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 themin your records.org allows (at least it did a while ago) to link not only to a filebut also to a specific version of a file.You could do small modification in the protocol-files as you need themand 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 isimportant if you might plan link to a lot of external files. Imagingyou overwrite a file by accident or because you can't remember youreferred to the original file already. A normal link would quietlypoint to the new file and would not be in-sync with anything youmentioned 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 PCreachable from all your other devices) you could easily add data fromwithin the lab, go to your office to add more data and at a certainpoint merge all this together. Both PCs could work offline and onlyneed to be online for check-in and check-out new data.Another benefit of combining org-mode and git... you can tag certainversions of your lab book. E.g. tag them whenever you write a paperand make a notice in org-mode. This enables you to get back to all themeasurement and reps. data evaluation results as you found them duringwriting your paper, even years and many many changes later (e.g. youmight improved your data analysis method over time but for the paperyou 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 mergingorg-files much more nice.Check here:Albeit I have to say I like to do all kind of stuff in org-mode, Ifaced problems using only org-mode as lab-notebook. Sometimes thingsin a lab are to numerous and to verbose to type them all in as theyhappen. Sometimes a little sketch, some quick scribbled note, etc.contains the real important data.... sentences like "Damn, Joe slammedthe door AGAIN", during an AFM measurement. Or in your case "Uhh..what are the funny little flakes in my buffer solutions".... I thinksometimes a keyboard still filters to much and hence org-mode mightnot really contain all the necessary info.As a summary:org-mode as a lab-book will work fine if you are strict in using itand force yourself to be verbose enough.Hope thats helpsTottiCC. There might be some legal issue with real lab books and electroniconce. Back in the good old time where scientists didn't publish eachand every result and where it could take many many months until somediscovery reached the other side of the planet, the laboratory bookswhere the legal evidence of the original work. If someone made a wrongclaim or someone accused someone else of falsify reporting, thelaboratory books where used to proof those claims. That is the reason,you find e.g. nicely archived laboratory books of all the greatscientists of the Bell laboratories. Not sure how much this is stillrelevant today.On 20 September 2012 03:49, Eric Schulte <eric.schulte@gmx.com> wrote:Eric Lubeck <eric.lubeck@gmail.com> writes:Hello Everybody,I had a look around the web for awhile, but couldn't find anyinformation pertaining to my particular needs. I hope somebody herewill be able to help me out.Anyway, I've been looking around for quite a while for the propersystem to set-up an electronic laboratory notebook in. I will beusing org-mode to document wet-lab experiments in addition tocomputational work.One of my particular concerns is this: I'm accustomed to using achronological laboratory notebook for recording all of my data. Theagenda views in org-mode seem to provide a means to retrievechronological information out of my outlines, but I would than need totimestamp every single entry in my outline. Is there a means fordoing this? Currently I am manually typing C-u C-c ! , but it wouldbe helpful to have something automatically configured to timestamp andplace the time in a drawer for any entry in a particular file.I believe such automated functionality may exist (although I don't useit personally). Take a look at this portion of the manual [1].My other question pertains to efficiently representing linked ornested data. I'd like to record my detailed laboratory protocols inanother outline. As most of my day-to-day work is using theseprotocols with minimal modifications, I'd like to record in my primaryoutline a property or hyperlink that points to the primary protocoland suggests that this days experiment "inherits" from the mainprotocol with given modifications. It would be really awesome if theprotocol tree could than pick up on these distant inheriting protocolsand transclude in the dates I have performed this protocol andsubsequent modifications from the "lab notebook" section. Is such atask possible with org-mode, or must I look towards a more traditionaldatabase?If I read this paragraph correctly, you want to be able to collect thedates from every entry in which a particular protocol was used. If youassign each protocol a short tag name, then you could tag each dailyexperiment with the date and the protocol used. Armed with your taggedheadlines Org-mode should provide everything required to search for andcollect your experiments based on tags, and to do things like collectthe dates on which each tag was used. Look at the tag and searchingsections of the Org-mode manual [2], and maybe look at the org-collectorin the contrib portion of Worg [3].Thanks,Eric LubeckFootnotes:--Eric Schulte