Apps for doing Research in Linux?

Software PureOS
1

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.

Gnome Latex works great and is one of the best apps for Latex format.

Zotero is a great application for research for references and bibliographies organization, supports Open ID login by OpenID Foundation

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

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

DataHub IO (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)

Joplin is great note taking to do list app, supporting markdown format
syncing with NextCloud (other sync options supported).

Firefox one of the best browsers that respect privacy and is not chromium based.

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.

My Current Goal is to try install and test out all of this apps in current PureOS any advice is welcome, I have already tested Linux Mint, NixOS, Manjaro and next on the list is PureOS PC, the PureOS seems to be great.

Regards, Alex

4 Likes
2

Seems like you got it pretty nailed down. I haven’t tried it but you can try abiword for composing, editing and viewing docs. I’d say go manjaro for your OS. Huge community, based on arch so very nice and only thing I could complain about it is compatibility with programs supporting deb first, rpm seconds and thirdly arch but the community is so big somebody probs made an awesome native solution already. I dunno. Just my opinion.

1 Like
3

Well I use Linux for about 10 year, I know few things :slight_smile: Thanks for your time will give your suggestions a try.

Fedora has being my main OS for many years, but I test out other Linux OS, PureOS, Manjaro yes, Linux Mint. (Already have the same post in Manjaro and Linux Mint).
Most of the popular. Debian Family (PureOS, Linux Mint, Elementary, Ubuntu) and Arch (Manjaro, Manjaro embeded). Red Hat Family (CentOS, Scientific Linux) even tried out Ubuntu Touch and few other mobile OSs.

For me personally Fedora is great due to RedHat extensive documentation and wonderful support for coding.
Yeah debian is probably great if you are regular desktop user, and Manjaro due to arch is on the cutting edge.
Regards, Alex

4

I used Fedora for several years and do think it’s a great choice. I recently switched to Pop!_OS because my laptop has an Nvidia card that wouldn’t always play well with Fedora.

I probably like Fedora more overall, but Pop! is great if you have Nvidia hardware.

Some software alternatives and other software I’ve liked. I really like the unified experience sticking with GNOME+GTK provides, so I’ve focused more on that:

Latex - Setzer
I just recently found this, but it’s a nice GTK-based editor, and if you install with Flatpak, it’s actually a nice way to download Latex as well.

Markdown - Marker
If you like using Markdown to write notes or other documents, this is another nice GTK-based editor, which is also easily installed with Flatpak.

Generic Text Editor - Gedit
Honestly, I find the GNOME-default Gedit to be perfectly fine for general code-writing. It’s got enough customizability with various plugins that it does exactly what I want of it.

Python/Jupyter Notebooks - nteract
If you use Jupyter Notebooks, but prefer the idea of having a desktop application rather than running it in your browser, nteract is great. This is Electron-based, not GTK, but I quite like it, particularly for quick development and testing of Python code, as well as for analysis tasks.

1 Like
5

LibreOffice is decent. Certainly the way to go if you need to open files coming from Mac or Windows. For writing papers, I tend to just use straight LaTex, with an appropriate template. For editing LaTex, split-screen emacs works great, since you can hook it up to auto-generate the PDF or HTML output and display it on save.

2 Likes
6

Thanks all for the suggestions, I have tried many of the apps mentioned and I am glad for the suggestions.

taylor-williamc yeah I have used PopOS, but Linux Mint seams easier to maintain (since I have many PCs and many different OS), I used PopOS on my System76 but moved to Linux Mint due to better support on my test PCs, also using Manjaro or NIXos interesting Linux OS I found recently. For Linux Newcommers I always recommend PopOS or Linux Mint over any other due to good community support, they are my go to OS for gaming.

lperkins2 not all research journals and conferences require LaTex markdown format, some want office docx or opne office, so Libre Office supports all of them, I usually write it all at first in simple text editor. Gnome Latex is very good options and integrates well with Libre Office (plus Zotero keeping track of bibliography).

7

Aye, that’s fair enough. It’s been a few years since I did anything that way. At the time, most everyone wanted .doc or .docx, but would generally accept .pdf. Given OpenOffice’s trouble with advanced formatting and fonts with MS Word compatibility, we used LaTex internally and shipped as PDFs.

Anyway, I forgot to mention gnumeric, GNU’s spreadsheet program. It’s decent overall, but not as polished as LibreOffice calc, but it does have a parametric solver out of the box, which is nice if you need it. I haven’t found another open source spreadsheet program which does.

2 Likes
8

Thanks for the input, I personally have not used spreadsheet program since 2010 I guess, I write the text in atom (Joplin First) or sometimes MC editor in terminal console, and just open and save the text in LibreOffice.
I also admit that the LaTex format is simple to use then all the doc and docx but corporations effect change.

Regards, Alex

9

I use LibreOffice for most things except for two issues.

  1. Excel spreadsheets with complex sheet to external sheet linkages don’t convert, so I have to stick with Excel in a certain case. (My HackMaster character sheets with common tables in another sheet with Hlooksup and Vlookups.)

  2. Word mail merges don’t convert for label printing. i have to stick with Word.

1 Like
10

Thank you everyone for the time+contribution to my post, this is a wonderful community I am glad I am part of.

I personally have not used spreadsheeet in years probably last time in office 2003 with WinXP before 2007.
and last few years after my company moved to slack like services for inter company messaging, I actually only check my email when I register for a service and few times per week just in case someone sends an email.

EDIT: Yesterday I had a 20 or 24h time limited before I can reply to the post as a new user, just an FYI in case it takes me about 1 day to reply again, it might not be by choice and if next day is full of work might be 2 days.

Regards, Alex

11

Thank you all for the input here I value your suggetions and your time, I will be leave the forum soon.
All the best to all here and to PureOS and Purism.

Best Regards.

12

Bye. Nice having you.