Sphinxtr: Creating a Portable PhD Thesis

To be totally fair, a sphincter (I'm assuming this is what you're referring to) refers to a circular muscle structure in the general case. Not just the butthole.

There are sphincters in your eyes.

There is a sphincter in your esophagus.

Your body is full of sphincters.

The anal sphincter is just one of many sphincters.

And now you really do know.

mirkules2• 14 years ago

That's irrelevant, because the association is ever-present.

As an example, if people lived on Venus, they would be called "Venerials" by the proper genitive form. Alas, doctors got to it first (Venus, Roman goddess of love...) so it was changed to "Venutians". (Source: Neil DeGrasse Tyson's podcast, StarTalk radio).

jonnathanson• 14 years ago

"Your body is full of sphincters."

I'm sorry, but this cracked me up. It brought out my inner Beavis and Butthead. I apologize. But, I mean, come on. Most people do associate the word sphincter with the butthole, and surely the creator should have known that. (Unless the, umm, cheeky association is intentional?)

bitwize• 14 years ago

Whoa, you mean we've got buttholes, like, all over? Cool. Huh huh huh.

muneeb• 14 years ago

This is awesome! I can totally see myself using this. We also need better make files for Latex. Changing one line, hitting make, and then watching crap fly across your screen is not a pleasant experience ...

jterrace19• 14 years ago

It's using http://code.google.com/p/latex-makefile/ which is a really awesome makefile. It has nice colored output and throws away all the garbage output.

qznc3• 14 years ago

At least you can build your own scripts around this stuff. Building LaTeX for me goes like this:

I use vim, change a line, and hit ":w". My git-onNotify [0] script detects a change and issues "make show". The Makefile uses rubber or latexmk to build a pdf, then issues "gnome-open $PDF", which opens the new version in my pdf viewer. If my screen is tiled, the preview on the side just updates.

Essentially, I just save my tex file and wait for the change.

[0] https://github.com/beza1e1/dot/blob/master/bin/git-onNotify

adiM• 14 years ago

How does this compare to existing text formats that generate multiple outputs, in particular pandoc (which supports an extended version of Markdown)?

andreasvc8• 14 years ago

The section on typography is actually about formatting. Also, an epigraph is not the same as a quotation:

     [...]
     2. (Literature) A citation from some author, or a sentence
        framed for the purpose, placed at the beginning of a work
        or of its separate divisions; a motto. Epigraphic

jterrace19• 14 years ago

Pull requests accepted :)

cmccabe3• 14 years ago

If the tex2html tool is poor, why not improve that tool? Re-inventing TeX seems like quite a waste of time.

Every time someone invents a new markup format for absolutely no reason, I die a little bit inside.

jterrace19• 14 years ago

This uses an existing format, restructuredtext, not a new markup format.

andreasvc8• 14 years ago

TeX and restructuredtext have very different goals. The first lets you specify every little typographical detail for a fixed page-oriented output. The latter focuses on a minimal set of semantic markup which can be used for different presentation media.

coliveira2• 14 years ago

What you said is just the difference between TeX and LaTeX. If you want just semantic meaning, use LaTeX without lower level TeX commands, then use an automated tool to convert it to html or other formats.

freeslave• 14 years ago

here's an eclipse based editor specifically built for writing/managing your thesis. http://www.chapterlab.com/

neonkiwi2• 14 years ago

Unfortunately this (good) product will take at least a generation to make it to the academic world.

I put my thesis together in HTML using Pandoc, customized to look a bit like a Tufte publication with margin notes. It had animations, anchor links when cross-referencing paragraphs, and in my eyes, made sense for a document like a thesis.

My committee members, on the other hand, were in consensus that a thesis should be a PDF with page numbers, not some multimedia document with hyperlinks. When I made a PDF[0] and submitted it to the university, someone even checked it to make sure the page numbering switched from Roman to Arabic at the correct point as stipulated by the submission guidelines (it didn't, hence my knowledge of their thoroughness).

Considering that universities today often don't even want a hard copy of a thesis, this is a world that is tied very strongly to the paper paradigm.

[0] Fortunately Pandoc did this quite nicely, though I did have to make a few changes to deal with citations. Incidentally, there is no good, cross-platform way to put an animation in a PDF.

jterrace19• 14 years ago

Yeah, my university formatting requirements are crazy also. This allowed me to have one source that outputs (nicely) to a bunch of different formats, including the university PDF requirement.

andreasvc8• 14 years ago

There's a good reason to require proper page numbers: citations. In general you can't refer to a particular passage in a huge HTML document. Anchor links are a technical solution, but that's not how normal citations work.

I think that more generally when a document becomes sufficiently complex it is better to use a page-oriented, typesetting approach. You'll want to fiddle with where certain page breaks and figures end up, and if you do that you might as well stick with one canonical format.

You can view it as the paper paradigm. Alternatively, you can also see it as sticking to a uniform, canonical format. Getting fluid layouts right is a very difficult problem, and manually getting the layout right for a fixed format is simply a much better solution for this purpose.

jterrace19• 14 years ago

The HTML format does generate multiple pages for different sections and chapters, completely configurable. The format above is the singlehtml format where everything is on one page. I'd much rather have a link to a specific anchor tag on a page that goes directly to where I want than a citation to a page number on a 200 page document.

neonkiwi2• 14 years ago

There's a good reason to require proper page numbers: citations.

Right, and I have even seen page numbers in citations of theses. It wasn't common in my field at least, but it happens. For a journal citation, generally page numbers tell you where in the volume that article is, not the content that is being referred to. I think there is flexibility in citations—one can refer to a figure, table, section or even paragraph number with at least equal clarity as a page number. There is convention here, I agree, and my point in my original post is that the convention is followed dogmatically rather than pragmatically in academia.

Getting fluid layouts right is a very difficult problem, and manually getting the layout right for a fixed format is simply a much better solution for this purpose.

I have given this topic a lot of thought. Partly from working on an HTML document for a thesis, partly because I've worked in the area of cognitive ergonomics. At the moment our tools aren't great for this, but that's really our fault as software designers. Fluid layouts should be better than fixed ones.

Concerns about fluid layouts are new, a byproduct of current technology. Printing technology didn't afford us these problems. You can remember when it was commonplace to see websites that contained text as bitmaps, to force readers to consume content as laid out by the designer. There were sites that rigidly spec'd font sizes and browsers that allowed that. Today, the best web designers accept the fact that content will be consumed on different screens (sizes and pixel densities) by users with different preferences. They design layouts that can gracefully handle a large font size stipulated by the reader, rather than design the way that a designer would for print.

So what is the underlying issue with fluid layouts?

Well, we have text that relates to graphics, and as Tufte points out in some great books on the topic, it's particularly useful (and historically very common) to have the relevant text presented in conjunction with graphics. That's an obvious point, but with fluid layouts this can unpleasantly 'break.'[0] This is a solvable issue (even using current web technologies), in a way that can evolve beyond what paper can do for us.

I'd like to see a markup that allows me to designate which graphics are relevant to a block of text, and have those figures shown together. For example, if the display allows it, once you start scrolling past a relevant figure it could slide to the margin of the text and stay pinned alongside as you read relevant text for reference. Perhaps the reader could select other figures to pin, or unpin figures as well.

Think of the number of times you've flipped between pages of a PDF to read text and look at the figure described. Sometimes I end up opening the same document twice and putting them on my screen side-by-side. That's the kind of hack us human factors types love putting in slide shows about how we should be designing for users.

With high-resolution displays getting to mass-market price points, we are only missing the right tools to take technical documents to the next level. As I said, this could be done in HTML, CSS and javascript today, but it's not author-friendly. Even if the tools did exist to make this easy, it would frowned upon in the academic world for being different. But some fields are more progressive than others, and eventually we'll move past the page as a paradigm. I've got to applaud the OP for taking steps in that direction.

My futurist speculation: the move away from pages in the scientific community will happen at the same time that it will move away from traditional journals as an idea distribution channel. I don't think that's in the immediate future, though.

[0] In fact, this often breaks with fixed layouts too, except it's only really bad during document creation. Think figure placements in LaTeX. Fortunately the document creator has to do this work once, and then all of the readers see the exact same thing. Better tools for fluid documents would make things friendlier for the author as well as the readers.

frisco• 14 years ago

This is what thesis writing procrastination looks like.

jterrace19• 14 years ago

To be fair, I only released it after my thesis was done :)

pmr_3• 14 years ago

I have written my Bachelor thesis in org-mode and was incredibly happy with it. There is certainly a difference in requirements for a PhD Thesis, but I cannot think of any missing feature or hard to overcome problem right away.

drothlis2• 14 years ago

What did you use to convert to pdf / html?

pmr_3• 14 years ago

org-mode comes with HTML/pdf/DocBook export and you can extend the exporter with your own formats.

kghose• 14 years ago

Also relevant: https://github.com/coolwanglu/pdf2htmlEX

jterrace19• 14 years ago

This is a nice project, but different goals. I don't want my HTML output to look like a PDF. I want it to look like a nicely formatted web document

abbot25• 14 years ago

As someone who did typeset his thesis not too long ago to forget all that lot of tiny tweaks I had to make to get a perfect print out from LaTeX, I would say that this project has a lot of issues. Some of them a more or less easy to fix, but some of them will be hard. Consider wrapping some specific paragraph in a \fussy / \sloppy pair, or hammering a specific float to this page, or ... (this list is really long). Not to mention bibliography tools. I don't claim that these issues are unsolvable, but the deeper you go into solving them the more you will discover that you are basically re-implementing LaTeX.

While the idea of multi-format thesis, or at least double format - PDF and HTML, is very compelling, I doubt there could be good enough solutions for that for any thesis which contains more then just text and some inconsiderate amount of figures/tables/formulae at all.

jterrace19• 14 years ago

Agreed, but for my case, I didn't really care too much about the PDF output. The printed version of my thesis is going to sit in my university library untouched forever. I'm much more concerned with having a semantically correct, searchable, beautiful HTML output.

abbot25• 14 years ago

Why not to go the other way round in this case? Typeset your thesis in semantically correct, searchable, beautiful HTML5, and then just add some specific CSS to get the hard print copy?

reeses• 14 years ago

You made me twitch from cumulative LaTeX PTSD.

"Just write and pay attention to content, not formatting," has led to staring at the clock, wondering how 5am came around so quickly more nights than I would care to admit.

God forbid you use Sweave.

I'm looking back 22 years and getting the twitch again. All that time I saved not playing with fonts, kerning, margins, and line height has been burned aligning figures or tables or yes, trying to get that frickin' float on a page at least vaguely proximal to its reference.

pserwylo• 14 years ago

Looks nice. Currently, I am quite happy writing my thesis in LyX [0], which outputs to various formats, including HTML.

I also have a script which periodically converts the source files from LyX to both HTML and PDF, then dumps them in the webroot of the Apache server running on my Uni computer. This folder has a .htaccess file which restricts access to my supervisors and myself using the Uni's LDAP server.

It works a treat for me.

[0] http://www.lyx.org/

Heliosmaster• 14 years ago

I don't get it, what's the problem on writing good handcrafted (no WYSIWYG editors) LaTeX?!

qznc3• 14 years ago

It seems out of place in a web-dominated world. Compare Brat Victor's "learnable programming" [0] or "Scientific Communication As Sequential Art" [1], which includes animated or interactive things.

[0] http://worrydream.com/LearnableProgramming/ [1] http://worrydream.com/ScientificCommunicationAsSequentialArt...

lrem2• 14 years ago

Looks cool. But I guess doing things like using IEEE classes is out of question? And does it really miss a way of typesetting inline math?

jterrace19• 14 years ago

It has inline math. I just forgot to add an example for it. If by IEEE style, you mean bibtex, then yes, you can easily swap the bibtex format.

lrem2• 14 years ago

I mean writing things meant for publishing in IEEE conferences, using the IEEEtran class.

Another concern is: is it practical to include figures drawn with Tikz? I find it the easiest way to lay out many things, but it effectively means LaTeX lock-in.

_hobgoblin_• 14 years ago

I read that as Sphincter...

Sphinxtr: Creating a Portable PhD Thesis

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