Publish your GreaseMonkey scripts
I knew it was possible to use GreaseMonkey scripts to change webpages to better suit our needs. I tried it once to get blog comments about scientific papers to show up in journal websites. Pierre and Stew have been creating several interesting scripts for postgenomic and connotea. What I did not know was that one could actually publish these scripts. I am all for publishing of smaller and finner grained scientific content but I have to say that this paper seemed like little more than a big blog post. Should we try to publish this type of work ?
Anyway :) ho ho ho , merry xmas everyone
Monday, December 25, 2006
Posted by Pedro Beltrão at 1:14 AM
9 comments:
I talked about this paper in the context of mashups recently, but I do agree that a blog or similar resource would have been the best place for it, otherwise Pierre can publish quite a few papers.
Should we try to publish this type of work ?
Yes -- on our blogs! This is exactly the sort of thing for which blogs (or experiment-wikis like Jean-Claude Bradeley's) are perfect.
(the link to deepak's post that I missed :)
One argument to try to publish this type of work on a journal would be to increase the awareness to these tools.
It would be nice to find new ways to reach the non tech crowd
Pedro,
That's the part that I try and figure out all the time. It's a tougher process than one might think. I think of the various people I have tried to introduce to all these tools, about 5% have picked up on them immediately, while another 2-3% grow into them. The rest just think I am a geek and all this will pass. The place to get people to start using blogs, wikis, etc is college (Insert Jean-Claude Bradley reference here) or even high school.
Another point ... in addition to promoting these tools as means to improve transparency and data access, perhaps we should also point out that they are also wonderful productivity tools
Just wanted to chime in on the "should we publish this kind of work" question (since I went ahead and published this one). The problem with blogs for publishing this sort of thing is that they often do not seem to reach the needed audience. The people that read geek-oriented blogs, such as Pierre Lindenbaum's, do not need to be informed about the existence and implications of technology like this, they usually already know. I think the main value of publishing this sort of work in a journal is that non-tech-geek scientists (such as most of those who make decisions about funding) will actually stand a chance of reading about it and becoming interested. That being said, comments from reviewers (who I assume are expert practicing bioinformaticians AKA geeks) indicated that most didn't know much, if anything, about GreaseMonkey etc. before reading the article.
p.s. I think it would be great if Pierre published more papers describing his exploits :)..
The other thing, of course, is that its still much more beneficial for an academic career to publish in journals than in blogs.
Thanks Benjamin for finding this blog and responding :). I agree with both your points. I argued as well that it could be worth publishing this tool to raise awareness. I guess I should not try to evaluate the effort you put into building this tool.
What I think what I was trying to discuss, in a more abstract way, was what constitutes a paper and what should be published in less formal and faster communication medium. What would be ideal was if scientists gave credit and paid attention to other forms of scientific communication (like blogs).
I don't think that the negative comments about the iHOPerator article are warranted.
I handled the peer review of that manuscript and three of the four reviewers thought that it was really interesting and important, with only one dissented on grounds of interest. I liked the article so much that I included it as one of our Research Highlights.
I think the point to recognise is that this sort of thing is still new to the average bioinformatician (I could find previous mentions of Greasemonkey only in such places as Linux Journal, but not in the biomedical literature) and if the publication gets Greasemonkey, Web 2.0 and the "semantic web" more attention, then that's great!
There's been a good deal interest in the article from the readers of BMC Bioinformatics, so I think we were well justified in publishing it.
Wow. That started quite the discussion.
At one level we are all on the same page. On another level on a different one.
Given the current environment where publication in a journal carries that extra weight and the fact that blogs, etc are not in the mainstream, I agree with Matt that publishing in a journal like BMC Bioinformatics is probably one of the few options people have available, and perhaps, this will get people more interested in cool applications like Greasemonkey.
On the flip side, it would be better if we started moving towards a world where greasemonkey scripts and various mashups could be spread virally via the web. In tech, one can build his/her cache like that, but not in science. Not yet anyway.
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