From mboxrd@z Thu Jan 1 00:00:00 1970 From: Eric Schulte Subject: Re: Using org-mode for laboratory notes. Date: Wed, 19 Sep 2012 12:49:27 -0600 Message-ID: <87a9wlalvs.fsf@gmx.com> References: <3EBF4F09D06D482C9F7BD50A74669FA8@gmail.com> Mime-Version: 1.0 Content-Type: text/plain Return-path: Received: from eggs.gnu.org ([208.118.235.92]:38627) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1TEPTU-0005AM-UA for emacs-orgmode@gnu.org; Wed, 19 Sep 2012 14:58:18 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1TEPTT-00009U-I6 for emacs-orgmode@gnu.org; Wed, 19 Sep 2012 14:58:16 -0400 Received: from mailout-eu.gmx.com ([213.165.64.43]:37982) by eggs.gnu.org with smtp (Exim 4.71) (envelope-from ) id 1TEPTT-00008o-8Q for emacs-orgmode@gnu.org; Wed, 19 Sep 2012 14:58:15 -0400 In-Reply-To: <3EBF4F09D06D482C9F7BD50A74669FA8@gmail.com> (Eric Lubeck's message of "Wed, 19 Sep 2012 09:15:35 -0700") List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: Eric Lubeck Cc: emacs-orgmode@gnu.org Eric Lubeck 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