Edge wander

In class today, we talked about the first Assemblethon paper. A student asked about the term “edge wander”, which comes from a paper by Ian Holmes and Richard Durbin. Figure 6 from the paper illustrates the basic idea. Edge wander is a problem in multiple sequence alignments, and often scientists manually adjust alignments based on […]

More JSmol2wp testing

As of version 0.7, I wonder whether having two posts with viewers causes applet name clashes. The prediction is that this would work while viewing one post, but not on the home page. This prediction turned out to be true. This first item loaded the first one from the next post, while the first item […]

Testing JSmol2wp

[jsmol pdb=’1LMB’ caption=’lambda repressor headpiece’ debug = ‘false’ wrap = ‘5’ commands = ‘arm = select 1-6:3, 1-6:4; color yellow;||| helix-turn-helix = select 33-52:3, 33-52:4; color yellow; hide hoh;||| helix 5 = select *:3,*:4; spacefill off; cartoon; select 84,87; color yellow; spacefill on; select *; hide hoh; hide *:1,*:2; #moveto 2 0 1 0 0 0 […]

What do Americans and Finns know about Ammonia?

Via Jon Eisen on twitter, Hal Levin at MicroBEnet has gotten himself into trouble with this post (now deleted as not reflecting the views of MicroBEnet). The part that annoyed readers (including me, after seeing the tweet calling it out). On May 8th, CNN reported on “Top 20 most polluted cities in the world.” An esteemed colleague […]

Who gets NIH grants and is it a problem?

Drugmonkey posts a graph from Grantome.org showing distribution of grants by institution. A series of follow-up posts at Grantome includes one that looks beyond the top 50 institutions and concludes: The NIH website reports that more than 80% of its budget goes to over 2,500 universities and research institutions. Yet for the R01 – which is arguably […]

Do architects get what we do in the lab?

This post is what I wrote in February of 2009 on the old blog. I was prompted to dig this post up by Virginia Postrel tweeting about this article in Slate. I pulled the text from a database dump of the old blog. The images are old too, but were not in the original post (found them in my […]

Human subjects and education research

At Retraction Watch, there’s a story of a paper about ethics training retracted due to IRB human subjects protocol problems. We tend to think of human subjects research as involving things like drug trials, but a lot of it is things like this: This was an IRB-approved paper-pencil study investigating how certain features of ethics […]

Genomes and phenomes

Via Jonathan Eisen, NSF is using a wiki to get input on genomes and phenomes BIO seeks community input on Genomes-Phenomes research frontiersJohn Wingfield, Assistant Director of the National Science Foundation Directorate for Biological Sciences (BIO), is pleased to announce the posting of a Wiki to seek community input on the grand challenge of understanding the […]

Open source communities are different

Via Althouse, Farhad Manjoo argues in the NYT that Brendan Eich had to resign because: Mozilla is not a normal company. It is an activist organization. Mozilla’s primary mission isn’t to make money but to spread open-source code across the globe in the eventual hope of promoting “the development of the Internet as a public resource.” As […]