Oh the horror

I just looked at Jim Watson’s genome I think. Thats not the scary part. What is shocking to me is how much work we have to do in order to make a user interface to human genomes that doesn’t make my head spin.

Sequencing is quickly becoming the easy the part. A freshly liberated ladder is of little help if I can’t figure out how to use it. We need more genomic cartographers.

The Genomic Cartographer:
1 part bioinformatician
1 part beautician
mix and serve

Update: This Genome Browser is looking promising.

University of Utah DNA Learning Center

The University of Utah deserves a huge amount of praise for a fantastic educational site about genetics.  Bright, lucid graphics.  Interactive features and multimedia (WOW!).   Well-written, lay-person friendly content.

The topics range from genetic basics, pharmacogenetics, to medical marijuana.  Check it out.

Making the Genome Usable

One can make a profession of figuring out how to make a piece of technology easy to use.  In the computing industry, we call this work "usability" or "human-computer interaction" or "interaction design".  Making the human genome easy to use is one of the challenges that lie ahead for the field of personal genomics. 

This is the first post on this blog with the tag "usability" and I’m using this occasion to celebrate what appears to be the first AJAX-driven genome browser, GBrowse (a prototype).  AJAX is a group of web technologies (named by the geeks at Adaptive Path) featured in many of the hot, new web applications like Google Maps. 

Will the genomics industry follow the example of the computing industry and have entire professions and degrees grow-up around making the human genome usable?

Ispecies Mash-up

Harbinger!  I-species is a mash-up of a variety of information sources…

Golden Eagle
Morel (Morchella esculenta)
Helicobacter Pylori
Toxoplasma gondii (see this post at The Loom)

Check it out!  See also the I-Species Blog

Hat tip Open Access News with this post…snip: “Once scientists see the value of freeing-up data, mashups will explode…”

Want more mash-ups?  Look no further

What consequence human health?

UPDATE: Sirna Therapeutics Animation of siRNA

I love biology animations.  Here is a cool one on RNA interference by Sirna Therapeutics (.mpg file).  (Compare with this flash animation also on RNA interference.) 

UPDATE: Upon looking at the Sirna animation on siRNA a second time, I noticed that the double-stranded RNA at the beginning is left-handed.  We could call it artistic license, but it is really just an error.  If it makes the artists feel any better, they are not the first to make this mistake.  There is in fact a rather long and glorified history of our collective handedness illiteracy as shown in the Left-Handed DNA Hall of Fame.  The hall of fame very well could have been called the Left-Handed RNA Hall of Fame because RNA, like DNA, is made of right-handed sugars.  Not to be misled, nature isn’t entirely right-handed, either.  In fact, nature is intriguingly uneven handed.

Two egregious handedness mistakes for an article on proteomics in a popular trade magazine inspired Chris Welch to pen a poem that would have inspired the muses themselves (with permission):

On your cover a very rare sight,
a helix that gave me a fright.
Did you forget that this spiral
called DNA is chiral,
and it normally twists to the right?
          –Chemical & Engineering News, Aug 14, 2000         

Exhibit: Art of Larry Gonick

The Bancroft Library at UC Berkeley has an online exhibit of original artwork from Cartoon Guide to Genetics (1991). 

(Thanks to The Eyes Have It for the pointer)

Web Design for Sciences: Digizyme

I must comment on my recent discovery of absolutely stunning work by Digizyme, a multimedia company focusing their efforts on the sciences.