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Thursday, July 9, 2009

New Tool: KeepNote

Obviously I haven't updated much here lately - I've been pretty busy and inspiration hasn't struck me much in the last few days to get anything written. However, I started using some new software this morning, and I'm enjoying it so much I figured I have to share.

One of the big problems I have, as a bioinformatician, is keeping track of all the notes and one off scripts I write. I don't want to use an SVN, because it's just a repository with no organization. I don't want to use a wiki, because it's a huge hassle to maintain for small projects, and I hate using text files.

The compromise, it seems, is to use standards compliant files with a hell of a wrapper around them that does the organization for you, and the one I found is called KeepNote. The project page and downloads can be found at The software is available for all major OS (Linux, Mac and even Windows), and can be installed relatively quickly and (for the most part) painlessly. (Linux builds are missing a library in the dependencies, but that can be figured out pretty quickly - just apt-get the missing lib and re-install if you hit this problem.)

While it may not fit everyone's workflow, my few hours of using it have already helped me get my tools organized and assembled in a logical manner, and it's allowed me to remove a load of files from my desktop. There are still bugs with it: I had to manually do some configuration of the the web browser, text editor and such before I could get started, but so far I haven't hit any of the bugs.

It also claims to help you organize notes - which I can clearly see. next time I go to a conference, I'll be using this for recording and organizing the usual 30-40 pages of notes I take.

For me, this falls under the heading of required tools for bioinformaticians and students alike and I look forward to seeing the project evolve and grow.

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Blogger Dan said...

Weakling! Why aren't all of your notes written on vi, in TeX, and re-compiled and backed up daily by a cron job?

July 9, 2009 4:48:00 PM PDT  
Blogger Anthony Fejes said...

And what do you think I did before Keepnote???

July 9, 2009 7:49:00 PM PDT  
Blogger Rod said...

Another (non-free) alternative for Mac, at least, is Yojimbo:

July 21, 2009 12:21:00 PM PDT  
Blogger Will said...

This tool is the jam. Great tip!

August 11, 2009 7:26:00 AM PDT  

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