Jack Park

I’m collecting a bunch of links and notes here. Not too much else. While tracking Open Notebook Science, I’ve stumbled on a bunch of practitioners such as Michael Barton’s blog. I found that link by way of a discussion about Jon Udell blogging libraries and open notebook science. Somewhere in there, trust me things move quickly, I landed on a Nature Networks (cool stuff!) site where they are talking about collaboration.  Nature Networks is a provision of the Nature Magazine where you can pre-publish your work as a means of establishing dates and so forth.

From the Nature Networks site, there is a link talking about a pre-nup for collaborations, which leads to a Nature news item about a failed collaboration. More good stuff.

Then, there is the blog on Science in the Open, one of many blogs of the Open Wetware community. From what I can tell, the idea is to use a wiki with a lab notebook template for doing science in the open, and using a blog to advertise and discuss the research.

From this blog, we gather a couple of interesting quotes:

During the early stages of my project I found it quite useful to blog, as it helped me to clarify my results and ideas while the project was still taking shape. I tried to do this about once a week, on a Friday, and summarise my latest results. Having this record of results was also helpful to refer to when discussing my latest findings. When we were writing the manuscript I also found it useful to browse back through all the entries I had created and include any ideas I had forgotten about. However, as the project progressed blogging became less important, as I had already produced my main findings and was more focused on writing the manuscript.

As for sharing information I found that writing a summary blog my research takes rather a large amount of effort. Furthermore my  blog is the only gateway to my research, and results only become available when I make the time and effort write them up. This therefore doesn’t satisfy Jean Claude Bradley’s criteria of no insider knowledge, but rather could be described as being selectively open about my research. On the positive side a blog post is a concise summary that distills my most recent progress in a way I hope is easily accessible to a casual reader. Another interesting point is that posting all my results online meant they were indexed by Google, as you would expect, but this also lead to some strange occurrences when searching online for material. For example searching for “Akashi & Gojobori”, a paper I based my work on, brings up two links to my blog ahead of the original manuscript. I find this a bit embarrassing, and I wonder if the paper authors have also encountered this?

With less time to spend on blogging, I also tried to stream my research using Twitter, sending short messages automatically using a bash script every time I committed an SVN update. While this approach takes a lot less effort on my part, I think this is the opposite end of the spectrum to blogging, and spews out large amounts of obscure repository check in messages. Ultimately I think it is of little interest for even someone directly involved in the project.

In summary, open notebook science has not really had a large positive effect on my research. I think that this is mainly because using a blog alone is not an effective method of communicating scientific progress, because it requires substantial effort on my part to update, and second tracking the current state of the research can be difficult. However, I still believe that the principles of open notebook science can be beneficial to my research. In the next couple of months I’ll try some new methods to see what does work.

This entry was posted on Wednesday, May 7th, 2008 at 11:09 pm and is filed under Thesis Research. You can follow any responses to this entry through the RSS 2.0 feed. You can leave a response, or trackback from your own site.