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Re: [O] Using org-mode for laboratory notes.

From: Russell Adams
Subject: Re: [O] Using org-mode for laboratory notes.
Date: Wed, 19 Sep 2012 12:08:21 -0500
User-agent: Mutt/1.5.21 (2010-09-15)

On Wed, Sep 19, 2012 at 09:15:35AM -0700, Eric Lubeck wrote:
> 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.

There's an emacs customization I use which binds F9 to insert NOW as
an inactive date & time stamp.

 ;; Insert immediate timestamp
 (define-key global-map (kbd "<f9>")
   '(lambda () (interactive)
      (when (eq major-mode 'org-mode)
        (org-insert-time-stamp nil t t)
        (insert "\n"))))

I use this in my org files. I outline my projects by major task or
product. Every time I change tasks or return to taking notes I just
hit F9 before I start typing.

Then at any time I can use the agenda in log mode and enable inactive
time stamps to show me a hyperlinked timeline.

> 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?

The only word I got here was "database". There is some support for
using property drawers for storing data and summarizing. If you had a
headline which you kept notes under and stored values in a property
drawer you may be able to manipulate it.

Good luck!

Russell Adams                            address@hidden

PGP Key ID:     0x1160DCB3           http://www.adamsinfoserv.com/

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