7 ms·

Writing a Ph.D. thesis with Org Mode

136 points by quazar 7y ago

pvaldes 7y ago
Could be be done, but does not feel like the appropriate tool. Org mode translates to a basic latex only, that is a huge waste of TeX power. I did my thesis entirely in LaTeX, so I have some experience in the theme, and it was a rollercoaster. There is always some really special table, graph, arrangement, extra space needs, that you can do only programming with the real stuff. Doing the same with org mode would have been stuff of nightmares (even if org tex has some nice qualities that LaTex does not have, like fast shrinkable text). I missed only a thing. Being able to do in situ calculus in LaTeX (filling columns and totals in tables excel style), but is not really the right tool for that so you can't blame TeX for that. The team of R+Latex filled the gape nicely. Apart of this, TeX environment has planned and build yet anything that you could dream when you write a PHD thesis. From basic, to really esotheric. Can be difficult sometimes, but is awesome.
- yur3i__ 7y ago
  You can insert any LaTeX markup in org mode as well as just using their syntax.
  - jimmy_dean 7y ago
    And you can inline display latex fragments. Not the prettiest display but it does the job!
  - _emacsomancer_ 7y ago
    This is more fragile than you would expect. If most of what you're doing is going to be LaTeX, it's easier just to write in .tex and eliminate the .org middle man. (I say this with a great love of Org mode, which I use everywhere else.)
    - pvaldes 7y ago
      Org mode would (probably) make a mess with R chunks included in the .tex file, for example. You can't compile from R to org to latex to pdf, so this can be a problem. Same problem with Python to Latex path if you put org in the middle of the way. By the way, I use .org files a lot also. Is handy for small and simple documents.
      - _emacsomancer_ 7y ago
        Even with plain LaTeX I've had trouble with Org mode trying to decide when to 'smartly' switch into maths mode, and what should be literal, e.g. `\latexfunction{...}` is sometimes translated as `\\\latexfunction{...}` because Org decides it should escape the backslash.
- brighter2morrow 7y ago
  What's the benefit of Latex over LyX? With LyX you can insert latex if you need it, but otherwise you are in a very nice Wysiwym environment
  - 0xADD1E 7y ago
    Really just a difference in preference in my experience. I personally really like declarative workflows.
  - davrosthedalek 7y ago
    Essentially, Emacs + makefiles :) Lyx is great for shorter things. I use it for presentations, where being able to see the images, colors, etc really helps. For longer stuff, with a lot of text, a nice editor has its advantages. And you can split of chapters in extra files easily and all that.
    - j88439h84 7y ago
      You can see the images in emacs with org previews. http://kitchingroup.cheme.cmu.edu/blog/2016/11/06/Justifying-LaTeX-preview-fragments-in-org-mode http://kitchingroup.cheme.cmu.edu/blog/2016/11/06/Justifying...
  - pvaldes 7y ago
    Writing LaTeX in emacs is faster
- makerofspoons 7y ago
  When I was doing my thesis I was a big fan of Mathematica's right click -> copy as LaTeX feature. It saved a lot of time entering formulas and copying tables from the notebooks I was using for analysis.
  - lol768 7y ago
    +1 for this, it really helped me. Also, Mathpix is neat - especially if you're citing results and need to include some equations from those papers.
    - fredguth 7y ago
      With arxiv papers, I usually download the Tex file and copy the formulas from there. Besides, sometimes you find interesting ideas that were commented due to space.
m000 7y ago
I'm not sure about other fields, but most theses in computer science these days are usually a stitch-up of your papers + some glue text/backstory. I.e. 80% of your thesis is already in LaTeX format. Org Mode only adds complexity to your workflow.
- kleiba 7y ago
  I doubt that anyone can be familiar with "most theses in computer science these days".
  - wolfram74 7y ago
    Depends on your threshold for "familiarity". Anyone currently working on theirs will likely have a number of friends/colleagues working on ones of their own, include second and third hand knowledge accumulated from conferences and likely any modestly sociable CS doctoral candidate would know at least the loose structure, if not 30 second blurb of quite a large number of theses in progress.
- kadal 7y ago
  Unless (like me) you write your papers in org-mode too!
- ska 7y ago
  That is very much dependent on department.
- analog31 7y ago
  This was common in the hard sciences way back when. I remember fellow students saying things like: "I have my three papers, that's three chapters, now I just need my intro and conclusions." In psychology, they had a phrase, which was: "Published and outa here." Some advantages: It meant your work was demonstrably publishable, you got 3 pubs out of it. Disadvantages: You were basically a hostage until your advisor agreed to let you publish 3 papers. It probably tended to flood the literature with papers of lesser quality.
deleted 7y ago
[deleted]
vipbababd 7y ago
You can insert any LaTeX markup in org mode as well as just using their syntax..
tgbugs 7y ago
I have been writing my thesis as an org-mode file in git that is automatically published [0] as a pdf every time I commit using a bash script tangled as a commit hook. Figures are (or can be) computed from live data, and org-ref can automatically manage and format all my references as I go without the insanity inducing workflows that one usually has to resort to. Another amazing thing about org-mode is that I can write a code block to hit a remote api (e.g. google docs) and fill and format entire chapters from a collaborative editing source that my advisor is comfortable using, C-c C-c and it is embedded in the document. Perfect for stitching papers together from a variety of sources. While there is a learning curve, the peace of mind of having a single tool that enables me to use any tool I need to use was such a relief after years of other painful writing and publishing workflows. If you are starting a PhD today and are going to do anything at all with code, I seriously suggest you learn org-mode. By the time you finish, not only will you have a PhD, but even if you don't you will have the power of one of the most amazing authoring tools under your command! (I would say, "Learn org-mode, simplify your life!" but emacs tends to lead to other complications). 0. https://orgmode.org/manual/Publishing.html https://orgmode.org/manual/Publishing.html
- ska 7y ago
  Back in the stone age when I did mine, my approach was more local, but similar. I wrote all the text in LaTeX using AucTeX package, but had a makefile and a commit hook (to CVS, later SVN, this was pre-git). All figures & tables etc. were generated from other make targets, which chained back to a mix of (usually) lisp code, matlab, or maple/mathematica. Oh, and figures generated by things like MetaPost. Structuring things at the chapter level .tex files made it all pretty manageable. I had figure dependencies on both input data and executable targets/scripts, so changing either would trigger a recompute, with the exception of some long running stuff - of course had global rebuild rules. I wrote many papers this way too, it was nice to know everything was synchronized properly. I did use org-mode to organize my work though. These days it would be on github and I probably wouldn't have lost it in a move.
- kmundnic 7y ago
  How do you deal with different sections from google docs? As in, how do you format these into markdown or latex sections? I've been working with psychologists and I've taught them the basics of a latex document, but I see how extracting the sections they have written from a google doc could be useful.
limist 7y ago
Back in the late 2000's I looked around for the right tool for my Ph.D. dissertation and quickly ruled out Word, Libre (or Open Office) Writer, or any wysiwyg tool, because they 1) lacked fast, easy ways to work at the structural (tree) level of the document, which is important when you have many sections and subsections to organize thoughts and arguments; 2) couldn't do mathematical notation well; 3) didn't integrate well with the reference management tool I was using then, Mendeley. As an Emacs lover, I soon found Org, and it was (and remains) the perfect tool, for working in plain text — which will never be obsolete, and works easily with git or version control. Then and now, nothing could match Org speed and flexibility: structural editing (creating nodes, moving nodes, promote/out-dent a node, demote/in-dent a node) was and is fundamental to Org (unlike Markdown etc), and it's ridiculously easy to reorganize thinking and writing as you go. You can export to LaTeX (or HTML) and customize formatting as needed, while also including code blocks from multiple languages. Integration with BibTeX was tight, and made handling hundreds of references easy. Where other writing tools for complex documents previously made me cringe and cuss, Org makes writing a pure joy, freeing the mind to work entirely on content and its structure.
auraham 7y ago
I liked the latex template, could you give more details about it? such as font name and so on.

136 points by quazar 7y ago

Could be be done, but does not feel like the appropriate tool. Org mode translates to a basic latex only, that is a huge waste of TeX power. I did my thesis entirely in LaTeX, so I have some experience in the theme, and it was a rollercoaster. There is always some really special table, graph, arrangement, extra space needs, that you can do only programming with the real stuff. Doing the same with org mode would have been stuff of nightmares (even if org tex has some nice qualities that LaTex does not have, like fast shrinkable text). I missed only a thing. Being able to do in situ calculus in LaTeX (filling columns and totals in tables excel style), but is not really the right tool for that so you can't blame TeX for that. The team of R+Latex filled the gape nicely. Apart of this, TeX environment has planned and build yet anything that you could dream when you write a PHD thesis. From basic, to really esotheric. Can be difficult sometimes, but is awesome.

yur3i__ 7y ago
You can insert any LaTeX markup in org mode as well as just using their syntax.
- jimmy_dean 7y ago
  And you can inline display latex fragments. Not the prettiest display but it does the job!
- _emacsomancer_ 7y ago
  This is more fragile than you would expect. If most of what you're doing is going to be LaTeX, it's easier just to write in .tex and eliminate the .org middle man. (I say this with a great love of Org mode, which I use everywhere else.)
  - pvaldes 7y ago
    Org mode would (probably) make a mess with R chunks included in the .tex file, for example. You can't compile from R to org to latex to pdf, so this can be a problem. Same problem with Python to Latex path if you put org in the middle of the way. By the way, I use .org files a lot also. Is handy for small and simple documents.
    - _emacsomancer_ 7y ago
      Even with plain LaTeX I've had trouble with Org mode trying to decide when to 'smartly' switch into maths mode, and what should be literal, e.g. `\latexfunction{...}` is sometimes translated as `\\\latexfunction{...}` because Org decides it should escape the backslash.
brighter2morrow 7y ago
What's the benefit of Latex over LyX? With LyX you can insert latex if you need it, but otherwise you are in a very nice Wysiwym environment
- 0xADD1E 7y ago
  Really just a difference in preference in my experience. I personally really like declarative workflows.
- davrosthedalek 7y ago
  Essentially, Emacs + makefiles :) Lyx is great for shorter things. I use it for presentations, where being able to see the images, colors, etc really helps. For longer stuff, with a lot of text, a nice editor has its advantages. And you can split of chapters in extra files easily and all that.
  - j88439h84 7y ago
    You can see the images in emacs with org previews. http://kitchingroup.cheme.cmu.edu/blog/2016/11/06/Justifying-LaTeX-preview-fragments-in-org-mode http://kitchingroup.cheme.cmu.edu/blog/2016/11/06/Justifying...
- pvaldes 7y ago
  Writing LaTeX in emacs is faster
makerofspoons 7y ago
When I was doing my thesis I was a big fan of Mathematica's right click -> copy as LaTeX feature. It saved a lot of time entering formulas and copying tables from the notebooks I was using for analysis.
- lol768 7y ago
  +1 for this, it really helped me. Also, Mathpix is neat - especially if you're citing results and need to include some equations from those papers.
  - fredguth 7y ago
    With arxiv papers, I usually download the Tex file and copy the formulas from there. Besides, sometimes you find interesting ideas that were commented due to space.

m000 7y ago

I'm not sure about other fields, but most theses in computer science these days are usually a stitch-up of your papers + some glue text/backstory. I.e. 80% of your thesis is already in LaTeX format. Org Mode only adds complexity to your workflow.

kleiba 7y ago
I doubt that anyone can be familiar with "most theses in computer science these days".
- wolfram74 7y ago
  Depends on your threshold for "familiarity". Anyone currently working on theirs will likely have a number of friends/colleagues working on ones of their own, include second and third hand knowledge accumulated from conferences and likely any modestly sociable CS doctoral candidate would know at least the loose structure, if not 30 second blurb of quite a large number of theses in progress.
kadal 7y ago
Unless (like me) you write your papers in org-mode too!
ska 7y ago
That is very much dependent on department.
analog31 7y ago
This was common in the hard sciences way back when. I remember fellow students saying things like: "I have my three papers, that's three chapters, now I just need my intro and conclusions." In psychology, they had a phrase, which was: "Published and outa here." Some advantages: It meant your work was demonstrably publishable, you got 3 pubs out of it. Disadvantages: You were basically a hostage until your advisor agreed to let you publish 3 papers. It probably tended to flood the literature with papers of lesser quality.

deleted 7y ago

[deleted]

vipbababd 7y ago

You can insert any LaTeX markup in org mode as well as just using their syntax..

tgbugs 7y ago

I have been writing my thesis as an org-mode file in git that is automatically published [0] as a pdf every time I commit using a bash script tangled as a commit hook. Figures are (or can be) computed from live data, and org-ref can automatically manage and format all my references as I go without the insanity inducing workflows that one usually has to resort to. Another amazing thing about org-mode is that I can write a code block to hit a remote api (e.g. google docs) and fill and format entire chapters from a collaborative editing source that my advisor is comfortable using, C-c C-c and it is embedded in the document. Perfect for stitching papers together from a variety of sources. While there is a learning curve, the peace of mind of having a single tool that enables me to use any tool I need to use was such a relief after years of other painful writing and publishing workflows. If you are starting a PhD today and are going to do anything at all with code, I seriously suggest you learn org-mode. By the time you finish, not only will you have a PhD, but even if you don't you will have the power of one of the most amazing authoring tools under your command! (I would say, "Learn org-mode, simplify your life!" but emacs tends to lead to other complications). 0. https://orgmode.org/manual/Publishing.html https://orgmode.org/manual/Publishing.html

ska 7y ago
Back in the stone age when I did mine, my approach was more local, but similar. I wrote all the text in LaTeX using AucTeX package, but had a makefile and a commit hook (to CVS, later SVN, this was pre-git). All figures & tables etc. were generated from other make targets, which chained back to a mix of (usually) lisp code, matlab, or maple/mathematica. Oh, and figures generated by things like MetaPost. Structuring things at the chapter level .tex files made it all pretty manageable. I had figure dependencies on both input data and executable targets/scripts, so changing either would trigger a recompute, with the exception of some long running stuff - of course had global rebuild rules. I wrote many papers this way too, it was nice to know everything was synchronized properly. I did use org-mode to organize my work though. These days it would be on github and I probably wouldn't have lost it in a move.
kmundnic 7y ago
How do you deal with different sections from google docs? As in, how do you format these into markdown or latex sections? I've been working with psychologists and I've taught them the basics of a latex document, but I see how extracting the sections they have written from a google doc could be useful.

limist 7y ago

Back in the late 2000's I looked around for the right tool for my Ph.D. dissertation and quickly ruled out Word, Libre (or Open Office) Writer, or any wysiwyg tool, because they 1) lacked fast, easy ways to work at the structural (tree) level of the document, which is important when you have many sections and subsections to organize thoughts and arguments; 2) couldn't do mathematical notation well; 3) didn't integrate well with the reference management tool I was using then, Mendeley. As an Emacs lover, I soon found Org, and it was (and remains) the perfect tool, for working in plain text — which will never be obsolete, and works easily with git or version control. Then and now, nothing could match Org speed and flexibility: structural editing (creating nodes, moving nodes, promote/out-dent a node, demote/in-dent a node) was and is fundamental to Org (unlike Markdown etc), and it's ridiculously easy to reorganize thinking and writing as you go. You can export to LaTeX (or HTML) and customize formatting as needed, while also including code blocks from multiple languages. Integration with BibTeX was tight, and made handling hundreds of references easy. Where other writing tools for complex documents previously made me cringe and cuss, Org makes writing a pure joy, freeing the mind to work entirely on content and its structure.

auraham 7y ago

I liked the latex template, could you give more details about it? such as font name and so on.