Re: Using org-mode for laboratory notes.

[Eric Schulte <eric.schulte@gmx.com>]

Eric Lubeck <eric.lubeck@gmail.com> writes:

> Hello Everybody, 
>
> I had a look around the web for awhile, but couldn't find any
> information pertaining to my particular needs.  I hope somebody here
> will be able to help me out.
>
> Anyway, I've been looking around for quite a while for the proper
> system to set-up an electronic laboratory notebook in.  I will be
> using org-mode to document wet-lab experiments in addition to
> computational work.
>
> One of my particular concerns is this: I'm accustomed to using a
> chronological laboratory notebook for recording all of my data.  The
> agenda views in org-mode seem to provide a means to retrieve
> chronological information out of my outlines, but I would than need to
> timestamp every single entry in my outline.  Is there a means for
> doing this?  Currently I am manually typing C-u C-c ! , but it would
> be helpful to have something automatically configured to timestamp and
> place the time in a drawer for any entry in a particular file.
>

I believe such automated functionality may exist (although I don't use
it personally).  Take a look at this portion of the manual [1].

>
> My other question pertains to efficiently representing linked or
> nested data.  I'd like to record my detailed laboratory protocols in
> another outline.  As most of my day-to-day work is using these
> protocols with minimal modifications, I'd like to record in my primary
> outline a property or hyperlink that points to the primary protocol
> and suggests that this days experiment "inherits" from the main
> protocol with given modifications.  It would be really awesome if the
> protocol tree could than pick up on these distant inheriting protocols
> and transclude in the dates I have performed this protocol and
> subsequent modifications from the "lab notebook" section.  Is such a
> task possible with org-mode, or must I look towards a more traditional
> database?
>

If I read this paragraph correctly, you want to be able to collect the
dates from every entry in which a particular protocol was used.  If you
assign each protocol a short tag name, then you could tag each daily
experiment with the date and the protocol used.  Armed with your tagged
headlines Org-mode should provide everything required to search for and
collect your experiments based on tags, and to do things like collect
the dates on which each tag was used.  Look at the tag and searching
sections of the Org-mode manual [2], and maybe look at the org-collector
in the contrib portion of Worg [3].

>
> Thanks,
> Eric Lubeck


Footnotes: 
[1]  http://orgmode.org/manual/Clocking-work-time.html

[2]  http://orgmode.org/manual/Tags.html

[3]  http://orgmode.org/worg/org-contrib/org-collector.html

-- 
Eric Schulte
http://cs.unm.edu/~eschulte