nodalpoint.org

I'm not much of an evolutionary biologist, but Jonathan Eisen asked for help and I can't resist. So, in the name of Science, and via the goodness of nodalpoint, here is some deserved Google Juice for various Trees of Life on the Web.

• Jonathan Eisen's "Tree of Life" blog
• Tree of Life Web Project
• Tree of life (science) - Wikipedia, the free encyclopedia
• Green Tree of Life at Berkeley
• Fungal Tree of Life Project
• Beetle Tree of Life project
• Fly Tree of Life project
• Mammal Tree of Life project
• Cypriniformes Tree of Life project
• Liverwort Tree of Life Project
• Early Bird Tree of Life project
• Angiosperm Tree of Life project
• Cnidaria Tree of Life Project
• Decapoda Tree of Life Project

There, I've done my bit for Science, now it's your turn. Spread the ❤ link love ❤,and since we will soon be celebrating the 200th anniversary of the birth of Charles Darwin, why not marvel at the coral / shrub / lungs of life too?

(CC-licensed Tree of Life picture by Phitar)

Steven Salzberg has an opinion piece in Genome Biology that talks about Wikis for managing genome annotation and the problem of bit rot in gene annotation (would that be annotation rot?).

I wrote a quick post about it. This harkens to the other gene wiki discussions on nodalpoint as well as some of the things Ian Holmes and his group are thinking about on the GbrowseAJAX mailing list.

Way back in Nodalpoint history (probably about a year ago), we had "paper of the month" posts. They were rarely monthly and often involved more than one paper, but I always thought that it was a nice idea. So here's a few that caught my eye this month.

Can someone explain to me how Katoh and Katoh get so many papers published? have a look at these pubmed search results.

By the way, is there any link on the web with the authors that occur most often in pubmed? There's no Pubmedbattle yet? (Well you could googlebattle it out but that's not very scientific). (As for Eric s. lander, he seems to be at 237 papers today).

Bioinformatics Resource and Solution for Science Students

(http://www.bisa.in)

Being a student of biological science, it happens so many times that a simple bioinformatics analysis takes too long or errant results haunt you. You may be or may not be familiar with computers and bioinformatics as the concept is not so clear to your mind. But in today’s ever growing research one needs to be familiar with all the aspects of biological sciences and BIOINFORMATICS is a profound candidate.BISA (http://www.bisa.in)offers number of resources and services for free.

BISA offers

Congratulations on an exciting new site, it looks like it's beginning to really shape up!

I figured maybe I can liven it up a bit with a small (beta) debut here. Maybe you'd like to have a look at my new (totally rewritten) software for bioinformatics analysis; it supports analyzing almost every type of file through some advanced information theory techniques. Try it and see, it's easy to use:

complearn.org

As promised, it's April 1st and here's my publication pick. Published in February, so not exactly paper of the month, but not to worry. "Serendipitous discovery of Wolbachia genomes in multiple Drosophila species" by Salzberg et al. is in the open access journal Genome Biology, abstract here and full access here. Hit "read more" for the details.

This is for those who are interested in plotting microbial genomes in circular plots. You can easily plot classification-type data or numerical data (microarrays, proteomics or other computational data) in the program GenomeViz. Here is the manuscript. GenomeViz is free for academic users. Any comments are most welcome.

Confused? Well, there was the "first draft genome" (2000), then there was the "almost finished genome" (2003) and now they are filling in the gaps. It's all explained admirably here.

When I gave one of my first talks at my current workplace on Perl, BLAST and genomic analysis, a nameless audience member asked me a question I have never forgotten. "It strikes me that what you're doing is rather desperate", she said, "wouldn't you be better off doing some experiments?"

At the time, I was rendered almost speechless (there is no polite way to answer such a question), but I've since learned that many biologists (at least at my current workplace...) are not aware of the paradigm shift brought about by computational biology. Namely, rather than stumble about choosing research topics and experiments almost at random, you can make intelligent use of information (i.e. process it computationally) and use that as a way to direct and focus your research.

The folks at the UGA CSB Lab seem to understand that, so next time you're faced with such a question, direct your questioner to something like this Powerpoint (sorry) slide.