you were talking about LibreOffice. I have corrected my previous post.

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Since this is an ongoing discussion (and quite an interesting one) can you please remove the [Closed] tag? In case others might want to discuss this as well?

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I wanted to share an experience sort of post as a blog, but discussion is always better even if I did not expect to find people interested in research topic on Linux, pleasant surprise.

Ari.

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We have all kinds around here.

:grin:

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yeah from all the Linux Communities I jumped at this is the most diverse, enjoyable and fun to be in.

Ari.

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"All the forums in all the distros in all the world--and you jumped into ours!"

Play it, Ari. :slight_smile:

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haha nice spin of Casablanca :smiley: this is actually my 7-th Linux dsitro community.
Ari.

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Various editors integrate LaTeX (emacs, vim, kate IIRC, ... ) or are speciallized for LaTeX (texmaker, texstudio, kbibtex, kile, ktikz, ... ), you could also run pdflatex from cli.
Personally, I use emacs with the spacemacs configuration and tex-layer. I also create most necessary graphics with tikz.

Another part of research is statistics and numerical mathematics: octave or R (for statistics).

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You'll find us by far the most fun forum.

And Linux does get spoken. Occasionally. :wink:

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thanks I work as a data scientist and data viz is last part of the story.
yeah I use octave sometimes, but I like R more, R cran has a lot of tools, and R studio is great + R Shiny has a webservice where you can just send link with the analyzes done and complete no large files.
https://www.rstudio.com https://shiny.rstudio.com
ReDASH is great also, they offer payed service or free community manage your self server.
https://github.com/getredash

Most of my work is the backend not front end part of the AI, so I use terminal 99% of time + browser for company webservices for administration stuff.

I agree.

I just wanted to add. Not that I do research (beyond googling memes and the random thing once in a while) but I just discovered kile for LaTeX. What a fantastic tool!
I'm learning it to replace Micro$haft Publisher for the Newsletters I make for a project.

Really love it. LaTeX is pretty slick too.

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is that in KDE Kile? https://kile.sourceforge.io/screenshots.php

???

Kile is what my coworkers use (the ones using latex, which are few) and what I plan to use if I get to make the shift in the following months (I mean the shift from graphical writing/formatting).

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Yes it is.

Microsoft Publisher
I've been searching for something to handle making newsletter. Linux is sorely lacking for Desktop Publishing. I stumbled onto kile. Which as I learn how to use it (and LaTeX) I think will fit the bill.

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I'm really impressed by it so far. I'm a total LaTeX newb but it's been really fun to learn and Kile just works and is surprisingly intuitive.

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Microfost I forgot them :smiley: I left that world many years ago for linux so don't keep track of the F they do. well writing papers and newsletters are kinda similar, you need to follow strict formatting since later on papers or journals are published online in a newsletter type of website.

I agree that kile OR any other latex editor can do the job, if you use KDE stick to kile, I moved from VLC to lollypop and gnome-videos since the DESKTOP evn. default apps works best in any linux distro.
any latex editor has a learning curve but worth it on the long run compared to graphical writing.

Ari.

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