06 May Electronic Lab Books
I’ve been thinking recently about how best to organize my research data and experimental records. I’m not sure my needs are the same as everyone else’s, but I doubt they are so very different. Mostly I want to record GenBank searches, phylogenetic analyses, little bits of perl code. Although I support open data, I choose not to before publication. To be honest I don’t even really understand the need or desirability of open lab books. Maybe I’ve just come across more unscrupulous people?
Here is what I think I need
- I want it to be electronic (obviously) as its easier to incorporate my results and code that way. Also I have almost forgotten how to write and typing is much easier.
- I want the format to be open, not proprietary. It is equivalent to me if it has good batch export to a common format e.g. RTF. That way I’m not locked in to a particular program or system. I have swapped between several by batch exporting my records as RTF and importing them to another program.
- It should have both a chronological listing format and good search functions
- It should be easy to insert pictures and resize if necessary.
- It should be easy to work with formatted text, headings, tables and lists
- Links to other entries are useful, as are tags and a good folder hierarchy.
So I have been thinking about (a) Wikis, web and blog software (b) MS Word and Google docs (c) Specifically-designed electronic laboratory notebooks (d) Journaling software. Here are some thoughts and where I am now.
A. Wikis, Web and Blog software
There are a lot of different wikis out there, some simple, some very powerful. You can set up a free wiki on a public server. OpenWetWare is a good example. I don’t want to go that route as I want to keep my experiments private until I publish. Some positives of wikis are that they can be published locally on your hard drive, or on a lab server. TiddlyWiki is a favourite of mine. Wikis give the possibility of sharing. If I had a student using this approach I could log in and read her lab book whenever I wanted. I’ve tried a few wikis and my feeling is that they are a little more difficult to use than necessary. I am used to the ease and power of word processors and well made software. The ones I have tried don’t have that sort of polish. I don’t really know enough about wikis. Is it possible to batch export entries? If I kept a wiki lab book, then found something better would it be easy to select all, export as (say) RTF and then import into my new favourite software? I suspect it may not be very straight forward. I don’t see wikis as the way to go, it doesn’t feel right for me.
Blogs are great, organized chronologically (just like a paper lab book), with the ability to insert pictures, tables and formatting. Again I worry about the sophistication of blogs. I suppose there are different varieties. But I have many of the same questions as of wikis. I am not yet convinced the software is good enough. Blogger is a bit horrible and buggy. Inserting pictures can be problematic. It doesn’t seem to be up to the standard I would expect of my main information storage system.
There are some excellent open source content management systems available. Joomla! for example is a free and powerful content management system for creating web sites. I think setting up templates for different experiments could be a useful way to go. But same complaints as above.
B. MS Word and Google Docs
The new version of MS Word (2008 on my Mac) has a notebook layout. This looks like it could be just the thing, but it isn’t. Its not well designed and I gave up on it within half an hour. Standard Word docs are a possibility too. But then each experiment would be in a separate document I guess, quite difficult to browse and organize them.
Google docs are a simple set of office applications that you use online. They are interesting as they are stored on Google’s servers. You can also mark a document as shared and select who has access to it. It might be a useful approach to showing your supervisor your work if you are a student.
C. Specifically-designed electronic laboratory notebooks
These are usually commercial, and concentrated on features like security, validation and audit trails of what changes were made when. There is a list of some software here and the wikipedia entry is useful. I don’t find these really meet my needs as I really don’t care about documenting my edits and validating my electronic lab book any more than I did my paper one. It might be different if you work in industry. I recently saw iPad though which is free and definitely worth a look. After testing it a bit though I don’t like the environment very much.
D. Journaling Software
These are applications for organizing databases of data in the form of notes, and other media. They are often very sophisticated and powerful. They tend to be operating system specific. I use OS X (most of the time) so the examples below relate to Macs, but Microsoft and Linux have similar stuff. I have used Journler until recently. This is a really excellent software package (US$35), but I have recently swapped to use MacJournal which costs the same. This is a similar program, not quite as well-designed as Journler but it does have the advantage of syncing with my .Mac account so I have the same data available at home and in the office. It turns out this is really important for me.
These journals are a database of entries. Entries can be formatted like a word processor document with styles and tables and inserted pictures. Tags and search facilities are good. Different types of media (e.g. PDFs, JPG) can be dragged in. Audio (or video) notes can be recorded and added simply. Chronological listing and folder structures are useful. Export of notes as html, PDF, RTF, text etc should ensure that the information is always accessible even if you stop using the software.
I am very impressed with information journals like Journler (see pic below) and MacJournal as electronic lab books. They fit my needs, are powerful and very polished pieces of software. I’ve realized that working in a nice software environment is more important to me than anything else. They don’t have the automatic publish to web strengths of blogs and wikis which I guess can be very useful to coordinate between lab members, or to allow a supervisor to routinely read a student’s book. They both do export as html though and hopefully this aspect will develop.