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

From: Torsten Wagner
Subject: Re: [O] Using org-mode for laboratory notes.
Date: Thu, 20 Sep 2012 10:44:49 +0900


one way which works rather differently is the combination of git and org-mode.
You could write your protocols in separate org-files and link to them
in your records.
org allows (at least it did a while ago) to link not only to a file
but also to a specific version of a file.
You could do small modification in the protocol-files as you need them
and check them into the git system.
Link to them and you will see the version you used for exactly this experiments.

Actually using something like git and a git sensitive link is
important if you might plan link to a lot of external files. Imaging
you overwrite a file by accident or because you can't remember you
referred to the original file already. A normal link would quietly
point to the new file and would not be in-sync with anything you
mentioned in your org-file.

Other benefits are gits diff, merge and change-recording capabilities.
If you set-up the git repro with entire lab-book on a server (a PC
reachable from all your other devices) you could easily add data from
within the lab, go to your office to add more data and at a certain
point merge all this together. Both PCs could work offline and only
need to be online for check-in and check-out new data.
Another benefit of combining org-mode and git... you can tag certain
versions of your lab book. E.g. tag them whenever you write a paper
and make a notice in org-mode. This enables you to get back to all the
measurement and reps. data evaluation results as you found them during
writing your paper, even years and many many changes later (e.g. you
might improved your data analysis method over time but for the paper
you still want to see the old stupid way how you dealt with the data).

Recently we got an org-file sensitive git-module, which makes merging
org-files much more nice.
Check here:


Albeit I have to say I like to do all kind of stuff in org-mode, I
faced problems using only org-mode as lab-notebook. Sometimes things
in a lab are to numerous and to verbose to type them all in as they
happen. Sometimes a little sketch, some quick scribbled note, etc.
contains the real important data.... sentences like "Damn, Joe slammed
the door AGAIN", during an AFM measurement. Or in your case "Uhh..
what are the funny little flakes in my buffer solutions".... I think
sometimes a keyboard still filters to much and hence org-mode might
not really contain all the necessary info.
As a summary:
org-mode as a lab-book will work fine if you are strict in using it
and force yourself to be verbose enough.

Hope thats helps


CC. There might be some legal issue with real lab books and electronic
once. Back in the good old time where scientists didn't publish each
and every result and where it could take many many months until some
discovery reached the other side of the planet, the laboratory books
where the legal evidence of the original work. If someone made a wrong
claim or someone accused someone else of falsify reporting, the
laboratory books where used to proof those claims. That is the reason,
you find e.g. nicely archived laboratory books of all the great
scientists of the Bell laboratories. Not sure how much this is still
relevant today.

On 20 September 2012 03:49, Eric Schulte <address@hidden> wrote:
> Eric Lubeck <address@hidden> 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

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