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

Keep on with the good work Cathal!

Some other resources, basically plugins for turning wordpress into a scientific paper

https://sites.google.com/site/wpscientists/home/plugins 

also its now easy to generate citable references using figshare, upload a figure/paper/graph/data and get a doi! 

As an example 

http://figshare.com/articles/Netroceros_bellicornis_Konow_lectotype_SDEI/779797

Netroceros bellicornis Konow lectotype SDEI. Andreas Taeger. figshare.
http://dx.doi.org/10.6084/m9.figshare.779797

Retrieved 12:26, Aug 23, 2013 (GMT)

On Fri, Aug 23, 2013 at 4:06 AM, Dakota Hamill <dko...@gmail.com> wrote:

And occasionally here, if I think it merits shouting
about.

I hope people share whatever they are working on, in whatever stage of development it is, whether they think it warrants a shout out or not.   For too long I was worried about something being "good enough" to share.  I think it's great to show off whatever you do, even if it's rudimentary, because to some people, that's inspiring enough.  Not every experiment one does has to shatter boundaries, and not every write-up has to be ready for submission to a journal for peer review. 

I find motivation to be a roller coaster ride, at times extremely high, and at other times, extremely low.  I look to posts on here, big or small, grandiose or simple, for motivation to get back in the lab.  

I think it would be very beneficial to setup links to everyone else's blogs or websites/projects they are working on, such that if someone stumbles across one blog, they could be linked to anothers in the community.  Since News.DIYBio is down, maybe we should start another thread where we can all post links to our websites?  

On Thu, Aug 22, 2013 at 6:51 PM, Cathal Garvey <cathal...@cathalgarvey.me> wrote:

I don't really expect this to see much, if any, use. For me, it's an
exercise in actualised musings about the future of academia. I
presently record all of the work I'm happy to share on blogposts and
twitter, yes. And occasionally here, if I think it merits shouting
about.

But, say I wanted to share positive results on an experiment that
generated new knowledge in a meaningful, if small, way. There's a
reason we write science the way we do; impersonal, explicit,
formalised. It's a whitepaper of knowledge, and a deliberate effort on
the part of the experimenter to remove her/himself from the process and
open it up to criticism.

For this, I don't think blogposts in the casual form we're used to are
sufficient, but neither do I think we need an intermediary to measure
"scientific merit"; our peers will do just fine, thank you; that's how
science began, after all.

So, because I like to write in markup and hack on code, a markup format
to assist in writing explicit, formatted, impassionate scientific
literature seemed a worthy evening's work. Others may feel similarly,
or may decide to press on using LibreOffice or Wordpress' rich-text
editor. The standard layout, impersonal voice, and quality of the
research are what matter, not the method used to achieve it.

And no; there's not much of any of that yet in DIYbio. Indeed, I doubt
many will publish their research as "DIYbio". Rather, I think we'll
continue to trailblaze opening  up science to the "masses", and
meanwhile showing up a lot of assumptions about how science itself
should be done, and those who want to generate knowledge will carry on
calling it "science", not "diybio" or "biohacking". Me? I'm in it for
something else, right now. But I'll always be a scientist in spirit,
and the future of the field is wide open.

On Thu, 22 Aug 2013 18:37:46 -0400
Avery louie <inact...@gmail.com> wrote:

> It seems like there may be a slight case of putting the horse before
> the cart here.  Do people actually want to share what they are
> doing?  If so, why are they not already doing it using the mailing
> list, twitter etc. how easy will it be to use?  I am not saying this
> is bad, I am just pointing out some things to think about.
>
> --A
>
>
> On Thu, Aug 22, 2013 at 6:23 PM, Cathal Garvey
> <cathal...@cathalgarvey.me
> > wrote:
>
> > Hi all,
> > Inspired by the notion, I've partially written a python script that
> > implements the idea of a "Markup language for Academic Authorship".
> >
> > It's not ready, it won't dump a paper for you yet, but it has most
> > of the basics ready:
> > https://gitorious.org/plod/plod
> >
> > Included is an unfinished "paper" for demonstration purposes. If you
> > compile, you'll get a simple layout that demonstrates citation
> > formatting, but you'll only notice the abstract extension at work if
> > you look at the html and note the class and id attributes.
> >
> > The gist:
> > 0. It's not ready, so seriously; don't bother if you're not
> > interested in hacking on the code and making it ready.
> > 1. It's Extended Markdown, using the Markdown package from PyPI
> > (required): https://pypi.python.org/pypi/Markdown/2.3.1
> > 2. It has (currently) two custom extensions:
> >     - one is a "fencing" scheme for defining the abstract as a
> >       separate, named HTML block so it can be styled and laid out
> >       differently: The abstract is surrounded in
> > "@@@" (@=a=Abstract) to achieve this.
> >     - the other is a citation format like what I wrote up earlier in
> >       this thread. If this format is desired (you can always do it
> >       manually), it is written as "{{ <fieldname> <contents...> |
> >       <field2> <contents...> }}". To actually place citations just
> > use the "footnotes" extension as included in Extended Markdown;
> >       follow the cited statement with "[^tag]", then define later
> > with "[^tag]: {{ <citation block> }}". The tag can be anything
> >       memorable; it will be replaced with a number in order of
> >       occurrence. The citation block will be placed either at the
> > end of the document, or wherever "///References List///" is found.
> > 3. The "metadata" extension allows definitions of metadata at the
> > very beginning of the document, which is not rendered into the final
> > document but alters its rendering. At present, only "title" is
> > used; it becomes the HTML page title, and until a better way to
> > automatically detect the paper title is cooked up, this is the only
> > way. 4. The "attributes" extension is enabled, and is used to set
> > the class/id of some elements that vary between papers, like the
> > title; you'll see in the example "test1.md" document that the title
> > is followed by {: #paper-title }, an ugly format used by the
> > extension to add "paper-title" as the HTML ID of the paper title. A
> > postprocessor extension might resolve the page-title issue more
> > cleanly but would require some sort of standard title formatting
> > anyway to distinguish it.
> >
> > Other than the above, it's standard extended markdown; you format
> > the same way and you process the same way. It compiles to HTML and
> > can be embedded in a template (read the script to see how the
> > template works, if given). Indeed, that's the whole point; right
> > now, it just compiles to a flat HTML file, but with the right
> > HTML/CSS template, it could compile to a properly formatted "paper"
> > as you might read on PLoS or Pubmed.
> >
> > A lot of nice things remain that could be implemented better. I
> > would like to see these features:
> > 1. Framed images, for figures with explanatory subtext.
> > 2. Insertion of other markdown documents, allowing a source file to
> > be separated, perhaps so important tables can be handled
> > independently and compiled into the main source as needed. Would
> > also be handy for larger works, to be broken into chapters.
> > 3. "Cited by", though this would probably require a central
> > database of citations to check with, which is pretty out of theme
> > with peer-produced academic literature.
> >
> >
> > On Fri, 16 Aug 2013 14:14:35 +0100
> > Cathal Garvey <cathal...@cathalgarvey.me> wrote:
> >
> > > My "criticisms" of wiki were directed at "wiki-only", not "wiki as
> > > well".
> > >
> > > In other words, if your files are written in a standard,
> > > machine-parseable format that's accessible somewhere, then
> > > rendering and displaying on a wiki is nice for human navigation
> > > between papers and references (although with proper linking
> > > within pages it shouldn't matter whether they're all hosted on
> > > the same site/wiki.), and provides a visual set of modifications
> > > to the file over time.
> > >
> > > However, the "wiki" is little better than a Wordpress install for
> > > this purpose; the usual purpose of a wiki is to be
> > > human-editable, but if it's merely a rendering of a source file
> > > stored elsewhere, then changes made to the wiki will not be
> > > passed back to the file.
> > >
> > > But, having "wiki-only", while having the advantage that it's
> > > human-editable (preferably by author/editor only!) and the
> > > presentation *is* the file, has the disadvantage that it's poorly
> > > machine parseable, making conversion into other formats and
> > > analysis less friendly to meta-study and development. The
> > > machine-parseable "wikisource" is usually stored as a database
> > > entry somewhere rather than as a readily-accessible file to a
> > > passing bot.
> > >
> > > Also, wikitext, while originally as simple as Markdown, has sort
> > > of devolved a bit, and has some non-obvious syntax which means
> > > lots of checking syntax guides during authorship: does the bar
> > > character come before the link or after the link? How do you do
> > > alt-text again? References ditch the normal syntax entirely and
> > > look like a horrid mix of wikitext and html.
> > >
> > > So, I'm not a big fan, but it's still far
> > > friendlier, machine-parseable and standardised than most other
> > > alternatives. Even LaTeX is terrible these days; it appears the
> > > primary goal of LaTeX developers over time has been to guarantee
> > > backwards compatibility rather than to develop a great markup
> > > format. Doing anything useful requires ten or more plugins which
> > > don't come as standard with LaTeX. The "development environment"
> > > for new authors is forbidding. While Markdown is poorly
> > > standardised too, it comes with more batteries and compiles
> > > optionally to basic LaTeX if you really want to do hardcore
> > > layout work.
> > >
> > > I'm contemplating devoting an evening into making a "scientific
> > > article compiler" in Python for Markdown; any suggestions on what
> > > you'd like to see most in an application like this? Or how you'd
> > > like to see it implemented? I'm assuming that the default
> > > presentation format these days is HTML but will look into
> > > creating a layout that can be printed to a niceish PDF, too.
> > >
> > > On Thu, 15 Aug 2013 12:33:44 -0700
> > > Nathan McCorkle <nmz...@gmail.com> wrote:
> > >
> > > > That seems like a good list of 'wants' for what a software for
> > > > this might be.
> > > >
> > > > I disagree about your wiki coment... It's stored as markdown but
> > > > rendered as html, why would you try to parse rendered HTML?
> > > > It's not cloud only, you can definitely run a local wiki, or
> > > > download the markdown and render it in some custom LaTex
> > > > prettifier or something else. On Aug 14, 2013 7:02 AM, "Cathal
> > > > Garvey" <cathal...@cathalgarvey.me> wrote:
> > > >
> > > > > 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 <nmz...@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
> > > > > > <scoc...@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.
> > > > > > >
> > > > > > > --
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twitter: @drbrian

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