FOSS and FLOSS Writing, Research and Productivity Tools

Here is a list of writing, research, productivity and online collaboration tools, focusing on FOSS and FLOSS, most of it running cross-platform.

Operating Systems
Linux Mint
Linux Mint is a Linux distribution based on Debian and Ubuntu,[4] with an alternative Linux Mint Debian Edition (LMDE) based purely on Debian. Mint provides full out-of-the-box multimedia support by including some proprietary software such as Adobe Flash.

Operating Systems (discontinued)
Artist X
ArtistX is an open source GNU/Linux distribution designed from the ground up to transform your personal computer into a fully capable audio/video and graphics production studio in a shortest time as possible. ArtistX incorporates all the necessary open source video and audio codecs, as well as full support for 2D and 3D graphics.

Operating Systems
Open Artist
openArtist tries to collect and combine creative software into one distribution, ready to use. Some of these programs are just not found in Ubuntu/Debian repositories, are built from scratch and packaged into openArtist’s repository. Also the Personal Package (ppa) archives play a siginficant role in openArtist. Canonical has made a fine invention when setting up Launchpad and their ppas. Many people build their own versions of programs, drivers etc, and openArtist tries to use the best ppas around to provide a stable, up-to-date distribution and program base.

Collaborative writing
Etherpad
Etherpad allows you to edit documents collaboratively in real-time, much like a live multi-player editor that runs in your browser. Write articles, press releases, to-do lists, etc. together with your friends, fellow students or colleagues, all working on the same document at the same time. All instances provide access to all data through a well-documented API and supports import/export to many major data exchange formats. And if the built-in feature set isn’t enough for you, there’s tons of plugins that allow you to customize your instance to suit your needs.

Sites that run etherpad (normally deleted after 30 days on inactivity!):
http://typewith.me/ (US)
http://piratepad.net/front-page/(Sweden)
http://www.edupad.ch/ (Switzerland)
https://www.etherpad.servus.at (Austria)
http://openetherpad.org/ (US)
http://primarypad.com/ (UK)
http://etherpad.netluchs.de (Germany)
http://www.piratenpad.de/ (Germany)
http://piratepad.nl/ (Netherlands)
http://piratepad.eu/ (Beta) (Luxemburg)
http://meetingwords.com/ (US)
http://titanpad.com/ (Austria)
http://pad.telecomix.org/ (Sweden)
http://livepad.eu/ (Sweden)
http://pad.planka.nu/ (Sweden)
http://publishwith.me/ (France)
http://pad.candan.fr (France)
http://lullapad.com/ (US)

Collaborative calculating
Ethercalc
Your data is saved on the web, and people can edit the same document at the same time. Everybody’s changes are instantly reflected on all screens. Work together on inventories, survey forms, list management, brainstorming sessions and more!

Survey
Limesurvey
LimeSurvey (formerly PHPSurveyor) is a free and open source on-line survey application written in PHP based on a MySQL, PostgreSQL or MSSQL database, distributed under the GNU General Public License. As a web server-based software it enables users using a web interface to develop and publish on-line surveys, collect responses, create statistics, and export the resulting data to other applications. Users can use rich text in questions and messages, using a rich text editor, and images and videos can be integrated into the survey. The layout and design of the survey can be modified under a template system. Templates can be changed in a WYSIWYGHTML editor. Additionally, templates can be imported and exported through the template editor. Once a survey is finalized, the user can activate it, making it available for respondents to view and answer. Likewise, questions can also be imported and exported through the editor interface. LimeSurvey has no limit on the number of surveys a user can create, nor is there a limit on how many participants can respond. Aside from technical and practical constraints, there is also no limit on the number of questions each survey may have. (via Wikipedia)

Organizing references
Referencer
Referencer is a GNOME application to organize documents or references, and ultimately generate a BibTeX bibliography file. It is designed with the scientist/researcher in mind, and “document” may be taken to mean “paper” in general, although Referencer can deal with any kind of document that BibTeX can. (via Wikipedia)

Organizing references
Zotero
Zotero /zoʊˈtɛroʊ/ is free and open-source reference management software to manage bibliographic data and related research materials (such as PDF files). Notable features include web browser integration, online syncing, generation of in-text citations, footnotes and bibliographies, as well as integration with the word processors Microsoft Word, LibreOffice, OpenOffice.org Writer and NeoOffice. It is produced by the Center for History and New Media of George Mason University (GMU). (via Wikipedia)

Note taking
Scrivener
Scrivener is a word-processing program and outliner designed for authors. Scrivener provides a management system for documents, notes and metadata. This allows the user to organize notes, concepts, research and whole documents for easy access and reference (documents including rich text, images, PDF, audio, video, web pages, etc.). Scrivener offers templates for screenplays, fiction, and non-fiction manuscripts. After writing a text, the user may export it for final formatting to a standard word processor, screenwriting software, desktop publishing software, or TeX. (via Wikipedia)

Note taking
LyX
LyX is an advanced open source document processor running on Linux/Unix, Windows, and Mac OS X. It is called a “document processor”, because unlike standard word processors, LyX encourages an approach to writing based on the structure of your documents, not their appearance. LyX lets you concentrate on writing, leaving details of visual layout to the software. LyX automates formatting according to predefined rule sets, yielding consistency throughout even the most complex documents. LyX produces high quality, professional output – using LaTeX, an open source, industrial strength typesetting engine, in the background. (via website)

Writing
LyX-Outline
LyX-Outline is a forthcoming add-on to the popular document processor, LyX, that will give it many of the same features as the writing tool, Scrivener. This add-on is a recognition that writing is about more than just plugging away at a piece of prose until it is finished. It’s also about tracking down loose ends, trying to visualize structure, and avoiding as many dead-ends as possible. In a word, it’s about getting from first to final draft by the quickest route possible, which may not necessarily be a straight line. (via website)

Distraction free Writing
FocusWriter
FocusWriter is a simple, distraction-free writing environment. It utilizes a hide-away interface that you access by moving your mouse to the edges of the screen, allowing the program to have a familiar look and feel to it while still getting out of the way so that you can immerse yourself in your work. It’s available for Linux, Windows, and Mac OS X, and has been translated into many different languages. (via website)

Writing – Word Processors
Latex word processing

Latex templates for Masters and PhD thesis:
Latex-Templates
MIT – thesis template
Sharelatex templates
PhD thesis templates

Writing – Word processing, Calculation, Presentations
LibreOffice
LibreOffice is a free and open source office suite, developed by The Document Foundation. It was forked from OpenOffice.org in 2010, which was an open-sourced version of the earlier StarOffice. The LibreOffice suite comprises programs for word processing, the creation and editing of spreadsheets, slideshows, diagrams and drawings, working with databases, and composing mathematical formulae. (via wikipedia)

Paper organizer
gPapers

This is gPapers, the open-sourced, Gnome based digital library manager. Think of it as an iTunes for your PDFs. I’ve written this mostly because my desk looks like this. You read a lot during your PhD, and keeping printouts on your desk in a giant stack just doesn’t scale. Necessity is the mother of invention…

http://gpapers.org
Installation Instructions (Linux)

Maps
Openstreetmap

Wikipad and Dokuwiki
Wikipad
Dokuwiki

PDF viewer and merger
Okular – pdf viever with highlight feature
Evince – pdf Document viewer
PDFsam – split and merge pdf files

Plagiarism checker
Ithenticate
Plagiarisma
Grammarly
Copyscape

Other useful programs
Shutter – Screenshot maker
Simple Screen Recorder – record your screen and make a tutorial video
Argunet – built argumentation maps
Freemind mindmapping tool
cb2bib – extract bibtext data from pdfs

LINKS – Books and research paper databases
Library.nu
AvaxHome
Library Genesis
Bookfi
Docstoc

IM, VOIP Chat & File xchange:
TOR messenger
Jit.si
BlinkZulip Group chat

Search engines
List of academic search engines
Google scholar, Google books
Philpapers
Archive.org
Semantic scholar

Research Directories
JAR – Journal of artistic research
Directory of Open Access Journals
Academia.edu
Researchgate
Refworks

FTP & Cloud
Owncloud
Filezilla

DVD backup and Video converter
Handbrake

Learning management software
Moodle system

Emulators
Wine – run windows programs on Linux

Inventory tracking
partkeepr.org

Find more tools and programs at PRISM-BREAK and FOSSfind