Sandra Porter
sporte
Posts by this author
August 14, 2007
What 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…
August 10, 2007
Here'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?
August 9, 2007
I 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…
August 8, 2007
Biologist 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,…
August 8, 2007
Some 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…
August 6, 2007
In 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,…
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…
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…
August 3, 2007
Last 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…
August 2, 2007
What 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…
August 1, 2007
Drug 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…
July 31, 2007
I 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…
July 30, 2007
Amateur 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…
July 30, 2007
If 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…
July 28, 2007
In 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…
July 27, 2007
I've had some requests for some more molecular puzzles since the last one that I posted (see A DNA puzzle ). One person liked it so much he even blogged about it.
So, here's one for you to chew on over the weekend.
This puzzle is a variation of an activity in Exploring DNA Structure, a CD/lab…
July 25, 2007
Not content with his recent exploits in human experimentation and cavorting with Plosites in San Francisco, Professor Steve Steve jetted across the country once again, last week, hitting both both Blacksburg, VA and Seattle, WA, and creating pandemonium wherever he went.
And raising the question…
July 24, 2007
What do people do in bioinformatics software companies?
tags: biotechnology careers, biotechnology, career+descriptions,
bioinformatics
In our old conference room, in our last office, we used to have this little card on a stand, entitled "Sun's universe of stars." Over the years, we watched…
July 23, 2007
Last week I found a bug in the new NCBI BLAST interface.
Of course, I reported it to the NCBI help desk so it will probably get fixed sometime soon. But it occurred to me, especially after seeing people joke about whether computer science is really a science or not, that it might surprise people…
July 18, 2007
If you missed reading some of the comments on yesterday's post, I highly recommend that you go back and catch up.
I especially want you all to pay close attention to the comments from Deepak and Keith Robison. Like me, they work in industry and not in an ivory tower. Unlike me, they actually…
July 17, 2007
I had an enlightening experience recently, after I wrote some bioinformatics activities, under contract, for a community college. At the end of the project, the person at the college asked me if the activities were anything like the things that a "bioinformatics technician" would do on the job.…
July 16, 2007
BLAST is a collection of programs that are used to compare sequences (DNA, RNA, or protein) to larger collections of sequences that are stored in databases. I've used BLAST as a teaching tool for many years, partly because it's become a standard tool for biological work and partly because it's…
July 15, 2007
At the Seattle Art Museum's new sculpture garden, we can read all the signs.
The artworks are easily offended.
The unsanctioned baby eaglets have disappeared.
The grass won't grow without your help.
We pay attention to the grass.
July 15, 2007
Professor Steve Steve, recently accused of consorting with a certain Washington madam came clean today with an alibi that he claims, proves the allegations are nothing more than malicious lies.
Dr. Steve insists that he was at the Fred Hutchinson Cancer Research Center doing experiments with…
July 13, 2007
Although, I didn't believe it when I first saw it. With all the years that I've heard (or taught) that all DNA is antiparallel, it was hard to believe my eyes.
Yet here is parallel DNA, with both strands oriented in the same direction, right here on your monitor. And the commenters were correct.…
July 12, 2007
By now, many of you have probably seen the the new BLAST web interface at the NCBI. There are many good things that I can say about it, but there are a few others that caught me by surprise during my last couple of classes.
tags: blast, BLAST tutorial, science education
Because of these changes,…
July 11, 2007
What do people in biotechnology do on the job?
What can students do with a science degree once they've finished college? Some answers can be found at the "Life Sciences Central web site. Created by the Workforce Development Council of Seattle-King County, this is a wonderful resource for anyone…
July 10, 2007
Okay, all of you biochemists and molecular biology types. I have a puzzle for you that I found by accident during a lecture. Yes, I was the one lecturing and the notes will be posted soon.
In the meantime, here's your puzzle: What's unusual about this pair of bases?
tags: DNA structure, DNA ,…
July 9, 2007
It was only a couple of weeks ago but it seems like years. I had spent a month learning how to use most of the features on my shiny new phone and we were in Alaska using Google maps to find our way around Fairbanks.
My thumbs were getting sore, but so what? I could a give a slide show on my…
June 28, 2007
When we make primer sequences for an assay, two characteristics we're concerned with are the specificity of the primers and the sensitivity.
We can use blastn to evaluate whether or not our primers are likely to work.
Specificity: The specificity of a primer set is related to whether the primers…