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I am beginning to write some short stories and I am trying to find some software that may aide me in brainstorming.

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Freemind is a commonly-used program for mind-mapping.

With a little practice, it can easily become a medium for your own thinking process. One of the best features of Freemind is that you can define your own key-mappings, which makes it more productive than other mind-mapping (brain-storming) tools out there. Also, though it is a mature software, it is still actively developed; so you can expect more features coming in as time goes by.

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Zim is another wiki-like program that allows you to take notes and brainstorm. It also works with WikiWords and will auto-link notes.

It's a little more difficult than Tomboy to setup, but it's a lightweight and powerful note-taking and brainstorming tool.

Zim is in the repos.

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I find I waste time trying to use fancy mind-mapping tools. Instead, I like using a "distraction-free" writing environment such as:

  • PyRoom or JDarkRoom: Full-screen, text-only writing. Forget about formatting. Stop glancing at the clock, and do NOT pause to check your email.
  • Typewriter: True to its name, this text editor has no backspace. Just write. You can come back to it later. (Extract the download until you reach Typewriter.jar)
  • Single-line visibility in gedit: Blinders for your text editor. Only the current line is visible, so there is no opportunity to get side-tracked rethinking your previous ideas.
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basket is pretty good for it too. It is not so graphical or map oriented, but it allows ideas to be freely explored and different items to be moved around and grouped.

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  • How I miss basket and its predecessor KnowIt!
    – dotancohen
    Jan 21, 2016 at 10:49
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I like to use Tomboy for note-taking and for brainstorming. It works really well, and you can organize all your thoughts into different "notebooks" to keep everything together. IT works with wikiwords, so you can type a word LikeThis and it will automatically link to the note called LikeThis. If there's no note by that name, Tomboy will create it.

Tomboy is automatically installed, or if it isn't, it's in the repos.

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