MathGroup Archive 2005

[Date Index] [Thread Index] [Author Index]

Search the Archive

Re: Mathematica Notebook Organiztion

  • To: mathgroup at
  • Subject: [mg56825] Re: [mg56816] Mathematica Notebook Organiztion
  • From: DrBob <drbob at>
  • Date: Sat, 7 May 2005 04:16:38 -0400 (EDT)
  • References: <>
  • Reply-to: drbob at
  • Sender: owner-wri-mathgroup at

WRI, please take notice. David is truly a guru on visual presentation and organization of information.


On Fri, 6 May 2005 03:01:35 -0400 (EDT), David Park <djmp at> wrote:

> I've made this a new topic because we have rather drifted off from the
> subject of writing packages to the subject of using notebooks in the best
> manner.
> It is my view that Mathematica notebooks (and similar such entities) are an
> entirely new publishing form. They FAR SURPASS printed books and articles
> because of the ability to interactively meld text, calculations, graphics
> and animations in one document. Theodore Gray deserves a lot of credit for
> his work on this concept. We are still learning how to use this media. But
> things are not perfect yet and Professor Siegman has touched on some issues.
> There is no reason that the Initialization and Routines Sections couldn't be
> at the end of the notebook. The Input cells in these Sections should be made
> into Initialization cells (and choose NOT to save as an AutoSave package).
> That way one doesn't have to necessarily evaluate a notebook from the top.
> The initializations are automatically performed when the first statement,
> anywhere, is evaluated. I like to make my notebooks such that a reader can
> start at any Section and begin evaluating. If this is not possible because
> of a rigid progression in the sections then the reader should be so
> instructed.
> Often I will select the Initialization and Routine section headings and
> change the FontColor to Gray. I also often add "Automatically Initialized".
> This subdues the sections and tells the reader he can generally ignore them.
> Sections are not automatically opened when Initialization cells are
> evaluated. My experience is that the sections remain closed. Also you can
> select a Section and completely evaluate it without ever opening it, or
> seeing the results. (I've had super geniuses complain that they evaluated my
> notebook but got no results, simply because they didn't know how to open
> Sections!)
> Graphics code can be put in closed cells in the running sections. It doesn't
> necessarily have to be put in the Routines section. That way you can
> intermix text, calculations and graphics in a smooth manner. The only
> problem is getting the reader to evaluate the closed cells, even if it has
> been carefully explained in an Introduction. They are so thin and small new
> readers often overlook them. It might be nice if one had the option of
> having a closed cell display a cell tag. It would also be nice if closed
> cells could be opened and closed in the same way as Sections.
> It is also possible to generate proofs, derivations or step by step
> calculations by interspersing Print statements with %% referenced
> statements. These can also be put in closed cells so that the main code is
> hidden.
> For printing (It will take some time for people to give up the security
> blanket of printed documents - inferior as they are!) there is no reason why
> some Sections can't be open and others closed.
> Professor Siegman's case:
>    Section
>    Text (a few paragraphs introducing the section)
>    Subsection
>    Subsection
> is a good point. I don't see any direct way around it other than making the
> Text an Introductory Subsection, which may be objectionable because it is so
> short, or manually closing these Text cells, but this is too difficult for
> the reader to work with. Perhaps there might be a FrontEnd command that
> gives the "outline view".
> Another approach would be to make a Table of Contents Section. The various
> items in the Table of Contents could actually be links to the corresponding
> sections of the notebook. This is like pdf documents where there is often a
> table of contents with links in the side bar. It requires extra work to
> write the sections, but then it also requires extra work in a pdf document.
> It would also be nice to have the following construction:
> 	Section
> 	Text and Input cells
> 	BoxSection
> 		Text and Input cells
> 		End of BoxSection marker
> 	Text and Input cells
> where the BoxSection could be closed or terminated, and subsequent Text and
> Input cells would NOT be part of the BoxSection, but part of the containing
> section. The BoxSections would be like boxes in textbooks which contain a
> side discussion without interrupting the main flow of material. (Possibly
> there could be a way to have manual grouping only in some subsection of a
> notebook, but I would much prefer a more versatile automatic grouping
> because manual grouping is too subject to abuse.)
> I have only looked a little at the Author's Tools application. It does give
> information about constructing Help documentation, which I omitted to
> mention in an earlier posting. But otherwise I haven't figured out just what
> Author's Tools does for one in the way of constructing better notebooks for
> readers. I wish WRI had provided a short elegant example with the
> application.
> It might also be nice to have the ability to construct stand alone browsers.
> Then the categories in the browser would be like the table of contents. In
> essence, authors would write Mathematica browsers, in which Mathematica
> notebooks formed the various chapters and sections.
> I wish that there were better standard notebook styles supplied with
> Mathematica. I find many of the standard ones useless. WRI needs to hire
> Edward Tufte, or someone equivalent, to design some notebook styles. It
> certainly is preferable to use a standard style because then one can count
> on readers having it.
> I would like to see one more Section level in notebooks. I would like to see
> the default to have GroupOpenCloseIcons on all the Section levels - but NOT
> on anything else. (Especially not on Input/Output groups.) The triangular
> open/close icons are intuitive to new readers - the cell brackets are not. I
> would like to see a better balance, actually a smaller range, of font sizes.
> In the Default style, for instance, I think the Title font size is much too
> large, and the Text font size is too small. The Text, Input and Output font
> sizes should be reasonably close in size. After all, text cells and
> Input/Output cells are of equal importance (IMHO) and should better blend.
> Look at any technical article or book and you will see that the equations
> and text have roughly comparable font sizes.
> David Park
> djmp at
> From: AES [mailto:siegman at]
To: mathgroup at
> Agreed, this is the sensible way to [include routines in notebooks], and how
> I generally do it.
> But two gripes about the result:
> 1)  In PhD dissertations, journal papers, books, reports, the (sometimes
> lengthy) "Routines" are most commonly are sent to the end, e.g. are
> stuck in Appendices, and the Initialization (or Introduction) section is
> immediately followed by the important (to the reader) sections such as
> Calculations and Results.  Among other things that lets you easily
> select and print the Introduction, the Calculations and the Results to
> toss in a file folder or (three-hole-type) notebook, leaving off the
> lengthy Routines stuff.
> Mathematica doesn't make it easy to organize its notebooks that way.
> 2)  In my (limited) experience if I use Automatic Grouping and try to
> close groups to see only the section headings (to get an overview of the
> notebook structure and faster scrolling to , this doesn't work right
> (i.e., the way I want it!) unless the cell structure is strictly
> hierarchical.   E.g., if I have repeated cell sequences in the form
>    Section
>    Text (a few paragraphs introducing the section)
>    Subsection
>    Subsection
> closing these groups so I'll see just the Section headings does not
> close the Text cells, although it does close the Subsections (maybe I'm
> not doing things right?).
> Also, closing the Routines section, then running the notebook from the
> top (to get a fresh start) opens the Routines section, doesn't it?

DrBob at

  • Prev by Date: Re: letrec/named let
  • Next by Date: Re: Mathematica Notebook Organiztion
  • Previous by thread: Mathematica Notebook Organiztion
  • Next by thread: Re: Re: Mathematica Notebook Organiztion