# Software/App for electronic research notebooks

I want to keep a research notebook for my computational "experiments". Basically, I should at least be able to write text and attach images like plots. Other nice features to have would be

2. latex equations
4. being able to transfer data
5. dating and version control
6. open-source tool

I am already familiar with trello and tiddlywiki. Trello is good for attaching stuff and organising tasks, but I need a notebook where I attach a plot, write stuff around it, attach another below it. It doesn't have a paper or canvas. Tiddlywiki is a little painful for attaching pics and equations, the file bloats, it seems I am keeping a blog.

What is a good, free electronic notebook tool for research/lab work?

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I just saw springpadit.com, but I don't know how good it is. Anybody used it? –  highBandWidth Apr 10 '12 at 19:14
Related question on Nonlinear Note Taking? –  user107 Apr 10 '12 at 20:06
Hello, highBandWidth: Welcome to Academia.SE. As a moderator, I have to agree with Nunoxic that the question is similar to the Nonlinear Note Taking. Please indicate in which sense the question is different, or it may be better to merge or close the question. –  aeismail Apr 11 '12 at 4:38
If anything, this question is better than the nonlinear note taking one as it is more detailed with specific desired requirements. Please keep it open. –  David Ketcheson Apr 11 '12 at 6:04
@aeismail, the reason I asked this question was that [Nonlinear Note Taking][1] is too focused on trees and mind-map structures. Lab notebooks (the physical kind used in wet-labs etc.) are not really the same as mind maps. [1]: academia.stackexchange.com/q/109/634 –  highBandWidth Apr 11 '12 at 16:15

For uploading papers and annotating them, I use mendeley. To organize my citations, I use citeulike which is nifty for it bibtex entry generation. I also use Jabref locally on my computer to manage my papers.

I am into numerical simulations as well and I generally add my results to latex documents (figures and all) as I eventually need it in a latex format for my dissertation! Plus this way, I save time!

Have you tried google notebook? I haven't used it in at least 3 years so I don't quite know how good it is now.

Good luck!

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If I'm not mistaken, Google notebook is going to be merged with Google Docs very soon. –  user107 Apr 10 '12 at 20:07
Google notebook is down: Google recently stopped development on Notebook, which means it's no longer open to sign-ups by new users or being improved. –  Piotr Migdal Apr 11 '12 at 11:55

For the last month, I have been using Gitit for this purpose. That link goes to a live demo where you can try it out. It satisfies all your requirements:

1. It's a wiki, so you can easily make links between pages.
2. It's built on pandoc, which understands TeX and uses MathJax to render it (it technically renders a subset of TeX, but it's a pretty substantial subset)
3. It's actually a Git repository, so you can upload anything you want to it. Or just put your figures out on the web (via figshare or a public Dropbox link) and link to them.
4. Same as 3.
5. Again, it's Git.
6. It is open source: https://github.com/jgm/gitit

As a bonus, you can put it out publicly on the web if you want (or just run it locally on your machine). I run it on an internal server at my University and my students and post-docs use it to. Thus it's a convenient way to share information as well.

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Check out GitHub hosted blogs using what's called "jekyll": -http://jekyllrb.com/ -https://github.com/mojombo/jekyll (see the wiki tab for example sites) -Easy way to start: use jekyll bootstrap or octopress

Jekyll is just a bunch of code that makes it easy to have stuff that you have on blogs/lab notebooks: tags, pagination, etc.

Some cool things are that its free, open source, versioned, handles images/papers/etc, can integrate comments (I use Disqus).

It does require a bit of a learning curve over other blog platforms, but its well worth it.

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The good thing about jekyll is that you can add files and they can go into version control along with your text/notes. The bad(?) thing is that unlike a lab notebook, you can't drag and drop images and visually mark/annotate stuff. –  highBandWidth Apr 11 '12 at 16:21

Came across this website today. Christoper Mayo piece on using Evernote for Research.

http://www.princeton.edu/~cmayo/evernoteresearch.html

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I am trying nixnote, its open source cousin. Looks good so far. I couldn't figure out if there was a way to attach arbitrary files, eg. to keep a copy of the dataset I ran or obtained along with the note describing it. –  highBandWidth Apr 12 '12 at 21:51

# Org-mode

I use Org-mode to organize and track my research. It is an Emacs major mode that seems to hit most of your requirements. The .org files are plain text which should guard against bloat and lets you access them anywhere, even when you do not have Emacs or Org-mode available.

Org-mode has linking capability to any type of file, as well as to specific locations in a document.

latex equations

Org-mode has support not only for LaTeX equations but for a number of programming languages via org-babel. You can include the code blocks inside your .org file.

Because it is only a text file, this sort of behavior can be accomplished through the linking mechanism. The links can be to other documents/papers on your machine or URLs. Visiting a URL in Org-mode will open your browser to the requested link.

being able to transfer data.

I am unsure what you are looking for here. Org-mode has a nice built-in table editor with automatic column width adjustment and some spreadsheet behavior. If you do not want the actual data in the .org file, you can always link to do the data. If you are looking to import data into the file directly, Org-mode has a function org-table-import that will parse TAB or whitespace separated data into an Org table.

dating and version control

I use Org-mode to track my time spent on various research items. You can set the headings in Org-mode to behave like multi-state TODO lists and assign time to them. Most headings start as TODO, switch to STARTED when I clock in on them, and then I can update them to DONE when I am finished. It can also generate reports based on your tracked time. For example, I use a built-in report for the last week to help generate weekly research updates.

I handle my version control and distribution through Dropbox, but since the files are plain text any version control system you are comfortable with should work fine.

open-source tool

Org-mode is open source.

Org-mode also can be set to display inline images, so even though the actual .org file stays in plain text for VCS, when you open the file in Org-mode you can view the images, and comment on them accordingly.

While the .org files themselves are plain text, Org-mode has a number of export options, including LaTeX, PDF, HTML, DocBook, OpenDocument and others. So if you want to turn your research notebook into something more visually appealing than a plain text file, there are many options. I would recommend this paper for a good description of what Org-mode can do in a research environment.

The downside is that it is a mode for Emacs. If you are not already using Emacs it has a steep learning curve and can require extensive customization to get things running exactly the way you want. Org-mode and AUCTeX (the Emacs LaTeX mode) are the reasons I spent the time to learn to work with Emacs and I have not been disappointed. However, if you are looking to get something up and running quickly (and are not already familiar with Emacs) it may not be your best option.

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It sounds like you're looking for something like http://figshare.com

It's part of Digital Science, which is part of the same family of companies as Nature Publishing, but I know the guy who runs it and I think he's really sharp & going about things the right way.

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figshare seems a like a place to host individual files, whether images, pdfs or datasets. Do people actually use it to keep daily records and the like? –  highBandWidth Apr 12 '12 at 21:53

I personally use VoodooPad, which is basically a personal wiki, in conjunction with LaTeXiT for latex equations. I've found it to work very well; you can store many things in it, including papers. It's all text-based so you can back up using Git or whatever you like. They have a free version. Not open source.

I'm surprised nobody's mentioned Evernote. They claim you can put anything at all in it, and from what I've seen, that's true. Backup to Evernote cloud. Free, not open source.

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