A request for opinions or experiences: as part of my interest in reproducibility (you did read last weeks article on reproducible analysis, right?) , I’ve been looking at electronic lab notebooks. I’d really like to structure my research and protocols in a better way, being able to search and retrieve them with ease, seeing what I did. As it happens, my employer has an interest in ELNs as well, except more towards the wetlab end of things. How can the bench scientist easily record what they did, what results they got and share these with a lab or supervisor?
Thinking about my list of desired features, I ended up with
Must allow saving and summarizing the methods and results of lab procedures
Must make results secure (i.e. only seen by permitted users) and sharable (i.e. can be seen by selected users), i.e. access control
Should be centrally stored/backed up
Should have timestamping or versions (i.e. tracking of modifications)
Should have rich editing tools (i.e. user friendly, no wiki markup)
Should be cross platform (must work on Windows at least, this is what we use)
Should allow the inclusion of rich data including images and spreadsheets
Prefer free / cheap / open source solutions, if only so we have hack on and extend them
Prefer data stored in open formats not binary
Prefer a large community and ongoing development
It turns out there’s a lot there. Deep investigation of these is hampered by several factors – time, availability of a demo, etc. – so this is perforce a superficial examination. See below for a summary. Bad stuff or showstoppers are highlighted in red, good-stuff or selling point in green, uncertain points in blue. (Blank squares – either the point was moot or I couldn’t find out enough to even guess.)
Some brief thoughts:
- Damn, do some companies make it hard for you to find out about their product. The most you can get is a bit of glossy brochure, without getting into a conversation with a salesperson.
- Similarly, some companies are very secretive about price. Make a request for a quote and you’ll be besieged by a salesteam wanting to “discuss” it with you. (“Discuss” here meaning “What’s the maximum you can afford? That’s the price!”)
- It’s not all bad – many of the web-based products provide a demo.
- Curiously, there’s a lot of activity in the industrial and chemistry worlds (presumably due to IP concerns) and less in biology.
- It’s disappointing to see so many open source projects having gone defunct. Still, running a complex OS project is a tough, unpaid job.
- Web-based seems the only way to go – for deployment, backup, uniformity of experience. Flashy, AJAX interfaces are still fairly rare for web-based ELNs. However, I convinced that a good UI is critical – if it’s hard to use, people won’t use it.
- There are some reports of people using iPads for lab entry. [looks at budget allocation] Good for them I guess.
So here’s where you come in:
- What’s your experience with ELNs, for bioinformatics or elsewhere?
- Are there any features or problems you can forsee?
- Any obvious candidates I’ve missed?
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About the AuthorOriginally a laboratory scientist, PM stumbled into the world of computational biology in the dark days when Perl, CGI and C++ were tools of choice. Since then, he has lived and worked in Australia, South Africa and the UK on topics ranging from macroevolution through phylogenetics to computational embryology. Currently he works for the Health Protection Agency (UK), chasing and tracing pathogens and their evolution.
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