Andy Maloney
Question to the community: Where do you draw the line with what you post in your open notebook? For instance, do you keep your notebook focused and only post results/failures with your experiments, or do you make a point to post things that are tedious lab necessities such as "mixing solutions, analyzing data, or cleaning..."?
It makes sense to catalog everything you do in the lab so that you can see how your time is appropriated. That way when you return to your notebook, you can see how much time it takes to do things. But, is it necessary? I'm on the fence about this one since there are pluses and minuses to both sides of the argument. - Andy Maloney
I try and just keep notes as I go. It's always the minor detail you don't think work recording that is the critical piece of information you want six months down the track. The mixing solutions one has bitten us a few times when one lot of buffer was good and one was bad. I've certainly never regretted putting too much in the notebook. On the other hand those details probably aren't helpful to _most_ people looking at it from the outside. An ideal system would keep the trivia hidden in a "standard" view but have it there somewhere so that you could dig in if you needed to. - Cameron Neylon
Cameron: I know exactly what you mean about mixing buffers as I'm making one right now that doesn't seem to be working. Perhaps I should make a category in my notebook that I tag things that I think are "lab drudgery". - Andy Maloney
Taking Cameron's idea a little further: top layer = homepages for each project, featuring an intro and any published work; second layer = lab notes focused on experiments; third layer = everything that happened in the lab and was recorded, by a human or by a machine. That way readers could choose their own level of detail. In my daydreams every lab links to this kind of layered notebook directly from their own homepage... - Bill Hooker
Steve Koch pointed out that I have been lax lately with posting to my notebook. I agree with him completely. However, what I have been doing lately seems to me more along the lines of engineering necessities and not science. Thus, no postings as of late from me. But it seems that even posting the engineering nightmares I have to go through to make science is important as well. - Andy Maloney
Bill: I've tried to implement your idea in my notebook. This is not trivial and is proving to be quite time consuming to try and tag my entries properly so that there is some sort of layering affect. Both for my own sanity and those that may come across my page. - Andy Maloney
One negative idea I have about posting everything to my notebook probably has to do with how I feel about Twitter. No one cares (or at least they shouldn't care in my opinion) about how I had to order more vials. Of course, I may be taking that sentiment too far when it comes to my notebook. - Andy Maloney
Not to say Twitter is bad. It's great for those that want to use it. - Andy Maloney
"it seems that even posting the engineering nightmares I have to go through to make science is important as well" -- absolutely. This is exactly the kind of tacit knowledge that gets lost, and rediscovered, and lost, and rediscovered, and so on. If you solved a problem, engineering or scientific, then you did something that someone else might be able to use. Perhaps running out of vials (I assume it's because Koch keeps using them to store his crack) is a relatively trivial problem, and you might not write it up in your notebook. On the other hand, if you discovered a way to get the same vials at 1/10th of the cost that most people pay, then you found something useful. The key, I think, is to write up your notes in such a way that someone facing the same problem will come across your solution by searching. No one is likely to browse an Open Notebook -- they will come to it by searching, and make their way through it in the same fashion, looking for the bits they can use. It's no different in principle from the way we use PubMed -- we don't browse that, either, and most of it is useless to any single researcher. - Bill Hooker
+1 Bill and the challenge remains how to make it both easy to record all of that detail effectively and to make the right thing easily discoverable when someone somewhere wants it. - Cameron Neylon
I would not log 'making solutions', never logged that on books. But what I do is put the date on which a solution was made (date and maker's initials) and that gets logged in the experiment. Same with chemicals like antibodies: when I aliquot I tape the bottle label to the notebook and the 'internal' tag/batch that identifies the tubes in the freezer. The internal reference is what I record in the experiment book, but can be tracked back to original source. (This has come in handy at the time to claim a replacement from manufacturers when batches are bad. ) - Kubke
In my imagination we have a little web widget which is part recipe and buffer calculation engine and part logging in of buffer making. This serves two purposes, it makes it appealing to log the creation of the buffer because you get that as a side effect of bringing up/calculating the recipe and it also allows you connect other automatic logging of e.g. a balance that could let you go back and check whether something was wrong later. But the user should only have to do the absolute minimum of intervention. If you can get that logging as a sideeffect of e.g. printing out a label it's even better. This wouldn't even be hard to implement, I just haven't found the time yet... - Cameron Neylon
I ask my students to keep a time log of what they do and observe. Invariably new students don't record enough detail. But that comes out naturally when I step through their logs and can't recreate exactly what they did - and I will comment on this directly in their notebook. Maybe they will remember a critical missing detail or maybe all that was learned from the experiment was what information to include next time. The real test for me is - could someone write a paper just reading the notebook and associated raw data files - or do they have to contact the researcher because information is missing. That's an ideal - but it is something to strive for. - Jean-Claude Bradley
This is a terrific discussion -- one that I plan to use with students when discussing the practice/ethics of recording science. From a social science perspective, the mere existence of thoroughly noted lab notebooks is quite interesting... - Mickey Schafer
Sure D :) - BTW there is a recent paper in J Chem Ed about using wikis for chem lab - unfortunately none of them are public - via Brent Friesen - Jean-Claude Bradley
Great discussion! My work is all theory and I don't get all my blackboard scraps into the notebook, though often I wish i had (learning that a camera is faster than LaTeX), while git records all the micro-level changes in the code so I just comment on the larger ones. I try and use tags to avoid the most useful stuff getting buried in the details but haven't found OWW Categories or search to be quite good enough for me. Open to suggestions for that one. - Carl Boettiger
Carl: Using OWW categories is a pain but, it is nice to have a page that links dynamically to all my notebook entries with specific category tags. I include a template in my notebook that allows me to write a short description about the entry and that description is visible in my DPL page. It's just a shame that I learned how to do this a year after I started my notebook, so I have a lot of pages not tagged properly. Oh, and put everything in your notebook. My lack of description in mine has caused me to have a very painful 2 weeks. - Andy Maloney