Comments on: Filling in the evolutionary blanks, genome by genome

By: Jonathan Eisen

Jonathan Eisen — Thu, 24 Dec 2009 16:13:39 +0000

Morgan -you can’t be as biased as I am and I just posted a “research blogging” article about this paper too … still figuring out research blogging’s system though so not sure it is working right

By: Morgan Langille

Morgan Langille — Thu, 24 Dec 2009 01:51:32 +0000

I was going to test out my new research blogging account by reviewing this paper. Oh well, I guess some may think I am a little biased being in his lab.

Nice review, and I think there is still lots of improvements to me made for viewing and analyzing comparative genomic projects.

By: Iddo

Iddo — Thu, 24 Dec 2009 00:50:14 +0000

The numerical gotcha is the least suckiest antispam mechanism I could find. All the graphical captchas take time to load, which makes commenting a drag…

By: Iddo

Iddo — Thu, 24 Dec 2009 00:07:46 +0000

IMG does have some annotation browser. Linking to that seems easy. Granted (pun intended), making a more sophisticated tree-able browser is somewhat non-trivial…

By: Jonathan Eisen

Jonathan Eisen — Thu, 24 Dec 2009 00:03:04 +0000

Well, the genome space browser is a great idea — but would be some work — I will suggest it to IMG people and to others — might make a good grant proposal —

I note, the numerical gotcha thing has issues when I click “back” after I forget to type it in once …

By: Iddo

Iddo — Wed, 23 Dec 2009 23:32:00 +0000

Thanks Jonathan. Both kinda lead to the same place. The GenBank (and Biotorrents) presence is well noted. But since GEBA is all about exploring genome space, I was half-expecting a clickable version of that tree you have in Figure 1, + some comparative genome browsing? JGI has the infrastructure for that with the IMG.

By: Jonathan Eisen

Jonathan Eisen — Wed, 23 Dec 2009 23:25:31 +0000

Also – the better GEBA site is http://img.jgi.doe.gov/cgi-bin/geba/main.cgi

Try that and you should find the genomes (I hope …)

By: Jonathan Eisen

Jonathan Eisen — Wed, 23 Dec 2009 23:18:29 +0000

Working on the JGI-GEBA pages – not sure why it is password protected from where you went. But I note, the data is all in Genbank. And it is also all in Biotorrents at http://www.biotorrents.net/details.php?id=38.