10 ms·

Madoko – Write full-blown academic articles in Markdown

242 points by talles 11y ago

talles 11y ago
By the way, I came to find Madoko while researching for Koka (it's written in it): https://news.ycombinator.com/item?id=10131071 https://news.ycombinator.com/item?id=10131071 Also, there's this presentation: http://research.microsoft.com/apps/video/default.aspx?id=238813 http://research.microsoft.com/apps/video/default.aspx?id=238...
decasia 11y ago
Site seems to be offline, but in addition to what talles mentions, there's these: http://madoko.codeplex.com/ http://madoko.codeplex.com/ http://research.microsoft.com/en-us/um/people/daan/madoko/doc/reference.html#sec-performance-and-license http://research.microsoft.com/en-us/um/people/daan/madoko/do... http://webcache.googleusercontent.com/search?q=cache:azgHiPZpp2MJ:https://www.madoko.net/+&cd=1&hl=en&ct=clnk&gl=us http://webcache.googleusercontent.com/search?q=cache:azgHiPZ...
- talles 11y ago
  Actually, it was my mistake, it's https://www.madoko.net https://www.madoko.net (it's not working without www). Could someone correct it?
  - sctb 11y ago
    Thanks! We updated the link.
shadowfiend 11y ago
For what it's worth, there's also `asciidoc` and its implementation asciidoctor (http://asciidoctor.org http://asciidoctor.org). It has an both official JVM and JS packages in addition to the Ruby version, as well. Notably missing is math support, however, because rather than Madoko's approach of using LaTeX and then using a LaTeX-to-HTML renderer, asciidoc renders directly to HTML (or Docbook, or LaTeX). IMO, the end result doesn't necessarily look like an academic article placed on an HTML page… But it's nicer for consumption in a browser—the whole asciidoctor site is generated from asciidoctor. EDIT: this means asciidoc is a better fit for documentation, in book or article or whatever form—but I think once it gains math support (which they're working on) it would be quite useful for this as well.
- krapht 11y ago
  I don't understand what you mean about lacking math support. I am writing math exercises using asciidoctor right now, as it integrates with Mathjax. I would highly recommend asciidoc over markdown for scholarly work in succint plain text. Markdown is limited in its capabilities by design, as evidenced by all the different flavors of Markdown extension. It's what I would use to write an e-mail or blog post. Asciidoc, in the design of the language, anticipated extension and post-processing and has better support for using it as part of a complete document processing toolchain. After all, it's just syntax sugar for DocBook XML.
jordigh 11y ago
Oh, wow, this could be great. LaTeX only for the math, markdown for everything else. What if you need to futz with margins and styles or use a publisher's standard .sty file?
- suncanon 11y ago
  I concur -- do any of the markdown environments listed above accept imported .cls latex style files? Would they even be compatible? It seems like this would be essential for writing research papers according to a conference's template. If so, I would definitely use....
  - jamessb 11y ago
    When Pandoc converts Markdown to LaTeX, it uses a template that speciefies what header and footer material to add (http://pandoc.org/README.html#templates http://pandoc.org/README.html#templates). You could modify the default template to use whatever style file you want. Pandoc also supports references with a .bib file, and inserting TeX math formulae between dollar signs.
    - lelandbatey 11y ago
      Exactly. I've been using raw markdown processed with Pandoc as my sole document-creation tool for the past 3 years and it's worked excellently so far. Pandoc's pretty awesome.
AaronO 11y ago
You also might want to take a look at GitBook (https://www.gitbook.com/ https://www.gitbook.com/). It supports both Markdown and AsciiDoc and is used by authors to write books, documentation, research-papers (GitBook has great TeX support, in all outputs: web, pdf, epub, mobi). (Here's a math heavy book for example: http://jandeleeuw.gitbooks.io/bras1/content/blockrelaxation/bls.html http://jandeleeuw.gitbooks.io/bras1/content/blockrelaxation/...) The format and toolchain itself is open-source (https://github.com/GitbookIO/gitbook https://github.com/GitbookIO/gitbook) There's a ecosystem built on top of that such as a Desktop Editor (https://www.gitbook.com/editor https://www.gitbook.com/editor), plugins (http://plugins.gitbook.com/ http://plugins.gitbook.com/), and more ... I don't want to hijack the current thread, Madoko seems really cool, I thought some of you might be interested in a more established solution. I'm happy to answer any questions ! Disclaimer: I'm one of the GitBook co-founders
- k__ 11y ago
  Hehe, I had the same idea for my master thesis. A asciidoc academic paper editor. Still not finished it, since I wanted to make it realtime collaborative.
- bachmeier 11y ago
  > GitBook has great TeX support You probably want to update your website in that case: "Markdown, books are written using the markdown or AsciiDoc syntax. TeX support is planned."
  - haddr 11y ago
    Ahh, I also was thinking there is some TeX templating support... What they have is only KaTeX for math formulas.
  - AaronO 11y ago
    By TeX support I meant that we fully support TeX equations. The website mentions TeX but means LaTeX, I'll get that fixed, sorry for the confusion. Our TeX support allows you basically to write Markdown/Asciidoc and use TeX formulas wherever you need to, which gives you the best of both worlds (the simplicity of Markdown and the power of TeX formulas).
JohnHammersley 11y ago
It's interesting seeing the different approaches to combining the power of a structured formatting language with the ease of use of a (relatively code free) text editor. I'm one of the founders of Overleaf [1], and we've taken the route of keeping the full power of LaTeX there for anyone that needs it, but providing a 'Rich Text mode' [2] overlay for those who prefer a less code-like experience. If you give it a try, let us know what you think! [1] https://www.overleaf.com https://www.overleaf.com [2] https://www.overleaf.com/blog/81 https://www.overleaf.com/blog/81
- Phemist 11y ago
  I wrote my master's thesis in overleaf about a year ago, because my laptop was starting to break down and I needed a solution that allowed me to easily switch between university computers without having to constantly set-up my workspace on each individual PC. That was before the rich content editor was implemented, but I loved the experience nonetheless. The whole thesis was, next to my research, an exercise in cloud-based software. VM's on Cloud9, Code repo on github and my text editor on overleaf. Thanks a lot for making it available to a poor student like me!
  - JohnHammersley 11y ago
    Thanks, that's great to hear! :) I'm impressed you used your thesis as a testbed for cloud-based software, hope it didn't cause any/too much additional stress! If you generated any datasets during your work, you may also want to check out figshare[1] as a handy data repository. [1] http://figshare.com/ http://figshare.com/ (Note - we work in the same office as figshare, so this is probably a biased recommendation!)
    - Phemist 11y ago
      Thanks for the link! My thesis was basically a data analysis project, improving on work my supervisor did prior to me starting my thesis. Figshare is good to keep in mind, but I don't think I'd have had much use for it, as the whole point of my thesis was to get certain figures within a reasonable time. I actually had quite a lot of fun figuring out how to get everything working in the cloud. Set up my home desktop as my personal computer "cluster" (i5 processor, so a cluster of 4 cores!), I find it hard to work in an environment that I tend to do other stuff besides work in. Derived a small representative dataset from the massive one I had to quickly iterate over my analysis scripts in Cloud9 (while having github take care of my revision history). Then ssh'ing into my desktop PC whenever I needed to run the scripts on the full data set. I considered adding a section on open science and cloud-based software to my thesis, but in the end decided not to due to a lack of time. Open science is based on open source principles, where everything that can be shared should be shared. The Cloud VM angle is quite interesting in this sense, as being able to share the machines that software for a research project was ran on is often quite difficult (or nigh impossible), and a cloud-based VM seems to bridge this gap somewhat. In theory, anyone could log-in to the VM and play around in the workspace I set up for my thesis project, not that many would want to I suppose.
deleted 11y ago
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storrgie 11y ago
I'm not sure if I'll have an opinion that isn't commonly shared, so I figured I'd elucidate: I deeply love the simplicity of using markdown + LaTeX, however I realize that I'm somewhere on the gradient of complexity where I'm sacrificing some power for simplicity. Currently I think the tool that is used most is pandoc, and there are some offshoots that give pandoc more 'academic' power, like scholdoc. I've just been hoping that the pandoc world would progress (add more scholarly features) so that I could continue to keep my own data locally, manage it in my own vcs, and process it with a makefile. The only reason I see to hop on the software as a service bandwagon is for collaborative real-time editing (and some projects benefit greatly from this). I'll plug sharelatex for that, primarily because their model releases the software so that you can run your own if you don't want to pay for the service.
- etherealmachine 11y ago
  Is Madoko a SAAS app? If so I'll note another problem - madoko.net is currently timing out when I go to access it; any data inside is stuck there for the duration. On the Markdown+LaTeX note, I wrote my own Markdown parser (https://github.com/etherealmachine/markdown https://github.com/etherealmachine/markdown) to drive my github.io site (https://etherealmachine.github.io https://etherealmachine.github.io). Basically it's what you describe - easy mixing of Markdown+LaTeX to construct nice looking HTML.
  - dimgl 11y ago
    You can download Madoko and run it yourself. http://madoko.codeplex.com/ http://madoko.codeplex.com/ http://research.microsoft.com/en-us/um/people/daan/madoko/doc/reference.html http://research.microsoft.com/en-us/um/people/daan/madoko/do...
astazangasta 11y ago
Or, just use LaTEX? What makes this better? Pure TeX is hardly that esoteric, and extra power is there if you want it.
phelimb 11y ago
There's also "paper-now" which uses Jekyll Now + GitHub Pages. https://github.com/PeerJ/paper-now https://github.com/PeerJ/paper-now https://peerj.github.io/paper-now/ https://peerj.github.io/paper-now/
- tjohns 11y ago
  I hadn't heard of paper-now. I really like what they've done with the sidebar. My only complaint is that I'd imagine reading academic articles in an ultra-thin sans-serif font might get tiring after a while.
jbssm 11y ago
This is really nice. Does it allow to work on multi file documents? i.e. when wiring a big document like a thesis, it's nice to have the chapters divided by different files.
gkya 11y ago
Emacs' Org-mode is pretty good for writing articles. It can be configured to use whatever package / setting one wants while exporting to tex / pdf, e.g. use some .sty files (presumably, I haven't needed them yet), or use the beamer class to make a slideshow. It can be integrated with the ESS package so that it can be used as a live programming environment for R, or whatever else the package supports. And it also supports todo lists, agendas, and any sort of note-taking from the first moment. Example config for latex export (although I do not write academic articles): https://github.com/cadadr/emacs.d/blob/c81ff8afa3ca4ab553013c0e5151c3595391aedb/gk/gk-org.el https://github.com/cadadr/emacs.d/blob/c81ff8afa3ca4ab553013...
- bachmeier 11y ago
  I wouldn't recommend org-mode for writing professional documents. It is more unstable than any other major piece of software I've used. I use it daily, but not for writing. Things get changed in each release, the documentation is rarely in sync, and in a lot of cases major changes are not documented at all. I learned the hard way. I wrote some presentations using org-mode. Then they changed the exporters without updating the documentation. It would be especially problematic to write an academic article in org-mode, because you might have to return a year or two later, and that's not when you want to find out how much has changed since you last worked on the paper.
  - gkya 11y ago
    One can keep the intermediary .tex files should they export to pdf. Or for any substantial project one can fix the version of org, as other projects do so with the versions of the compiler or of the libraries. Still, if you are correct, then it is a problem for every user. I haven't encountered such problem in my use, although my use of ox-latex has been rather superficial (some homeworks, a tiny CV).
  - krupan 11y ago
    It's true that org-mode is a bit of moving target, but the basic syntax for document formatting doesn't change. If you are really worried about this you could record/archive which version of org you used to put your paper together.
michaelmior 11y ago
> The editor has ‘hick-ups’! I'm not sure if this is a joke I'm missing, but "hiccups" is the spelling of the term referring to involuntary inhalation as well as (informally) a minor difficulty or setback[0]. A "hick" is an unsophisticated person[1]. [0] http://dictionary.reference.com/browse/hiccup?s=t http://dictionary.reference.com/browse/hiccup?s=t [1] http://dictionary.reference.com/browse/hick?s=t http://dictionary.reference.com/browse/hick?s=t
michaelmior 11y ago
> Can I write my academic paper, manual, book, thesis, etc. in Madoko instead of LaTeX? For me a strict requirement for this is that I can use a particular template and document class. Unfortunately I don't have any choice as to what the particular format is. It's not clear if Madoko makes this possible.
- twblalock 11y ago
  This is the problem if you want to publish. A lot of journals want .docx or Latex files, not PDFs, and they will simply reject submissions that don't comply with their requirements. It would be nice if journals would accept Markdown, but frankly I don't expect that to happen anytime soon.
  - michaelhoffman 11y ago
    Pandoc is a great solution for converting Markdown into LaTeX and you can add arbitrary LaTeX code at the beginning and end of the output.
  - suncanon 11y ago
    Even if your journal accepts PDFs, michaelmior's comment raises an important issue that a LaTeX style template cannot be imported into most (or all?) of these Markdown editors. This would be a great feature to add, IMO!
    - cls59 11y ago
      The issue with that is that a LaTeX template is turing-complete. Doing a meaningful import of arbitrary journal styles without re-implementing TeX is a very, very, very hard problem.
    - yid 11y ago
      > Even if your journal accepts PDFs, michaelmior's comment raises an important issue that a LaTeX style template cannot be imported into most (or all?) of these Markdown editors. Perhaps it would be easier to go the other way -- to modify a Markdown parser to output a simple subset of Latex that can fit into most common academic templates.
sampo 11y ago
> Madoko also automatically synchronizes your changes to the cloud storage every 30 seconds or so. Does it make a new push to GitHub every 30 seconds?
dllu 11y ago
A few months ago I created my own Markdown-like lightweight markup language supporting LaTeX equations, which can be compiled to either HTML or LaTeX: http://lawrence.lu/programming/dllup/ http://lawrence.lu/programming/dllup/
mpnordland 11y ago
For School most of my papers require MLA formating. I found a mla latex template and so now I just use pandoc and that template to do my papers. When they want a docx I also made an odt template that I the use libreoffice to convert to docx. If madoko had an option to do that, then I'd be interested, otherwise it's no use to me.
Avshalom 11y ago
Well the html rendering is quite nice but Markdown is so limited it seems like you're just writing latex with '['s replacing some of the '('s.
rayalez 11y ago
To achieve the same functionality on my blog I use: - Pelican - static website generator, like Jekyll but in python. - MathJax to render Latex It is easy to synchronize Pelican with dropbox or github, and it is incredibly convenient. You can use this article: http://technivore.org/posts/2014/01/03/blogging-with-dropbox-and-pelican.html http://technivore.org/posts/2014/01/03/blogging-with-dropbox... To configure it in such a way that all the updates happen automatically. For example I can simply write an article in Editorial on my iPad, and it gets immediately published/updated, without me having to do anything at all, exactly zero mouse clicks.
antman 11y ago
Scholarlymarkdown is nice and I like the way you can add captions and references to equations and images. http://scholarlymarkdown.com/ http://scholarlymarkdown.com/
Animats 11y ago
Perhaps someday there will be computer programs where you can write things without typing in funny codes. TeX embedded in Markdown seems painful. How about writing in a restricted subset of HTML, as some forums (notably Slashdot) allow? <h1>, <h2>, .., <title>, <p>, <i>, <b>, <blockquote>, and a few others let you do what Markdown does. For math, there's MathML: Square root of two: <math><msqrt><mn>2</mn></msqrt></math>
- FraaJad 11y ago
  I written TeX embedded in markdown the time with Pandoc for reports and papers. It's much easier than writing all TeX.
  - FraaJad 11y ago
    wow, what was i thinking when i wrote that sentence? doesn't make any sense.
- ska 11y ago
  MathML is not a full replacement for TeX, and if we are talking about actual publication of papers/books rather than web content then neither HTML nor MathML are really up for the job.
- simplyinfinity 11y ago
  >Perhaps someday there will be computer programs where you can write things without typing in funny codes. You mean like ms word or open office ?
mangecoeur 11y ago
Not sure how this is really different from pandoc markdown...
mhartl 11y ago
Softcover [1] covers many of the same bases as well. Actually supporting all of LaTeX's features in HTML is basically impossible, though, so no matter which tool you use it's best to go in with tempered expectations. [1]: http://www.softcover.io/ http://www.softcover.io/
anotheryou 11y ago
Yet another Markdown flavor... Markdown is really not sufficient, this markup looks very cool but I'm missing compatibility again. I'll see if I can make it yellow cms compatible when exporting html...
- dimgl 11y ago
  The Madoko document states that it implements different flavors and extends it slightly. > Madoko is fully compatible with basic Markdown syntax and passes the entire test suite. It also implements most extensions, like Github flavored markdown, PanDoc, Markdown Extra, and multi-markdown, and it adds quite a few features itself to make it really useful for writing academic and industrial documents.
davidcollantes 11y ago
Typora (http://typora.io/ http://typora.io/) does similar, but it is an OS X application (Windows coming, so the author says).
- dimgl 11y ago
  Can you do LaTeX on Typora?
  - davidcollantes 11y ago
    I am not sure it can, yet. It can do Math, so far. I have opened an issue on Github requesting it.
  - davidcollantes 11y ago
    It can! See https://twitter.com/Typora/status/637495313259892740/photo/1 https://twitter.com/Typora/status/637495313259892740/photo/1
anotheryou 11y ago
pfew, but the generated html is ugly (missing breaks, strange inline styles and classes)
coliveira 11y ago
Good try, but in fact it is useless to use something other than Latex to write academic articles. Most journals in mathematics and engineering accept Latex, but I have never seen one accepting markdown. Which means that you will have to convert to Latex source anyway -- and in many cases make sure that the Latex code uses the style package of the publisher. This seems to me just to be asking for more trouble.
cetra3 11y ago
We use a simple md2pdf script internally that takes a markdown, throws on the company logo & font, and produces a pdf document. Process is md (vim/mou) -> cmark -> wkhtml2pdf -> pdf This works well for us, but would be nice if we could sort of merge this with an online wiki of some sorts.
- creshal 11y ago
  Have you considered pandoc? That allows to reduce it to md → pandoc → pdf, and in my experience pandoc generates much better PDFs (working links, etc.)
SZJX 11y ago
Doesn't org-mode already a kind of do that? I think it will handle most of the requirements just fine, handle LaTeX when necessary and what's better is that it comes within emacs allowing all kinds of easy customizations and extensions.

242 points by talles 11y ago

By the way, I came to find Madoko while researching for Koka (it's written in it): https://news.ycombinator.com/item?id=10131071 https://news.ycombinator.com/item?id=10131071 Also, there's this presentation: http://research.microsoft.com/apps/video/default.aspx?id=238813 http://research.microsoft.com/apps/video/default.aspx?id=238...

decasia 11y ago

Site seems to be offline, but in addition to what talles mentions, there's these: http://madoko.codeplex.com/ http://madoko.codeplex.com/ http://research.microsoft.com/en-us/um/people/daan/madoko/doc/reference.html#sec-performance-and-license http://research.microsoft.com/en-us/um/people/daan/madoko/do... http://webcache.googleusercontent.com/search?q=cache:azgHiPZpp2MJ:https://www.madoko.net/+&cd=1&hl=en&ct=clnk&gl=us http://webcache.googleusercontent.com/search?q=cache:azgHiPZ...

talles 11y ago
Actually, it was my mistake, it's https://www.madoko.net https://www.madoko.net (it's not working without www). Could someone correct it?
- sctb 11y ago
  Thanks! We updated the link.

shadowfiend 11y ago

For what it's worth, there's also `asciidoc` and its implementation asciidoctor (http://asciidoctor.org http://asciidoctor.org). It has an both official JVM and JS packages in addition to the Ruby version, as well. Notably missing is math support, however, because rather than Madoko's approach of using LaTeX and then using a LaTeX-to-HTML renderer, asciidoc renders directly to HTML (or Docbook, or LaTeX). IMO, the end result doesn't necessarily look like an academic article placed on an HTML page… But it's nicer for consumption in a browser—the whole asciidoctor site is generated from asciidoctor. EDIT: this means asciidoc is a better fit for documentation, in book or article or whatever form—but I think once it gains math support (which they're working on) it would be quite useful for this as well.

krapht 11y ago
I don't understand what you mean about lacking math support. I am writing math exercises using asciidoctor right now, as it integrates with Mathjax. I would highly recommend asciidoc over markdown for scholarly work in succint plain text. Markdown is limited in its capabilities by design, as evidenced by all the different flavors of Markdown extension. It's what I would use to write an e-mail or blog post. Asciidoc, in the design of the language, anticipated extension and post-processing and has better support for using it as part of a complete document processing toolchain. After all, it's just syntax sugar for DocBook XML.

jordigh 11y ago

Oh, wow, this could be great. LaTeX only for the math, markdown for everything else. What if you need to futz with margins and styles or use a publisher's standard .sty file?

suncanon 11y ago
I concur -- do any of the markdown environments listed above accept imported .cls latex style files? Would they even be compatible? It seems like this would be essential for writing research papers according to a conference's template. If so, I would definitely use....
- jamessb 11y ago
  When Pandoc converts Markdown to LaTeX, it uses a template that speciefies what header and footer material to add (http://pandoc.org/README.html#templates http://pandoc.org/README.html#templates). You could modify the default template to use whatever style file you want. Pandoc also supports references with a .bib file, and inserting TeX math formulae between dollar signs.
  - lelandbatey 11y ago
    Exactly. I've been using raw markdown processed with Pandoc as my sole document-creation tool for the past 3 years and it's worked excellently so far. Pandoc's pretty awesome.

AaronO 11y ago

You also might want to take a look at GitBook (https://www.gitbook.com/ https://www.gitbook.com/). It supports both Markdown and AsciiDoc and is used by authors to write books, documentation, research-papers (GitBook has great TeX support, in all outputs: web, pdf, epub, mobi). (Here's a math heavy book for example: http://jandeleeuw.gitbooks.io/bras1/content/blockrelaxation/bls.html http://jandeleeuw.gitbooks.io/bras1/content/blockrelaxation/...) The format and toolchain itself is open-source (https://github.com/GitbookIO/gitbook https://github.com/GitbookIO/gitbook) There's a ecosystem built on top of that such as a Desktop Editor (https://www.gitbook.com/editor https://www.gitbook.com/editor), plugins (http://plugins.gitbook.com/ http://plugins.gitbook.com/), and more ... I don't want to hijack the current thread, Madoko seems really cool, I thought some of you might be interested in a more established solution. I'm happy to answer any questions ! Disclaimer: I'm one of the GitBook co-founders

k__ 11y ago
Hehe, I had the same idea for my master thesis. A asciidoc academic paper editor. Still not finished it, since I wanted to make it realtime collaborative.
bachmeier 11y ago
> GitBook has great TeX support You probably want to update your website in that case: "Markdown, books are written using the markdown or AsciiDoc syntax. TeX support is planned."
- haddr 11y ago
  Ahh, I also was thinking there is some TeX templating support... What they have is only KaTeX for math formulas.
- AaronO 11y ago
  By TeX support I meant that we fully support TeX equations. The website mentions TeX but means LaTeX, I'll get that fixed, sorry for the confusion. Our TeX support allows you basically to write Markdown/Asciidoc and use TeX formulas wherever you need to, which gives you the best of both worlds (the simplicity of Markdown and the power of TeX formulas).

JohnHammersley 11y ago

It's interesting seeing the different approaches to combining the power of a structured formatting language with the ease of use of a (relatively code free) text editor. I'm one of the founders of Overleaf [1], and we've taken the route of keeping the full power of LaTeX there for anyone that needs it, but providing a 'Rich Text mode' [2] overlay for those who prefer a less code-like experience. If you give it a try, let us know what you think! [1] https://www.overleaf.com https://www.overleaf.com [2] https://www.overleaf.com/blog/81 https://www.overleaf.com/blog/81

Phemist 11y ago
I wrote my master's thesis in overleaf about a year ago, because my laptop was starting to break down and I needed a solution that allowed me to easily switch between university computers without having to constantly set-up my workspace on each individual PC. That was before the rich content editor was implemented, but I loved the experience nonetheless. The whole thesis was, next to my research, an exercise in cloud-based software. VM's on Cloud9, Code repo on github and my text editor on overleaf. Thanks a lot for making it available to a poor student like me!
- JohnHammersley 11y ago
  Thanks, that's great to hear! :) I'm impressed you used your thesis as a testbed for cloud-based software, hope it didn't cause any/too much additional stress! If you generated any datasets during your work, you may also want to check out figshare[1] as a handy data repository. [1] http://figshare.com/ http://figshare.com/ (Note - we work in the same office as figshare, so this is probably a biased recommendation!)
  - Phemist 11y ago
    Thanks for the link! My thesis was basically a data analysis project, improving on work my supervisor did prior to me starting my thesis. Figshare is good to keep in mind, but I don't think I'd have had much use for it, as the whole point of my thesis was to get certain figures within a reasonable time. I actually had quite a lot of fun figuring out how to get everything working in the cloud. Set up my home desktop as my personal computer "cluster" (i5 processor, so a cluster of 4 cores!), I find it hard to work in an environment that I tend to do other stuff besides work in. Derived a small representative dataset from the massive one I had to quickly iterate over my analysis scripts in Cloud9 (while having github take care of my revision history). Then ssh'ing into my desktop PC whenever I needed to run the scripts on the full data set. I considered adding a section on open science and cloud-based software to my thesis, but in the end decided not to due to a lack of time. Open science is based on open source principles, where everything that can be shared should be shared. The Cloud VM angle is quite interesting in this sense, as being able to share the machines that software for a research project was ran on is often quite difficult (or nigh impossible), and a cloud-based VM seems to bridge this gap somewhat. In theory, anyone could log-in to the VM and play around in the workspace I set up for my thesis project, not that many would want to I suppose.

deleted 11y ago

[deleted]

storrgie 11y ago

I'm not sure if I'll have an opinion that isn't commonly shared, so I figured I'd elucidate: I deeply love the simplicity of using markdown + LaTeX, however I realize that I'm somewhere on the gradient of complexity where I'm sacrificing some power for simplicity. Currently I think the tool that is used most is pandoc, and there are some offshoots that give pandoc more 'academic' power, like scholdoc. I've just been hoping that the pandoc world would progress (add more scholarly features) so that I could continue to keep my own data locally, manage it in my own vcs, and process it with a makefile. The only reason I see to hop on the software as a service bandwagon is for collaborative real-time editing (and some projects benefit greatly from this). I'll plug sharelatex for that, primarily because their model releases the software so that you can run your own if you don't want to pay for the service.

etherealmachine 11y ago
Is Madoko a SAAS app? If so I'll note another problem - madoko.net is currently timing out when I go to access it; any data inside is stuck there for the duration. On the Markdown+LaTeX note, I wrote my own Markdown parser (https://github.com/etherealmachine/markdown https://github.com/etherealmachine/markdown) to drive my github.io site (https://etherealmachine.github.io https://etherealmachine.github.io). Basically it's what you describe - easy mixing of Markdown+LaTeX to construct nice looking HTML.
- dimgl 11y ago
  You can download Madoko and run it yourself. http://madoko.codeplex.com/ http://madoko.codeplex.com/ http://research.microsoft.com/en-us/um/people/daan/madoko/doc/reference.html http://research.microsoft.com/en-us/um/people/daan/madoko/do...

astazangasta 11y ago

Or, just use LaTEX? What makes this better? Pure TeX is hardly that esoteric, and extra power is there if you want it.

phelimb 11y ago

There's also "paper-now" which uses Jekyll Now + GitHub Pages. https://github.com/PeerJ/paper-now https://github.com/PeerJ/paper-now https://peerj.github.io/paper-now/ https://peerj.github.io/paper-now/

tjohns 11y ago
I hadn't heard of paper-now. I really like what they've done with the sidebar. My only complaint is that I'd imagine reading academic articles in an ultra-thin sans-serif font might get tiring after a while.

jbssm 11y ago

This is really nice. Does it allow to work on multi file documents? i.e. when wiring a big document like a thesis, it's nice to have the chapters divided by different files.

gkya 11y ago

Emacs' Org-mode is pretty good for writing articles. It can be configured to use whatever package / setting one wants while exporting to tex / pdf, e.g. use some .sty files (presumably, I haven't needed them yet), or use the beamer class to make a slideshow. It can be integrated with the ESS package so that it can be used as a live programming environment for R, or whatever else the package supports. And it also supports todo lists, agendas, and any sort of note-taking from the first moment. Example config for latex export (although I do not write academic articles): https://github.com/cadadr/emacs.d/blob/c81ff8afa3ca4ab553013c0e5151c3595391aedb/gk/gk-org.el https://github.com/cadadr/emacs.d/blob/c81ff8afa3ca4ab553013...

bachmeier 11y ago
I wouldn't recommend org-mode for writing professional documents. It is more unstable than any other major piece of software I've used. I use it daily, but not for writing. Things get changed in each release, the documentation is rarely in sync, and in a lot of cases major changes are not documented at all. I learned the hard way. I wrote some presentations using org-mode. Then they changed the exporters without updating the documentation. It would be especially problematic to write an academic article in org-mode, because you might have to return a year or two later, and that's not when you want to find out how much has changed since you last worked on the paper.
- gkya 11y ago
  One can keep the intermediary .tex files should they export to pdf. Or for any substantial project one can fix the version of org, as other projects do so with the versions of the compiler or of the libraries. Still, if you are correct, then it is a problem for every user. I haven't encountered such problem in my use, although my use of ox-latex has been rather superficial (some homeworks, a tiny CV).
- krupan 11y ago
  It's true that org-mode is a bit of moving target, but the basic syntax for document formatting doesn't change. If you are really worried about this you could record/archive which version of org you used to put your paper together.

michaelmior 11y ago

> The editor has ‘hick-ups’! I'm not sure if this is a joke I'm missing, but "hiccups" is the spelling of the term referring to involuntary inhalation as well as (informally) a minor difficulty or setback[0]. A "hick" is an unsophisticated person[1]. [0] http://dictionary.reference.com/browse/hiccup?s=t http://dictionary.reference.com/browse/hiccup?s=t [1] http://dictionary.reference.com/browse/hick?s=t http://dictionary.reference.com/browse/hick?s=t

michaelmior 11y ago

> Can I write my academic paper, manual, book, thesis, etc. in Madoko instead of LaTeX? For me a strict requirement for this is that I can use a particular template and document class. Unfortunately I don't have any choice as to what the particular format is. It's not clear if Madoko makes this possible.

twblalock 11y ago
This is the problem if you want to publish. A lot of journals want .docx or Latex files, not PDFs, and they will simply reject submissions that don't comply with their requirements. It would be nice if journals would accept Markdown, but frankly I don't expect that to happen anytime soon.
- michaelhoffman 11y ago
  Pandoc is a great solution for converting Markdown into LaTeX and you can add arbitrary LaTeX code at the beginning and end of the output.
- suncanon 11y ago
  Even if your journal accepts PDFs, michaelmior's comment raises an important issue that a LaTeX style template cannot be imported into most (or all?) of these Markdown editors. This would be a great feature to add, IMO!
  - cls59 11y ago
    The issue with that is that a LaTeX template is turing-complete. Doing a meaningful import of arbitrary journal styles without re-implementing TeX is a very, very, very hard problem.
  - yid 11y ago
    > Even if your journal accepts PDFs, michaelmior's comment raises an important issue that a LaTeX style template cannot be imported into most (or all?) of these Markdown editors. Perhaps it would be easier to go the other way -- to modify a Markdown parser to output a simple subset of Latex that can fit into most common academic templates.

sampo 11y ago

> Madoko also automatically synchronizes your changes to the cloud storage every 30 seconds or so. Does it make a new push to GitHub every 30 seconds?

dllu 11y ago

A few months ago I created my own Markdown-like lightweight markup language supporting LaTeX equations, which can be compiled to either HTML or LaTeX: http://lawrence.lu/programming/dllup/ http://lawrence.lu/programming/dllup/

mpnordland 11y ago

For School most of my papers require MLA formating. I found a mla latex template and so now I just use pandoc and that template to do my papers. When they want a docx I also made an odt template that I the use libreoffice to convert to docx. If madoko had an option to do that, then I'd be interested, otherwise it's no use to me.

Avshalom 11y ago

Well the html rendering is quite nice but Markdown is so limited it seems like you're just writing latex with '['s replacing some of the '('s.

rayalez 11y ago

To achieve the same functionality on my blog I use: - Pelican - static website generator, like Jekyll but in python. - MathJax to render Latex It is easy to synchronize Pelican with dropbox or github, and it is incredibly convenient. You can use this article: http://technivore.org/posts/2014/01/03/blogging-with-dropbox-and-pelican.html http://technivore.org/posts/2014/01/03/blogging-with-dropbox... To configure it in such a way that all the updates happen automatically. For example I can simply write an article in Editorial on my iPad, and it gets immediately published/updated, without me having to do anything at all, exactly zero mouse clicks.

antman 11y ago

Scholarlymarkdown is nice and I like the way you can add captions and references to equations and images. http://scholarlymarkdown.com/ http://scholarlymarkdown.com/

Animats 11y ago

Perhaps someday there will be computer programs where you can write things without typing in funny codes. TeX embedded in Markdown seems painful. How about writing in a restricted subset of HTML, as some forums (notably Slashdot) allow? <h1>, <h2>, .., <title>, <p>, <i>, <b>, <blockquote>, and a few others let you do what Markdown does. For math, there's MathML: Square root of two: <math><msqrt><mn>2</mn></msqrt></math>

FraaJad 11y ago
I written TeX embedded in markdown the time with Pandoc for reports and papers. It's much easier than writing all TeX.
- FraaJad 11y ago
  wow, what was i thinking when i wrote that sentence? doesn't make any sense.
ska 11y ago
MathML is not a full replacement for TeX, and if we are talking about actual publication of papers/books rather than web content then neither HTML nor MathML are really up for the job.
simplyinfinity 11y ago
>Perhaps someday there will be computer programs where you can write things without typing in funny codes. You mean like ms word or open office ?

mangecoeur 11y ago

Not sure how this is really different from pandoc markdown...

mhartl 11y ago

Softcover [1] covers many of the same bases as well. Actually supporting all of LaTeX's features in HTML is basically impossible, though, so no matter which tool you use it's best to go in with tempered expectations. [1]: http://www.softcover.io/ http://www.softcover.io/

anotheryou 11y ago

Yet another Markdown flavor... Markdown is really not sufficient, this markup looks very cool but I'm missing compatibility again. I'll see if I can make it yellow cms compatible when exporting html...

dimgl 11y ago
The Madoko document states that it implements different flavors and extends it slightly. > Madoko is fully compatible with basic Markdown syntax and passes the entire test suite. It also implements most extensions, like Github flavored markdown, PanDoc, Markdown Extra, and multi-markdown, and it adds quite a few features itself to make it really useful for writing academic and industrial documents.

davidcollantes 11y ago

Typora (http://typora.io/ http://typora.io/) does similar, but it is an OS X application (Windows coming, so the author says).

dimgl 11y ago
Can you do LaTeX on Typora?
- davidcollantes 11y ago
  I am not sure it can, yet. It can do Math, so far. I have opened an issue on Github requesting it.
- davidcollantes 11y ago
  It can! See https://twitter.com/Typora/status/637495313259892740/photo/1 https://twitter.com/Typora/status/637495313259892740/photo/1

anotheryou 11y ago

pfew, but the generated html is ugly (missing breaks, strange inline styles and classes)

coliveira 11y ago

Good try, but in fact it is useless to use something other than Latex to write academic articles. Most journals in mathematics and engineering accept Latex, but I have never seen one accepting markdown. Which means that you will have to convert to Latex source anyway -- and in many cases make sure that the Latex code uses the style package of the publisher. This seems to me just to be asking for more trouble.

cetra3 11y ago

We use a simple md2pdf script internally that takes a markdown, throws on the company logo & font, and produces a pdf document. Process is md (vim/mou) -> cmark -> wkhtml2pdf -> pdf This works well for us, but would be nice if we could sort of merge this with an online wiki of some sorts.

creshal 11y ago
Have you considered pandoc? That allows to reduce it to md → pandoc → pdf, and in my experience pandoc generates much better PDFs (working links, etc.)

SZJX 11y ago

Doesn't org-mode already a kind of do that? I think it will handle most of the requirements just fine, handle LaTeX when necessary and what's better is that it comes within emacs allowing all kinds of easy customizations and extensions.