This is my list of GNU/Linux tools for academic, educational, and research purposes which all are free software. I tried to pick up choices as simple as possible here just to represent every basic category and further I hope you could see more alternatives if you want. I also listed several specific tools like GNU Octave and Parallel which are proven to be useful for certain researches. On the other hand, I deliberately did not list LaTeX tools here as I already chosen LibreOffice for that category. I made every proprietary software name italicized here so you can spot them on easier. Happy researching!
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LibreOffice
Tool for writing all text documents. On other OS, this is equal to MS Word, Excel, and PowerPoint with abilities to write math equations, draw diagrams and flowchart, plus make database, plus many more extensions. Zotero bibliography tool, for example, helps you creating citations and bibliographies easily on LibreOffice Writer. On Ubuntu and most GNU/Linux distros, this tool is preinstalled already.
https://www.libreoffice.org
Firefox
Tool for surfing the internet. It is also preinstalled on Ubuntu and most distros. The important thing is that it is used by many people including researchers and it has tremendous amount of extensions available including for research purposes. Zotero, for example, works by "Save to Zotero" button on Firefox.
https://www.mozilla.org/firefox
Zotero
Tool for managing research references, bibliography, and citations. This tool integrates well to Firefox browser and LibreOffice word processor so you can make standard paper or thesis with nice citations. This is equal to Mendeley. Zotero is not preinstalled but is available as stand alone program plus Firefox and LibreOffice addons (old versions were simply an addon to Firefox).
https://zotero.org
StarDict
Dictionary for almost all languages. You can install the software and later add up dictionary files as you wish from repositories[1][2][3][4]. StarDict is not preinstalled but available on Ubuntu and most distros to be installed manually. If your research involves foreign languages, you will find this tool very helpful.
http://stardict.sourceforge.net
Inkscape
Tool for drawing and making illustrations. This is equal to CorelDRAW. Inkscape is not preinstalled but available on Ubuntu and most distros to be installed manually.
https://www.inkscape.org
GIMP and G'MIC
GIMP is tool for photo retouching. This is equal to Photoshop. G'MIC is tool for image processing, often paired with GIMP, which can help your research if it involves images. With GIMP you can easily adjust things such as brightness, color, contrast, etc. from images you are researching for further processing e.g. doing optical character recorgition (OCR) with Tesseract. For research example in this field, read David Revoy's interview. GIMP and G'MIC are not preinstalled on Ubuntu and most distros but can be easily installed.
https://www.gimp.org
https://gmic.eu
Fcitx and Mozc
Tool for writing text not in Latin alphabet script i.e. Arabic, Japanese, Chinese, Russian, etc. Fcitx and Mozc are preinstalled on Ubuntu, but not in most distros, however they are available to install manually.
https://fcitx-im.org
https://github.com/google/mozc
PDFSAM
Tool for splitting and joining PDF document. You can use this tool to join several documents with chapter order you choose. You can use it too if you wish to separate a document into parts with range you choose. You can find this tool helpful also for making digital journal which consists of PDF parts. PDFSAM is not preinstalled but available to be installed manually.
https://pdfsam.org/pdfsam-basic
Simple Scan
Tool for scanning physical paper documents into digital files. It is preinstalled on Ubuntu and most distros. It is a part of GNOME desktop environment.
https://launchpad.net/simple-scan
Tesseract
Tool for optical character recognition (OCR). This tool can help you to automatically write down text (either hand-written or printed) from photo without typing manually. Tesseract is the tool used by Google Inc. to detect text in images, videos, mobile devices, and Gmail spam detection. Read more about Tesseract use at Dedoimedo and LinuxJournal and Splitbrain.
https://opensource.google/projects/tesseract
Cheese
Tool for webcam. It is also preinstalled on Ubuntu and many other distros. You can use this if you research about image processing or pattern recognition for example. It is also part of GNOME.
https://wiki.gnome.org/Apps/Cheese
Audacity
Tool for editing digital audio and recording it also. It is not preinstalled on Ubuntu and most distros so you need to install it manually. You can use this if your research involves voices or sound.
https://www.audacityteam.org
digiKam
Tool for photo management especially to import them easily from any camera. This tool is not preinstalled on Ubuntu and most distros but you can install it manually.
https://digikam.org
Orca and Magnifier
Accessibility tools for vision or hearing impaired people. Orca helps speak-out-loud text on screen, while Magnifier helps zoom out things on screen. With these tools you can help yourself if you have difficulties, and help other researchers if they have ones. Fortunately, both are already preinstalled on Ubuntu and many other GNOME-based distros.
Orca, text to speech
Magnifier, zoom in and zoom out
Specific Tools
In order to keep this article simple, I separated field-specific tools from the main part. I also tried to make this particular list as simple as possible so later you could extend yourself to find more alternatives if you wish because I mention the website links. I believe you could learn so much just by reading each website of tools here.
- GNU Octave: equal to MATLAB, a mathematical simulator. But if you need Simulink alternative, use Scilab.
- GNU PSPP: equal to IBM SPSS, a statistical tool.
- GNU R: equal to IBM S language, for statistical programming.
- GNU Health: a medical and hospital information system tool.
- FreeGLUT: library to help you create (implement) OpenGL-based graphical programs e.g. video game or computer graphic projects.
- QGIS: equal to ArcGIS, a geographical information system.
- gEDA and KiCAD: equal to Multisim and EAGLE, a set of electronics design and simulation tools. See excellent example in real-life by Purism Librem project.
- GNU Parallel: a parallel processing tool. See amazing example in huge data processing (25TB) here.
- Mesa 3D: the free software OpenGL implementation on GNU/Linux.
- GNS3: equal to Cisco Packet Tracer, a computer network simulation tool.
- Wireshark: wiretapper tool to analyze how computer network works.
References
- https://linuxrig.com/tag/linux-academics
- https://bmcresnotes.biomedcentral.com/articles/10.1186/1756-0500-4-434
- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3091616
- https://opensource.com/article/20/1/teach-physics-open-source
- https://www.researchgate.net/publication/266883914_Open_source_software_in_teaching_physics_A_case_study_on_vector_algebra_and_visual_representations
- GNU Parallel https://www.biostars.org/p/63816
- https://help.ubuntu.com/community/OCR
- https://en.wikibooks.org/wiki/OpenGL_Programming
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