Bio::Blogs #8
Editorial musings
Welcome to the eight edition of the bioinformatics blog journal Bio::Blogs. The archive from previous months can be found at bioblogs.wordpress.com. When this carnival was started, more than eight months ago, it had the primary objective to serve as sort of display for some of the best bioinformatics blog posts on the web and to create incentives for other people to promote their blogs and join in the conversation.
Looking back at the past Bio::Blogs editions I would like to think that we have manage to come with with many interesting posts about bioinformatic conferences, tools and useful computational tips like the DNA analysis series by Sandra Porter (I,II,III,IV,V,VI). Bio::Blogs has also been use to promote tools that have been published in blogs like the Genetic Programming Applet from Pierre and research like the correlation between protein-interaction likelihood and protein age (I and II) that I worked on.
Not everything went as I would hope. The submissions to Bio::Blogs have not picked up as I would expect. Some of this can be explained by poor promotion of my part but it is also due to the small size of the bioinformatics blogging community. In any case I think it is worth maintaining Bio::Blogs up and running for some more time before thinking about stopping this experiment.
In this edition a PDF version of all the posts has been created for anyone interested in downloading, printing and reading some fine posts over coffee or tea. Leave comments or send an email (bioblogs at gmail.com) with your thoughts/ideas for the continuation of this blog journal.I think this printed version also gives a more concrete impression of the potential of blogging for scientific communication.
News and Views
GrrlScientist submitted a report on a recent Science paper describing how moths use their antennae to help them stabilize their flight. Apart from some nasty experiments were they authors removed and glued parts of the antenna the work features some interesting neurophysiology analysis used to characterize the sensitivity of the antennae.
From my blog I picked an entry on network reconstruction. I think the increasing amounts of omics data should be better explored than it currently is and network reconstruction methods are a very good way of achieving this. In this paper, Jason Ernst and colleagues used expression data to reconstruct dynamic transcription regulatory interactions. I will try to continue blogging about the topic in future posts.
Comentaries
PLoS ONE was launched about two months ago and it has produced so far an amazing stream of publications. However the initially proposed goal of generating discussions online to promote post-publication reviews as been lagging. Stew and Alf wrote two commentaries (summited by Greg) regarding the progress of PLoS ONE. They both discuss the current lack of infrastructures to stimulate the online discussions at the PLoS ONE site. Stew goes even further by providing to anyone interested a nice Gresemonkey script to add blog comments to the PLoS ONE papers. I hope Chris Surridge and the rest of the PLoS ONE team start deploying soon some of the tools that they have talked about in their blog. They need to make ONE feel like home, a place were a community of people can discuss their papers.
From Deepak we have a post dedicated to what he dubs EcoInformatics. The importance of using computational methods to analyze ecological changes from the molecules to the ecosystems. The problems range from data access to data management and analysis. The complexity and the different scales of organization (i.e. molecules, environment, ecosystems, disease) make this a very promising field for computational biologists.
From ecological changes we move on to human evolution. Phil tries to introduce the possibility of humanity using technology to improve itself. Having a strong interest myself in synthetic biology and man-machine interfaces I would say that we are still far away from having such control. It is nevertheless useful to discuss the implications of emerging technologies to better prepare for the possible changes.
Reviews and tips
I start this section with a post from a bran-new bioinformatics blog called Bioinformatics Zen. Michael Barton submitted his post on useful tips to get organized as a dry lab scientist. I agree with most of his suggestions. I have try to use slightly fancier methods of organizing my work using project managing tools but I end up returning to a more straightforward folder based approach as well.
Neil Saunders sent in a nice tutorial on building AJAX pages for bioinformatics. It is a very well explained introduction with annotated code. If you were ever interested in learning the basics of AJAX but never invested time in it, here is a good chance to try it.
Thursday, March 01, 2007
Posted by Pedro Beltrão at 7:39 PM
Labels: Bio::Blogs, carnivals
5 comments:
Hi Pedro,
I also share your point of view about the small size of the bioinformatics blogging community. When I started my own blog more than one year ago I imagined that It would be the scientific community the most aware of those tools (blogging, social bookmarking, social network...) but I was wrong. Most posts about bioinformatics are always written by the same people and social networks remain empty. But I'll continue to blog just to share my own interests and to keep a personal archive about tips and tricks about bioinformatics.
Yep
The life science blogosphere (and medical one) have grown a lot in the past year, but the bioinformatics/computational biology space has remained pretty static. Like Pierre, I expected the bioinfomaticians in the world to be the most ready to take to blogging, etc.
I am going to keep at it. Who knows. Someday the tide might change. Certainly if traffic is anything to go by, readership has gone up significantly.
I think that bioinformatics/computational biology is perhaps not as well-suited to blogging as other subjects. Most science blogs focus on interesting stories in the media, research or papers. A few science bloggers are essayists who write their posts like book or magazine articles.
Bioinformatics is really just a collection of computational methods. I might blog about Perl in the service of bioinformatics, but I could just as well be blogging about Perl in the service of anything. Or even just Perl.
Perhaps blogging is also not a characteristic of the working style or personality of many bioinformaticians. When we write code we aim for conciseness and efficiency - achieve the most with as few lines as possible. It's not really something about which you'd write an essay.
I view my blog in the same way as Pierre - an online archive of biohacks, useful primarily for me and available for others if they're interested.
So where next? Maybe readers respond better to a single, centralised information portal: "if you want bioinformatics knowledge, this is where you go". I guess postgenomic aims to do that, but it seems to miss a lot of sources (such as <cough> my blog). Nodalpoint aimed to be a portal in its early days. Perhaps the next incarnation of that site will feature some new tools for aggregating information.
I think there's still a place for our blogs - just not a very big place.
We worry more about impact and relevance that need be - many of the small notes that you've left out there are helpful in their own right. Any such posts might reach a handful of people only but this community is an interesting addition that would be difficult to create with any other medium.
Don't waste your time promoting, continue to write good posts - people who are interested in blogging and bioinformatics will find the community quickly anyway but only stay when there's something useful.
Roland Krause: I know a lot of people that still can't find any interest in blogging. Most people end up saying that the few interesting things in blogs are buried under a lot of other garbage. I can't blame them , it is true. I think that there is still a barrier to finding the community of people that share your interests in the blogosphere. It is a very dynamic and loosely connected social network. The hope was that something like bioblogs could serve as an introduction to the bioinformatic blogging community. Maybe you are right, if there is an interest people will join in. Also, maybe a site like Nodalpoint does this already better than bioblogs could ever do. One possibility would be just to move bio::blogs to Nodalpoint on a more permanent basis and let it be more like a monthly roundup of the other blogs.
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