I've now been using Mathematica for about a year, and am starting to get a somewhat unwieldy collection of notebooks. Sometimes I've figured out how to do a particular task in one of them, and want to use that again, but have to search through what I've done.

To tackle this, I've cobbled together a script that generates an html page for all the notebooks that I've checked into my source code repository (I happen to be using github to store my notebooks, latex, and other source code), and can put comments in that generated html file about what I did in each notebook, including any special techniques that I learned to accomplish the task. By way of example, I can list these with something like on this page.

From a local copy of my source repository I generate something similar, allowing a click on the various notebooks to view them with the CDF player.

I'm able to navigate my collection of notebooks well enough this way, but was curious how other people tackle the same organizational problem?

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    $\begingroup$ By a crazy directory structure and file-naming scheme, often helped by utilizing the "Search inside a file" feature on Windows. In other words, my pile of Mathematica notebooks looks much like the piles of notes on my desk... $\endgroup$
    – Eli Lansey
    Feb 2, 2012 at 21:20
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    $\begingroup$ I use folders and filenames. $\endgroup$
    – David
    Feb 2, 2012 at 21:21
  • $\begingroup$ Is this really a question about how to do something with Mathematica? $\endgroup$
    – Verbeia
    Feb 2, 2012 at 22:59
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    $\begingroup$ @verbeia, Perhaps, if Mathematica provides infrastructure for organizing and searching notebooks. $\endgroup$ Feb 3, 2012 at 0:17
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    $\begingroup$ I've been thinking of a system for exactly this. I was thinking of storing a database of notebook information (file path, title, tags) in a .m file and then making a notebook with a GUI for searching the database by tag and notebook contents. $\endgroup$
    – Andrew
    Feb 3, 2012 at 3:44

2 Answers 2


There are two answers to this question, and only one has anything to do with directory structure, and that only mildly.

The first answer is to structure the notebook itself using the style groupings provided. This will greatly enhance your ability to find something within any given notebook. For instance, as a materials physicist I use a model known as tight binding, and as part of my learning about how to apply it to a particular crystal structure, I have a notebook that I treat as a lab notebook. It has three main sections: Setup, Preliminary Testing, and Full Testing all at the highest level of the hierarchy. The least organized section is the Preliminary Testing, but even there I make ample use of Text cells to record my thoughts and observations. The other two sections make full use of the hierarchy to organize and group my examinations of the tight-binding method.

The second answer is packages. If you have some code that you find yourself referring to often, put in a package. Here I tend to use a rule of three, if I have to refer to or rewrite something 3 or more times, it needs to be in a package. It is here that a directory structure is helpful. In my case, my packages are currently organized into three directories: Quantum, Utilities, and Wien2k (a software package I've written interface scripts for) for a total of 16 packages.

I try to make each package somewhat complete in that they provide a full range of services. For example, the Wien2k package for loading their crystal structure files provides a full range of functions for accessing the structured information in those files, but sadly not saving them, as I haven't had the need to write it. But, some packages are just buckets of loosely related functions, and they're perfect that way.

  • $\begingroup$ So after you have a bunch of packages, organized into directories, you begin to have essentiall the same as at the start?? $\endgroup$
    – murray
    Sep 1, 2012 at 15:06

I use big, omnibus Notebooks with a deep section hierarchy rather than many smaller notebooks. These omnibus Notebooks then have a button on an installed palette for direct opening.

They look something like this:

Mathematica graphics

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    $\begingroup$ How big? Doesn't this become unwieldy? (Or does this notebook have hyperlinks to other notebooks -- which eventually would seem like a good idea.) $\endgroup$
    – murray
    Sep 1, 2012 at 15:07
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    $\begingroup$ @murray -- good question; not too big, and I'm careful to keep Graphics/Image objects out of the Notebooks most of the time and I turn off Cell edit tracking to minimize size. My largest Notebooks of this type are only around 3MB. Indeed adding another level of hyperlinks, from one of these Notebooks to others, rather than only from the Palette to the Notebooks, would be a good idea for any large projects. I don't have so many large projects that I cannot keep individual Notebooks for them and find them easily. $\endgroup$
    – Mr.Wizard
    Sep 1, 2012 at 19:55
  • $\begingroup$ Is there a way to remove all Output cells from a Notebook? $\endgroup$
    – a06e
    Mar 4, 2018 at 13:48
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    $\begingroup$ @becko Under the Cell menu I think you should have a Delete All Output command. Is that what you need? Is it missing, or do you need something else? $\endgroup$
    – Mr.Wizard
    Mar 5, 2018 at 1:46
  • $\begingroup$ @Mr.Wizard That's it, thanks! $\endgroup$
    – a06e
    Mar 5, 2018 at 13:04

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