transcriptfun

BlastViewer 2.3

Fri, 20 Mar 2009 21:54:48 -0700

BlastViewer 2.2

Mon, 22 Sep 2008 22:40:01 -0700

Jess - Thanks for the very interesting presentation on the microbial communities associated with...

Fri, 05 Sep 2008 11:48:06 -0700

Jess - Thanks for the very interesting presentation on the microbial communities associated with seagrass in Padilla Bay - an impressive amount of work!

Originally posted as a comment by Adelaide - back in seattle on gene|fish using Disqus.

"A seminar is, essentially, a group of people who come together to talk about a particular topic. If..."

Fri, 05 Sep 2008 10:03:50 -0700

“A seminar is, essentially, a group of people who come together to talk about a particular topic. If lecture classes tend to emphasize “coverage” through lectures and some reading, seminars tend to emphasize intense reading of books and articles or research into primary sources followed by a group discussion about what everyone is learning and what questions are arising.”

- Stephanie M. H. Camp
Department of History, University of Washington

Directions

Fri, 05 Sep 2008 09:33:36 -0700

Today I am pondering whether to go the route of Catalyst or make material more open. For the latter it would be some simple mix of Google Docs and tumblr.

Coffee and Donuts

Thu, 06 Dec 2007 09:03:19 -0800

Today we will meet in FSH 113 and as Kristi suggested refreshments will be provided. Though given how sickly everyone is, I decided it would be best if I brought in some orange juice. So it will be OJ and Donuts. Feel free to bring your own coffee.

The final week

Mon, 03 Dec 2007 12:02:35 -0800

It appears we will have some exciting presentations this Thursday. Looking forward to it. On Tuesday we will continue on with a review of sorts, building on your problem set answers. Class evaluations will also be filled out tomorrow in order to provide enough time Thursday for the presentations and audience questions.

I have a compiled a list of your suggestions from the last survey. We will discuss this tomorrow. Also your final quiz, survey, and problem set are available (though you will have to wait until Thursday to complete the problem set).

Beyond the Gene

Thu, 29 Nov 2007 08:23:32 -0800

Beyond the Gene:

A new, philosophical article in PLoS One by Evelyn Fox Keller and David Harel looks into the definition of a gene

Just made one of the last updates to the class website. All homolog pages are now accessible plus...

Thu, 29 Nov 2007 06:01:49 -0800

Just made one of the last updates to the class website. All homolog pages are now accessible plus hard links for quiz, survey, and today’s problem set.

Homolog pages look great. My kids really liked this one. If you interested in downloading the...

Tue, 27 Nov 2007 06:43:00 -0800

Homolog pages look great. My kids really liked this one.

If you interested in downloading the genomic_it scripts a compressed disk image file (7GB) is available. Today I will bring in some DVDs without NCBI databases (too big).

Today in class we will hear from Anne on a real world real time, and possibly from Colleen.

We will begin a quarter recap (to be finished next Tuesday) and time will be available near the end of class to work on your group projects.

A new quiz and new survey are available.

More homologs are rolling in over here, here, there, here, there, here, there, here, [current time:...

Wed, 21 Nov 2007 18:15:00 -0800

More homologs are rolling in over here, here, there, here, there, here, there, here, [current time: 7:14pm], there, here, there, and just barely here.[current time: 11:55pm]

via Bioinformatics Zen

Tue, 20 Nov 2007 10:21:19 -0800

via Bioinformatics Zen

GOLD: Genomes OnLine Database Homepage

Mon, 19 Nov 2007 14:07:43 -0800

GOLD: Genomes OnLine Database Homepage

Real-time lecture

Mon, 19 Nov 2007 14:01:58 -0800

For Tuesday lecture I do not plan on using the LCD so be sure to either download the slides or view online. It will primarily be a whiteboarding discussion.

That's one big table

Mon, 19 Nov 2007 13:04:25 -0800

In an effort to provide a real example of GO (talked about last week) I have uploaded a movie comparing NCBI Blast results and GO data on the Copepod ESTs. Basically, I tried to talk louder (I realize I say “basically” a lot). There is another quiz, quiz 8 for those of you keeping up. Tomorrow we will talk about real-time PCR.

23AndMe Will Decode Your DNA for $1,000. Welcome to the Age of Genomics

Sat, 17 Nov 2007 14:23:10 -0800

23AndMe Will Decode Your DNA for $1,000. Welcome to the Age of Genomics :

[WIRED Magazine]

Thursday's genomic_it shells are still going...

Fri, 16 Nov 2007 18:07:00 -0800

I know most of you have probably been refreshing your browser constantly to see what the next blast hit is. For those who are not, feel free to monitor the growth, repro, immune, and virulence groups’ respective blast on the unannotated EST database of choice.

First homolog available

Thu, 15 Nov 2007 10:55:00 -0800

First homolog available :

and more arriving, here,

Get ready for some command line

Thu, 15 Nov 2007 07:46:25 -0800

Please remember there is a quiz and survey waiting for most of you. Today’s problem set can also be found there. If your itching to listen to Tuesday’s discussion, check here. Recall your web project is due next week. And one final note.. I understand there is (was) a lot of information associated with this class, however in order to be proficient in bioinformatics, one of the primary skills is the ability to manage large amount of information generated on a regular basis. Hopefully you have aquired tools to assist you with this over the quarter. Based on the initial responses to the current survey we will likely take one period to do a big review.

Recent revisions regarding how the genome works [Yann Klimentidis' Weblog]

Wed, 14 Nov 2007 17:43:00 -0800

Recent revisions regarding how the genome works [Yann Klimentidis' Weblog]:

Via TAMU Anthropology in the News, I found this article from the Washington Post by David Brown called How Science is Rewriting the Book on Genes that gives an update on why things that were once thought to be rules in genetics are turning out not to be so cut and dry. Many of these are pretty well known.

A gene can code for many proteins, not just one, through alternative splicing

The regulation of genes might contribute more than previously thought to evolutionary change than the…