Hey,
Thanks for the good idea. I'll have to look into figuring that system out.
On the broader point of organizing the notebook, I am still having a bit of a
dilemma coming up with an effective system. My first thought was to just place
all my work in a dated hierarchy, such as with org-datetree. This would be
simple and mirror a conventional notebook, but would loose a lot of the logical
hierarchy possible with digital tools.
On the other hand, organizing all my experiments as a non-linear outline is
getting a bit messy. I found myself navigating around headlines everyday
searching for items I need to schedule for the next day. As my notebook gets
bigger, this system will probably get very inefficient. If i properly tag and
schedule my tasks for the day this should be less of a problem, but i still
foresee potential chaos if I get lazy. In addition to tasks I intend to record
other observations in the notebook that may not be associated with a recent
task, yet are important for me planning future experiments. Without proper
timestamps I could loose these observations over time.
This is where I came up with the idea of tagging all of my headlines with their
entry date and timestamp. Potentially such a system would enable me to view
the logical hierarchy of an experiment, but also view my work in the
conventional linear order.
Anyone have any other ideas for reasonable systems?
I'm also a bit confused about the proper way to implement such a system. I
imagine I could hack together some auto-timestamp property, but than it would
only apply to headlines, not to my nested observations in list form. For this
reason I have little used lists at all in org-mode, as it seems that any data
that could potentially be nested, such as with different tasks or properties,
must be converted back to headline form before it can be annotated. Am I
missing something?
Also, I have a general question about nesting headings demonstrated by the
below example.
* Today's Experiment :EXPERIMENT:
** Do today's Experiment :RATIONALE:
** Data link :DATA:
** Experiments are sad. :DISCUSSION:
** Repeat, but change X Tomorrow :FOLLOW-UP:
* Tomorrow's Experiment :EXPERIMENT:
** Yesterday's Experiment Failed :RATIONALE:
*** Determine if X was the cause
In the above case I have two options, to either continually nest all follow-up
experiments, or rely on a network of links to get me back to the data that led
to the follow-up experiments. Anybody have any advice on pursing either option?
Thanks for the help,
Eric Lubeck
On Wednesday, September 19, 2012 at 6:44 PM, Torsten Wagner wrote:
Hi,
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:
http://orgmode.org/worg/org-contrib/org-git-link.html
http://orgmode.org/worg/org-contrib/gsoc2012/student-projects/git-merge-tool/index.html
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
