My open science notebook
September 10th, 2007
I said, a month ago, that there would be an open science section for this month’s issue of Bio::Blogs. Unfortunately this wasn’t the case. There are a number of theories as to why this didn’t materialise, including global warming, the recent stock market panic, or the appointment of new British Prime Minister. However research has suggested that it was because I didn’t work on it; though the other reasons are linked to having had secondary effects.
I’m still very keen on the open notebook science movement: I think open collaboration will benefit everyone involved. So, when I should have been working on the Bio::Blogs special edition, I was instead tinkering with my small 80MB-of-RAM server, so that it could serve up two blogs without bursting into flame. Something rather tricky since just handling bioinformaticszen.com was becoming increasingly laboured. However after switching from apache to lighttpd with wp-cache, it’s now successfully running two blogs rather quickly.
“Two blogs?” I hear you cry. “Well that’s just self aggrandisement gone mad. What you write on one website is barely enough to keep me interested, let alone two.”
These are both valid points, though I am hurt to hear you say such things. In my defence the second blog is not about such trivialities as what cereal I ate for breakfast (I prefer toast), but rather my open science notebook. Anyone who is interested in reading about my research on how the atomic composition, or biosynthetic cost of a protein affects its expression can go to www.michaelbarton.me.uk. Even better (for me), they might be feeling generous enough to start a discussion in the comments.
What effect this shameless publicity will have, only time will tell, and I will be sure as to write here to let you know. As for the next Bio::Blogs special edition, I will try to work a little bit each week on it. How does before Christmas sound?
Creative Commons
The photo used in this post is taken from paulwatson on flickr and used under a creative commons licence.
September 10th, 2007 at 7:40 pm
Nice, maybe you can tell me how the open lab notebook was accepted by your boss and other colleague in your lab etc.
September 11th, 2007 at 11:50 am
No, this is a very interesting experiment you’re doing.
For my experience, usually lab-coworkers don’t collaborate very much in this kind of projects… but a blog can be very useful for yourself if you use it as a lab notebook.
For the Bio:Blogs special, don’t worry…. I think the real cause is the shrinking number of pirates since 1800 to today.
September 11th, 2007 at 1:46 pm
It is great that you are making your progress available like this!
Do you have any plans to host your actual laboratory notebook online with links to all raw data? If not, I wonder if you could post a sample page - I am curious if my assumptions about how researchers in different fields keep their daily notebooks (or if they even have lab notebooks like we do in synthetic organic chemistry).
September 12th, 2007 at 5:55 pm
The open notebook sounds like a very interesting idea. Like Konrad asked, I’m interested in knowing what does your boss think about this.
On a side note, if maintaining a server is an issue, why not use some hosted services such as blogger.com? Several science blogs that I read (e.g., The Tree of Life by Jonathan Eisen) are hosted there.
September 14th, 2007 at 9:40 pm
I am also curious to know how you approached your boss about this since I hope to do the same when I move to my next lab next year. I actually have a mini project in mind right now that I never discussed with my current supervisor, I might just kick it off on the blog too.
September 14th, 2007 at 9:41 pm
p.s - We don’t have a host for the next edition of Bio::Blogs (1st of October) anyone reading this wishing to host send an email to bioblogs(at)gmail.com :).
September 16th, 2007 at 10:03 am
[...] Bioinformatics Zen writes about open science notebook movement at My open science note book [...]
September 19th, 2007 at 4:56 pm
Sorry about the late reply to these comments, they are always welcome, I’m going on Holiday next week and I’ve been trying to get everything wrapped up before I go.
@Jean-Claude
I will put any data that is completely mine on the web, I am happy with this. However the data I am using has been generated by other people, so it’s not my place to make it available unfortunately.
I’m using my blog and google docs at the moment, but I think in future I will switch from google doc to a wiki, as it will be easier for people to contribute. I used google docs as it was easy to get started straight away.
@Konrad, Chuko, Pedro
You all asked the same question, but I don’t really have a definitive answer. There was never one point when I asked my boss “Can I all put all my data on the web?”. I’d always been experimenting with blogs and wikis since the start of my PhD, all of them internal. I had most recently been using a wiki, but other people couldn’t see it because it was on my computer.
I already had a server which I was running bioinformatics zen on, so I just created a second blog and started putting data on it, because it was external it meant everyone could see it - without have having to be on the university network.
I’ve had this blog for a while but didn’t really make noise about it, but then I got responses back from the journals who were all mostly pro open science, so I thought why not try and funnel some of the traffic from bioinformatics zen towards it to see I get any useful contributions? I had become some what disillusioned with science too, so I thought why not take a risk?
I think my supervisors know that anyone can read the posts, and I’m hoping the generous contributions of people towards my research will make the benefits obvious.