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Science

Lively discussion: how to cross-validate?

So today’s group meeting got a bit heated as Nafiz, Ashley, and Xiao touched on the finer points of how to cross validate. Machine learning people, your comments are welcome.  

How much do cows offset wind energy savings?

So I saw this Tweet from Michael Eisen a couple of days ago:   and those cows are destroying whatever gains clean energy creates https://t.co/DWRFj5x8Jj — Michael Eisen (@mbeisen) September 3, 2016   This was in reference to a Slate article by Dan Gross about how Iowa is leading the US  in renewable energy, specifically […]

NIH scaling back on model organism database funding: what you can do

TL;DR: NIH are scaling back funding on model organism databases, which will degrade annotation quality.  This can have far-reaching implications in many aspects of biology and computational biology. There’s a letter you can sign electronically, please do.  <http://www.genetics-gsa.org/MODsupport> I am hoping to write a more detailed post on why this is important, but for the […]

PLoS-1 published a “creationist” paper: some thoughts on what followed

As everyone knows by now, PloS-1 published what seemed to be a creationist paper. While references to the ‘Creator’ were few, the wording of the paper strongly supported intelligent design in human hand development. A later statement from the first author seemed to eschew actual creationism, but maintained teleological (if not theological) view of evolution, […]

Predicting protein function: what’s new?

(New: the paper was recently published in Genome Biology!) Long time readers of this blog (hi mom!) know that I am working with many other people in an effort called CAFA: the Critical Assessment of protein Function Annotation. This is a challenge that many research groups participate in, and its goal is to determine how […]

Family genetics in Star Wars (Warning: Episode VII spoilers)

So I saw Star Wars VII: “The Force Awakens” the other day. Great movie, which has mostly erased the shame of episodes I-III. Despite even more than the usual suspension of science, it’s a great SF flick. (Major spoilers below! You have been warned!) One mystery which will hopefully be resolved in the upcoming episodes […]

The Dark Matter Metaphor in Biology

Dark matter is a proposed kind of matter that cannot be seen, but that we believe accounts for most of the mass in the universe.  Its existence, mass, and properties  are inferred from its gravitational effects on visible matter. The most favored hypothesis is that dark matter is not  composed of baryons, the basic components […]

On cross-disciplinary ambiguity and conference comfort zones

I recently attended a conference which was unusual for me as most of the speakers come from a computer science culture, rather than a biology one. Somewhat outside my comfort zone. The science that was discussed was quite different from the more biological bioinformatics meetings: the reason being the motivation of the scientists, and what […]

I’m Moving and Hiring

Starting June 1, 2015, my lab is moving to Iowa State University in Ames, Iowa, and I’m very excited about this. I’ll be joining a growing cohort of researchers as part of a presidential “big data” hire the university has started a year ago. The research environment is superb, and there are some great bioinformaticians and genomics […]

Why scripting is not as simple as… scripting

If you haven’t read the transcript of Sean Eddy‘s recent talk “On High Throughput Sequencing for Neuroscience“, go ahead and read it. It’s full of many observations and insights into the relationships between computational and “wet” biology, and it is very well-written. I agree with many of his points, for example, that sequencing is not […]

A Simple Genome Annotator?

A question to genome annotators out there. I need a simple genome annotator for annotating bacteriophage genomes in an undergraduate course. Until now, we used DNAMaster but for various reasons  I would like to move away from that. Here’s what  I need for class: 1. Annotate a single assembled linear chromosome, about 50,000 bp, 80-120 genes, no […]

Friday bits and pieces: ebola, old software patches, microscopy and microbiomes

  Scammers are cashing in on the ebola scare. The news media is cashing in on the ebola scare. Politicians are cashing in on the ebola scare. Unfortunately, neither international healthcare nor biomedical research  are cashing in on the ebola scare.   I found the first software patch. Seems pretty robust.   Diet can influence certain autoimmune […]

Open Access: green vs. gold, and the culture of the disconnect

Four years ago I wrote about how Open Access would be adopted if it were convenient. Polls at the time showed that few scientists actively seek to publish OA, even though many support it. Reasons given, in no particular order: aiming for journals that were not OA and high publication fees. My conclusion was that researchers […]

Sequencing the frog that can save lives

TL; DR:  The genome sequence of the North American Wood Frog will tell us a lot about the genetic control of freezing and reanimating whole organisms. My friend and colleague, Dr. Andor Kiss is crowdfunding this project. If you would like to help, please go to experiment.com. You will get acknowledged by name in the paper. To […]

Work jargon scientists should have

Fakeference invitation: an email from Nancy, Sally or June, inviting you, for the second time (“perhaps you didn’t get my first invitation, there may be something wrong with my email”) to speak at a conference. The meeting has  5-10 Nobel laureates listed as invited speakers, and covers everything in science, from quantum mechanics to fish breeding. […]