RE: [DIYbio] Standardized DIYbio report format? WAS: Endophyte

[Sebastian Cocioba]

isolation and first successful sequencing
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A giant google drive folder? It would be neat to submit a paper for
community review and someone to compile a monthly journal of progress.
Maybe that will actually motivate people to DO science rather than talk
about it. I know there are a whole bunch of people actually conducting
science on the list...it would be nice to have many more.

Sent from my Windows Phone From: Jeswin
Sent: =E2=80=8E8/=E2=80=8E13/=E2=80=8E2013 9:53 AM
To: diy...@googlegroups.com; ben.g...@gmail.com
Subject: [DIYbio] Standardized DIYbio report format? WAS: Endophyte
isolation and first successful sequencing
On Wed, Aug 7, 2013 at 10:48 AM, Dakota Hamill <dko...@gmail.com> wrote:
>
> Ben: I understand what you're saying, there are times I read amazing
> articles or posts by people on how to build this or that and when I get t=
o
> the end, I say to myself, where is all the information and materials list=
!
> I've been quite busy during the week and have been writing these quick po=
sts
> at night. There is a section on the website that we had the intention (a=
nd
> still do) of filling with more detailed protocols. Since not everyone is
> entirely interested (like casual interested readers perhaps) in the exact
> buffer recipes, perhaps what I'll do is write a detailed reference sectio=
n

Can we get some sort of standard way to report the findings in the
DIYbio community? By standard, I mean, a specific file format (txt,
pdf, etc) with a specific template. The template should make it easy
to list materials, methods, results, conclusion, references. It should
be like a regular journal article except easily read by anyone and
easy to create [the report] by anyone.

And a place that accepts them as a repository would be nice, to keep
track of all the findings by people all over the world. Something like
github but I'm not sure what the general sentiment on github is. I
know Cathal uses it for his protocols.

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[Bryan Bishop]

On Tue, Aug 13, 2013 at 9:24 AM, Sebastian Cocioba <scoc...@gmail.com> wrote:

Can we get some sort of standard way to report the findings in the
DIYbio community? By standard, I mean, a specific file format (txt,
pdf, etc) with a specific template. The template should make it easy
to list materials, methods, results, conclusion, references. It should
be like a regular journal article except easily read by anyone and
easy to create [the report] by anyone.

How about yaml, because it's machine and human readable. Generic text doesn't tend to have that property. And don't get me started with pdf. :-)

- Bryan
http://heybryan.org/
1 512 203 0507

[Dakota Hamill]

Regardless of what format, I think it'd be great to have a collection of finished and reviewed works by people from the community.  I know there was a collection of pretty decent stuff on a German chemistry board I followed for a while, as well as one from sciencemadness.org.  People submitted things in .pdf with a common format and detailed lists or reagents, protocols, and pictures  The things I update on the blog are by no means finished or polished, and I never intended them to be that way.  Just like when writing a paper, the rough draft isn't the final copy, but it's still good to get people's feedback and opinions on the rough draft. 

There are some times when it's great to sit down and read through journal articles, and expect a really detailed layout of all the information, from materials to protocols an results.  Then there are times when it's enjoyable to just be able to peruse casually some of the work people are doing, if anyone happens to even update that, but a few blogs and people seem to.  I think there should be a place for both.  That's why I liked the DIYBio news feed.

Also, what's wrong with .pdf out of curiosity?  I'm not privy to any software or coding secrets really.

Generic text also looks pretty bland in a report format, feels like you're just reading something someone wrote in notepad.  I don't know how to describe .pdf's but, they always seem cleaner and have a completed look to whatever their contents are.  I wonder if there is something else that gives that same feeling or look?

[Jeswin]

On Tue, Aug 13, 2013 at 10:41 AM, Bryan Bishop <kan...@gmail.com> wrote:
>
> How about yaml, because it's machine and human readable. Generic text
> doesn't tend to have that property. And don't get me started with pdf. :-)
>

Ok, doesn't look too bad. But is it easy for anyone to learn and use?

I'm not really concerned about the output file format expect a single
format should be used.

What kind of report structure should be used? Something similar to
journal articles? How should the heading, body be organized? How are
references cited?

Finally, how do we deal with the loss of data/references on the
internet? The waybackarchive is nice but I'm not sure how complete
it's archives are. Blogs, personal websites come and go.