Comments on: My open science notebook http://www.bioinformaticszen.com/2007/09/my-open-science-notebook/ Sun, 07 Sep 2008 02:40:37 +0000 http://wordpress.org/?v=2.6 By: Mike http://www.bioinformaticszen.com/2007/09/my-open-science-notebook/#comment-2833 Mike Wed, 19 Sep 2007 16:56:21 +0000 http://www.bioinformaticszen.com/2007/09/my-open-science-notebook/#comment-2833 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. 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.

]]> By: Constructive Medicine » Blog Archive » Medicine 2.0 Blog Carnival http://www.bioinformaticszen.com/2007/09/my-open-science-notebook/#comment-2786 Constructive Medicine » Blog Archive » Medicine 2.0 Blog Carnival Sun, 16 Sep 2007 10:03:56 +0000 http://www.bioinformaticszen.com/2007/09/my-open-science-notebook/#comment-2786 [...] Bioinformatics Zen writes about open science notebook movement at My open science note book [...] [...] Bioinformatics Zen writes about open science notebook movement at My open science note book [...]

]]> By: Pedro Beltrao http://www.bioinformaticszen.com/2007/09/my-open-science-notebook/#comment-2756 Pedro Beltrao Fri, 14 Sep 2007 21:41:38 +0000 http://www.bioinformaticszen.com/2007/09/my-open-science-notebook/#comment-2756 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 :). 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 :).

]]> By: Pedro Beltrao http://www.bioinformaticszen.com/2007/09/my-open-science-notebook/#comment-2755 Pedro Beltrao Fri, 14 Sep 2007 21:40:30 +0000 http://www.bioinformaticszen.com/2007/09/my-open-science-notebook/#comment-2755 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. 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.

]]> By: chkuo http://www.bioinformaticszen.com/2007/09/my-open-science-notebook/#comment-2726 chkuo Wed, 12 Sep 2007 17:55:18 +0000 http://www.bioinformaticszen.com/2007/09/my-open-science-notebook/#comment-2726 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. 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.

]]> By: Jean-Claude Bradley http://www.bioinformaticszen.com/2007/09/my-open-science-notebook/#comment-2705 Jean-Claude Bradley Tue, 11 Sep 2007 13:46:05 +0000 http://www.bioinformaticszen.com/2007/09/my-open-science-notebook/#comment-2705 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). 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).

]]> By: Giovanni http://www.bioinformaticszen.com/2007/09/my-open-science-notebook/#comment-2703 Giovanni Tue, 11 Sep 2007 11:50:37 +0000 http://www.bioinformaticszen.com/2007/09/my-open-science-notebook/#comment-2703 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. 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.

]]> By: Konrad Förstner http://www.bioinformaticszen.com/2007/09/my-open-science-notebook/#comment-2693 Konrad Förstner Mon, 10 Sep 2007 19:40:08 +0000 http://www.bioinformaticszen.com/2007/09/my-open-science-notebook/#comment-2693 Nice, maybe you can tell me how the open lab notebook was accepted by your boss and other colleague in your lab etc. Nice, maybe you can tell me how the open lab notebook was accepted by your boss and other colleague in your lab etc.

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