sporte | August 20, 2007I'll continue with the remaining parts of my career series shortly, but for the time being, I want to bring your attention to a really good post on doing bioinformatics as a software professional, and some commentary on the question that never seems to go away: "do biologists need to be able to program?"
Thanks to GenomeWeb.
tags: biotechnology careers, biotechnology, career+descriptions,bioinformatics
From Paolo Nuin, we have a great interview with Dr. Alexei Drummond, author of BEAST, about his experience moving from academic biology to professional software development.
Many of…
sporte | August 17, 2007One time I was watching a football game on TV and they had a short quiz, called "You make the call" or something like that, and you had to watch a play and pretend to be a referee. A short video clip showed football players falling over each other. Then you were three possible calls that a refereee might make and asked to chose which was correct. After the commercial, the announcer would tell you which choice was right and explain why it was correct. I suppose this was a trick to make us watch the commercials, but I thought the game was kind of fun.
My SciBling "Mike the Mad" had a great…
sporte | August 16, 2007Thanks to Steven Colbert you can hear about DNA directly from Dr. Spencer Wells from the National Genographic Project.
I read about this video in the GenomeWeb Daily Scan and had to check it out.
Who would have thought scientists could be so funny?
Watch it quick! There was a note at the Comedy Central site saying the video expires on Sept. 15th 2007.
or you can go here and find out whether DNA could happen to you, too!
sporte | August 15, 2007Sometimes asking a question can be a mistake.
Especially when your question leads to more questions and having to question things that you didn't want to question, and pretty soon you begin to regret ever opening the file and looking at the data and asking the question in the first place.
Sigh. Take a deep breath.
Yesterday through a twist of fate, I ended up taking a look at the DNA sequences produced by two different base calling programs from the same chromatogram file, from an ABI 3730 DNA sequencing instrument. I thought they would be the same, or at least similar.
tags: DNA…
sporte | August 15, 2007Yes, you can!
Really, I thought this was going to be more challenging, but the nice folks at the NCBI have made a special personal genomics FTP site. You can also get Craig Venter's genome, and maybe even do some comparative genomics and see if one has a few deletions. After all, don't you want you find out who's is bigger?
Oh, I can tell this is going to be fun!
Get the traces at ftp://ftp.ncbi.nih.gov/pub/TraceDB/Personal_Genomics
sporte | August 14, 2007What do you do when base-callers disagree?
Okay DNA sequencing community, I want your help with this one. One of these sequences was called by phred and the other by the ABI KB base calling program.
Which one should I believe?
tags: DNA sequencing, DNA , base-calling programs
Sometimes I open up files and do short experiments just because - well, I'm curious. And sometimes I immediately wish I hadn't done that because what I opened looks like a larger can of worms than I really want to see.
These graphs show the quality of each base, in a DNA sequence, on the y axis and the position of…
sporte | August 10, 2007Here's a lovely DNA structure from our friend, human immunodeficiency virus I. I especially like the way that two heart-like shapes appear in the structure.
tags: DNA structure, DNA , molecular structure, biochemistry
Is nature ironic or what?
sporte | August 9, 2007I found that one of the most challenging things in moving from an academic institution to a software company was getting used to the difference between software engineers and biologists.
Now at last, we biologists can start to understand the mysterious ways of software engineers with this helpful reference from Silicon Glen.
Although, maybe we biologists do have something in common with the software engineers after all. I agree about on the talking frog. It would be pretty cool!
sporte | August 8, 2007Biologist 1: How many physicists does it take to write a research paper?
Biologist 2 (looks at the citation above): "all of them?"
I wrote about the challenges that biologists and computer scientists have in deciding who's on first. But after finding some physics papers in PubMed by mistake, I've decided that it must be much harder for the physicists.
How do the physicists decide which author goes where?
Do they all have to write out their individual contributions?
sporte | August 8, 2007Some maggots have gotten good press lately because of their helpful ability to clean out wounds by consuming dead tissue. Screwworms however; also known as Cochliomyia hominivorax, will never be welcomed in an operating room or anywhere else.
USDA Agricultural Research Service
These are the creatures of nightmares. During part of their lives, they live and travel as flies, and lay their eggs in the wounds of warm-blooded animals. When the eggs hatch, the screwworm maggots feed on the living flesh of the infested animals.
Fortunately, we've learned how to control the screwworm and we…
sporte | August 6, 2007In this, and the next post in this series, I want to answer some of the questions that came up in the comments.
One of the commenters on part II wrote that:
For most academic biology groups, however, being a bioinformatics specialist is a dead end job! People in these roles may or may not be PhDs, but they end up in fouth author hell - always the fourth author on hundreds of papers - which cuts no ice when it comes to institutional promotion boards.
Of course, he didn't ask for my opinion about this, but I'll share it anyway. And I want to hear from you.
Do you think this is a fair…
sporte | August 5, 2007
It could be geosmin.
We encountered geosmin once before in our butter but most people notice it, about this time of year, in their tap water.
Geosmin is a volatile compound that's made by soil bacteria like Streptomyces, as well as some plants like sugar beets, and cyanobacteria. It gets blamed quite often for making water taste like dirt. Only a small amount is required (10 nanograms per liter) for detection by the human palate (1) and it's been blamed for adding a "dirt-like" taste to many things like water, wine, apple-juice, and catfish.
So, late in the summer when everyone is…
sporte | August 3, 2007
Many medical conditions today are treated but never cured. Imagine, a child with a genetic disease like juvenile diabetes or hemophilia. This child will be taking expensive medications for their entire lives. In the case of some diseases the cost of the medications might be more than child or their parents can ever hope to earn in their lifetimes, much less spend on a life-saving drug.
This is one of the many reasons why people have placed such great hopes in gene therapy. If a disease results from a defective gene, and we could replace it or supplement it with a functional gene, perhaps we…
sporte | August 3, 2007Last Friday, we had another in the series of weird DNA structures. (You can see the first here).
I asked the audience to identify the unusual feature in this molecule. Here's the first picture:
tags: DNA structure, DNA , molecular structure, biochemistry
Here's the answer:
Steve L. guessed it correctly. This is not just DNA, it's a DNA:RNA hybrid. I circled a 2' hydroxyl group here to make it easier to see the difference. (Remember - the "D" in DNA stands for "deoxy.") The oxygens are red and it's easiest to tell the difference between the strands if you count them.
For extra credit -…
sporte | August 2, 2007What do malaria, sleeping sickness, yellow fever, and dengue virus have in common? Sure, they're all tropical diseases, but there's something else.
All of these diseases have some kind of insect vector.
image from the Public Health Library
tags: tropical disease, yellow fever, sleeping sickness, insect control,malaria
At one time, I thought it was merely a matter of an insect biting one organism and then transmitting the parasite to another organism because the parasite was stuck on the insect proboscis, or something like that, kind of like the way cold viruses might get transmitted…
sporte | August 1, 2007Drug Monkey has an interesting take on an article that I wrote the other day about publishing in biology.
I find it amusing that in some fields it's the most important to be first author and in others, it's the most important to be the last author, and sometimes we publish papers together in the same journals, and the people who read the article - gasp - probably never know!
Drug Monkey says we should let the reviewers decide on the authorship order.
I disagree, though. To paraphrase one of DM's commenters, the reviewers can't know who did what.
And, sometimes researchers don't…
sporte | July 31, 2007I don't usually blog about work for wide variety of reasons. But, last week, since I wanted to write about bioinformatics software companies, I broke with tradition and wrote about Geospiza as an example.
Naturally, I got some feedback about this. Some people liked it, but one of the most opinionated people said that I had given the software engineering and IT side short shrift and that I should write about that side a bit more.
Today, is my attempt at a remedy.
tags: biotechnology careers, biotechnology, career+descriptions,bioinformatics
The tip of the iceberg
This diagram was…
sporte | July 30, 2007Amateur astronomers unite! The pros want your help!
image from Astronomy Picture of the Day, Credit: NASA, ESA, A. Aloisi (STScI / ESA), Hubble Heritage (STScI / AURA) - ESA/Hubble Collaboration
I learned about this from the Washington Science Teachers Assocation.
Galaxy Zoo and the Sloan Digital Sky Survey are looking for your help in sorting out different galaxies. It's a cool opportunity for anyone to go where few non-astronomers have gone before and help do real science at the same time.
What does this involve?
Go to the Galaxy Zoo, peruse their tutorial, and learn how to pick…
sporte | July 30, 2007If you're in Seattle this week, and you're not going to the zoo concert on Wednesday night, you might enjoy this lecture series from the UW Genome Sciences department.
We missed the first two talks because of travel, but our college-age daughter and her friend persuaded us to go last Weds. and hear Debbie Nickerson talk about genetics and drugs.
Usually these sorts of talks are held during the school year and they're packed with high school students who're getting extra credit for attending and taking notes. This time it was different.
We looked around the room when we arrived, of course…
sporte | July 28, 2007In academic biology, scientific publications are a serious thing. People battle over positions in the author list and debate endlessly over who should be on the paper and who should not.
The funny thing is that sometimes we think that our rules and standards apply to other fields of science and assume that our conventions are, well, conventional.
If they're true for us, they must be true everywhere, right?
I was surprised, for example, when I learned that one of our (former) programmers didn't know there was a difference between peer-reviewed publications and the white papers that…