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So this is an odd fit, though really I think it's an odd fit for any site, so I thought I'd try it here, among my data-crunching brethren.

I came to epidemiology and biostatistics from biology, and still definitely have some habits from that field. One of them is keeping a lab notebook. It's useful for documenting thoughts, decisions, musings about the analysis, etc. All in one place, everything committed so I can look back on analysis later and have some clue what I did.

But it would be nice to move that into the 21st century. Particularly because even though the lab notebook system is decent enough for one person and documenting decisions, it would be nice to be able to attach plots from EDA, emails from data managers discussing a particular data set, etc.

I'm guessing this will involve rigging up my own system from an unholy union of many different bits, but is anyone currently using a system and have any recommendations?

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    $\begingroup$ I think it may be OK to grandfather (ie, leave open) this thread. $\endgroup$
    – gung - Reinstate Monica
    Commented Aug 25, 2016 at 14:26

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These are called Electronic Lab Notebooks (ELN).

Here are some of the open source options I've looked at:

  1. The Sage Notebook.

  2. The new IPython Notebook, which can now be run as a webapp on EC2 and Azure.

  3. Leo, which can be used with IPython and in many other ways.

  4. Various wiki, blogging, and CMS solutions.

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  • $\begingroup$ I ended up using a free Wikispaces wiki as my current experimental lab notebook substitute. $\endgroup$
    – Fomite
    Commented Oct 15, 2011 at 5:12
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My favorite: Evernote. You can tag entries (e.g., 'analysis', 'idea', etc.), you can paste pictures and graphics, and you can share notebooks with collaborators. And: it's basically free (well, freemium). But the free edition is absolutely sufficient for me.

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  • $\begingroup$ Furthermore, there are free apps for Android and iOS. $\endgroup$
    – Jose Zubcoff
    Commented Oct 12, 2011 at 8:05
  • $\begingroup$ +1 I find the mobile app for Evernote to be particularly useful when running around between labs or jotting down a thought when away from a computer. $\endgroup$
    – jthetzel
    Commented Aug 14, 2012 at 16:25
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I've never used it personally, but Microsoft has a piece of software in the Office suite called OneNote that accomplishes a similar goal to your e-lab notebook specifications. Refer to their website for more information. They also offer a free trial bundled with MS Office here.

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    $\begingroup$ @mbq have you found a decent Linux replacement for Onenote? $\endgroup$
    – andreas-h
    Commented Jul 3, 2013 at 14:18
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I found Xmind useful. You can attach anything, and tree structure is really useful for organizing. I especially like the feature where you can drill down into the node (topic). There are more similar software products which exploit the same concept.

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    $\begingroup$ Freeplane and Freemind are two free alternatives that I've used for various projects. A new fork of FreeMind is SciPlore MindMappings, which includes support for BibTeX references and importing bookmarks from a PDF. $\endgroup$
    – Wayne
    Commented Oct 12, 2011 at 12:35
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Personally I have found the Livescribe 'smartpen' a God send.

it merges the trusty 'old-world charm' of a traditional pen and paper notebook but inlcudes the ability to record sound (which it synchronises with your pen strokes) ready for later revision. NB- there is a downside and that is you have to buy special paper that works with the pen.....swings and round-a-bouts really

The audio/pen stokes an be uploaded onto the web and then attached to many of the other programs already higlihted above.

Students I teach (biomechanics) absolutely love this and find later studying of difficult concepts much easier than before (pre livescribe)

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You might want to check out the latest Zotero beta, which is now standalone and doesn't require Firefox.

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    $\begingroup$ Zotero is a bibliography manager, not a ELN. $\endgroup$
    – nico
    Commented Oct 12, 2011 at 16:05
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    $\begingroup$ @nico: I believe you can store anything you want in Zotero, including your own documents. It's not exactly an ELN, but it is free and would make it easy to include (and index) other materials as well. $\endgroup$
    – Wayne
    Commented Oct 13, 2011 at 1:06
  • $\begingroup$ sure, and it is great that you mentioned it (I use it a lot and it is amazing), but other opensource alternatives that are specifically thought as ELN exist, so why not using those? $\endgroup$
    – nico
    Commented Oct 13, 2011 at 6:51
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Check out this article, Beautifying Data in the Real World, from Nature Precedings for some ideas.

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    $\begingroup$ that is a nice article, but it would help to summarize some of the information in your answer $\endgroup$
    – Abe
    Commented Oct 12, 2011 at 14:35
  • $\begingroup$ Hi @Abe, Yes, that would be more helpful. I haven't read the article myself, finding it just yesterday and not being especially interested in the topic myself. I thought that I would share anyway. $\endgroup$
    – Charlie
    Commented Oct 12, 2011 at 15:43
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How about a Boogie Board? You can write your notes on a slate and record them as 's the same idea as the LiveScribe pen but you can save them as PDF files...It isn't out yet, but will be in less than a month.

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  • $\begingroup$ Onesoftwares download firefox 57.0 Free download. $\endgroup$
    – NomanJaved
    Commented Feb 10, 2018 at 16:48

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