Re: [DIYbio] Re: Standardized DIYbio report format? WAS: Endophyte isolation and first successful sequencing

The wiki parses Wikitext, yes, but the actual rendered wiki is standard
HTML and isn't designed explicitly for ease of parsing.

I'm also against relying on Wiki infrastructure because wikis are
"cloud only", in that rendering a wiki page to a local file is often
difficult, because of relative pathnames and image embeds, database
backed infrastructure, etc. - Yes, you *can* export to PDF, but PDF is
effectively a read-only data structure.

## Requirements for Ease and Academic Rigour
I think the ideal is a format that:
* Is easy for people to _read_.
* Is easy for people to _write_, requiring minimal reference and a
  shallow learning curve.
* Is already in widespread use if possible, so people have little to
  learn and plenty of support when they do.
* Allows image embedding.
* Allows dynamic styling, so it can be rendered into a pretty
  "Proceedings of DIYbio" frame.
* Allows easy linking, referencing and footnoting; critical for
  Scientific literature.
* Can be rendered into a matching document in most important formats
  for academic publishing standard: HTML (->Blog/Journal), LaTeX (->PDF)
* Has extensive software support already; don't shave yaks!

## Markdown Extra
I would like to suggest that Markdown, particularly a flavour of
Markdown Extra, would be ideal. If you're not familiar with the
Markdown syntax, it might hearten you to know that _this email is
written in markdown_. It was specifically designed to mimic how people
place emphasis, build lists, write titles and otherwise structure text
to be readable in the absence of pretty rendering.. except that it
allows you to then render that into a variety of formats.

Markdown normally renders into HTML, but there are LaTeX renderers and
Wikimedia-flavour wikitext renderers, and pandoc allows you to render
into anything from RTF to .doc, if you like. There are a bunch of
scripts and applications that specialise in posting markdown documents
to Wordpress blogs (which account for a two-figure percentage of all
known websites at present, so that's not to be sniffed at).

[Markdown Extra](http://michelf.ca/projects/php-markdown/extra/)
features referencing (in the form of footnotes), abbreviations, and
tables, all using fairly common-sense syntax. Markdown Extra is
supported in PHP and in Python's Markdown package (if the "extra" plugin
is loaded).

## Infrastructure
To store and manage publications, given the flexibility, you could have
a wiki or blog to publish rendered documents, and a more formal
repository that stores the Markdown source files and associated images.
That would cater to both ends of the technical spectrum; those that
just want a clear way to present data, and those that want crunchy
machine-parsable everything for meta stuff.

For DIYbio purposes, it would be pretty straightforward to knock
together a micro-publishing system where people submit their papers,
they are put up on a github[^1] repo where people can offer
issues and feedback (you don't need to know git to use the issues
feature, so it's non-techie safe) on the content of the document. When
it passes muster/review, it can be script-rendered and published to
wordpress and/or a wiki automatically.

Given that many people will already have dabbled with Markdown, and
those that haven't can already read it legibly (this email as
case-in-point), and the ease with which it could be rolled out and
diversified, I'd be strongly in favour of choosing it over something
over-lightweight and over-centralised like just-wiki, or overly
technical and offputting like LaTeX-and-git-only

[^1]: I say github and not gitorious because github has better support
for Markdown, sadly, and their issues interface is friendlier.

## Citizen Science Quarterly
With regard to the other publishing-relevant thread from Jacob, the CSQ
might be rebooting soon (!), and it would probably make Jacob's job a
lot easier if submissions could be trivially rendered into high-quality
HTML and LaTeX, for the online and print(?) editions respectively.

Thoughts?

On Tue, 13 Aug 2013 13:11:54 -0700
Nathan McCorkle <nmz787@gmail.com> wrote:

> Lots of journals already offer LaTex templates... so what's the best
> interface to magically transform plaintext blocks? A web form with
> blank text boxes and a submit button works, but it doesn't let people
> come back and edit it. Bryan says mediawiki (wikipedia) is hard to
> parse by a computer, but being a wiki which /does/ some formatting,
> the wiki engine /must/ be parsing it. I don't think mediawiki
> formatting is necessary though if we had a button to shove it all into
> a PDF... the wiki would just serve as a way to enter and edit the
> text. Leave the wiki unformatted save for some keywords to delineate
> different blocks that are needed for the LaTex template.
>
> On Tue, Aug 13, 2013 at 12:45 PM, Sebastian Cocioba
> <scocioba@gmail.com> wrote:
> > If someone with a knack for aesthetics can make a template and we
> > can vote on it? Try to get the ball rolling?
> >
> > Sent from my Windows Phone From: Nathan McCorkle
> > Sent: 8/13/2013 1:44 PM
> > To: diybio
> > Subject: Re: [DIYbio] Re: Standardized DIYbio report format? WAS:
> > Endophyte isolation and first successful sequencing
> > Maybe a template wiki page would suffice? You copy the template to
> > your own wiki page, then swap the template sections for your words.
> > Wikis are version controlled so edits are tracked, and there are
> > already collaboration tools built-in to each page (see wikipedia's
> > 'talk' page that goes along with each article).
> >
> > You can convert any text into a PDF format using some code, there'd
> > probably need to be a stylistic format chosen for this template.
> >
> > Maybe it'd be best to pick a stylistic format from one of the
> > current science publishers (they're all OK, though I don't really
> > care for 2 columns of text), then work out the wiki template and
> > the PDF generation stuff.
> >
> > --
> > -- You received this message because you are subscribed to the
> > Google Groups DIYbio group. To post to this group, send email to
> > diybio@googlegroups.com. To unsubscribe from this group, send email
> > to diybio+unsubscribe@googlegroups.com. For more options, visit this
> > group at https://groups.google.com/d/forum/diybio?hl=en
> > Learn more at www.diybio.org
> > ---
> > You received this message because you are subscribed to the Google
> > Groups "DIYbio" group.
> > To unsubscribe from this group and stop receiving emails from it,
> > send an email to diybio+unsubscribe@googlegroups.com.
> > To post to this group, send email to diybio@googlegroups.com.
> > Visit this group at http://groups.google.com/group/diybio.
> > To view this discussion on the web visit
> > https://groups.google.com/d/msgid/diybio/CA%2B82U9JHRRgiFBzNyTd47TNy05gkzJFQWxs_t9kk0jCJ9VSKDA%40mail.gmail.com?hl=en.
> > For more options, visit https://groups.google.com/groups/opt_out.
> >
> > --
> > -- You received this message because you are subscribed to the
> > Google Groups DIYbio group. To post to this group, send email to
> > diybio@googlegroups.com. To unsubscribe from this group, send email
> > to diybio+unsubscribe@googlegroups.com. For more options, visit
> > this group at https://groups.google.com/d/forum/diybio?hl=en Learn
> > more at www.diybio.org --- You received this message because you
> > are subscribed to the Google Groups "DIYbio" group. To unsubscribe
> > from this group and stop receiving emails from it, send an email to
> > diybio+unsubscribe@googlegroups.com. To post to this group, send
> > email to diybio@googlegroups.com. Visit this group at
> > http://groups.google.com/group/diybio. To view this discussion on
> > the web visit
> > https://groups.google.com/d/msgid/diybio/-5610509502223320986%40unknownmsgid.
> > For more options, visit https://groups.google.com/groups/opt_out.
> >
> >
>
>
>