bioinformatics
sporte | October 23, 2007It's hard to teach bioinformatics when schools work so hard to keep us from using computers.
Anecdotes from the past
Back in my days as a full-time instructor, I fought many battles with our IT department. Like many colleges, we had a few centralized computer labs, tightly controlled by IT (aka the IT nazis), where students were supposed to go to do their computing. Instructors also had a centralized computer lab, but over the years, we gained the right to have computers in our offices. Our major battle was whether or not we'd be allowed to use Macs.
There are certainly advantages in…
sporte | October 21, 2007Welcome Bio256 students!
This quarter, we're going to do some very cool things. We are going to use bioinformatics resources and tools to investigate some biological questions. My goal, is for you to remember that these resources exist and hopefully, be able to use them when you're out working in the biotech world. I don't believe that bioinformatics is a subject that you can really grasp without getting your fingers dirty. So, this course will include a lot of hands-on work.
My friend and collaborator at Johns Hopkins University has given me data sets from the past three years and we…
sporte | October 16, 2007A few weeks ago, I did some "back-of-the-envelope" calculations to explain to a reader why genome sequencing costs so much.
I estimated that, if JCV's genome were sequenced at the cost advertised by university core laboratories, his genome would cost about $128 million.
That was an estimate, of course. But what did it really cost?
Genome Technology asked J. Craig himself. In the October 2007 issue of GT, JCV estimates that the cost from the first Celera human genome project (guess who?) was about $100 million and that the cost of his most recent genome project was at least $70 million.…
sporte | September 9, 2007If you haven't, then hustle over to Mendel's Garden for a wonderful story about the monk and his life as a scientist, check out Gene Genie for best drawing of Craig Venter that I've ever seen; and if you're into computers, take a good long look at the lightning edition of Bio::blogs. I've visited them all out myself and I assure you, they're all a good time and chock full of fun links.
sporte | September 7, 2007During the past few Fridays (or least here and here), we've been looking at a paper that was published from China with some Β-lactamase sequences that were supposedly from Streptococcus pneumoniae. The amazing thing about these particular sequences is that Β-lactamase has never been seen in S. pneumoniae before, making this a rather significant (and possibly scary) discovery.
If it's correct.
tags: DNA sequence analysis, antiobiotic resistance , microbiology, blastn
The way this sequence was identified as Β-lactamase was through a blastn search at the NCBI. And in fact, it was correct to…
mikethemadbiologist | September 5, 2007125 taxa. This analysis is never going to end (stupid GTR models):
I'm getting annoyed....
Update: It took five days to run this thing. And, yes, that was after using ModelTest.
By the way, if you have no idea what I'm talking about, here's a post (without technical jargon) on likelihood and phylogenetics to introduce you to the basics.
sporte | September 5, 2007If you've read any of the many stories lately about Craig Venter or Jim Watson's genome, you've probably seen a "SNP" appear somewhere. (If you haven't read any of the stories, CNN has one here, and my fellow bloggers have posted several here, here, here, here, here, and here.)
You may be wondering, and rightly so: just what is a SNP?
Never fear, hopefully this post will answer some of those questions.
tags: DNA sequencing, DNA , SNPs, genetic testing
SNP stands for Single Nucleotide Polymorphism. That's a mouthful. It means some people, will have one base at a certain position, in a…
sporte | September 4, 2007
"Come quickly, Watson," said Sherlock Holmes, "I've been asked to review a mysterious sequence, whose importance I'm only now beginning to comprehend."
The unidentified stranger handed Holmes a piece of paper inscribed with symbols and said it was a map of unparalleled value.
Holmes gazed thoughtfully at the map, then slowly lifted his eyes and coldly surveyed his subject's beaming countenance. "You have an affinity for the ocean," said Holmes, "that you indulged to excess as a reckless youth. An experience as a medic in the military changed your life and gave you a reason to do more than…
mikethemadbiologist | August 29, 2007A while ago, I posted about eigenFACTOR, a bioinformatics tool that can be used to calculate the relative impact of scientific journals. Well, the eigenFACTORials have developed a whole buncha new stuff you can do with the program:
Maps of science. How different fields of science cite each other. And make sure you check out the groovy interactive map.
More data. eigenFACTOR now incorporates data from 1994-2005. There's also some really cool time series stuff you can do (here's the Philosophical Transactions of the Royal Society).
You can also search by publisher. Here's Demon…
sporte | August 24, 2007I began this series last week with a question about a DNA sequence that was published and reported to be one the first beta-lactamases to be found in Streptococcus pneumoniae. Mike has a great post about one of problems with this paper.
I think the data themselves are awfully suspicious.
So, last week I suggested that you, dear readers, go and find out why. I gave you a link to the abstract and a place to get started.
Perhaps that was too hard.
Sigh.
Okay, here's a little more help and another clue.
I highlighted the accession numbers. Post your guesses in the comments.
sporte | August 21, 2007
If you've read the previous posts on this topic, here and here, you're probably aware by now that I have this weird (okay, maybe fanatical) obsession with data. Or at least, with knowing if my data are right so I can get on with life, do the analysis and figure out the results.
My results from last week suggested that re-processing chromatogram data (from the ABI 3730) with phred was probably a bad idea, but still, I only had one data point and I really wanted to know if anyone had done a more thorough study and compared larger numbers of chromatograms.
Naturally, someone had.
tags: DNA…
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 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 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 | 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 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…
sporte | July 24, 2007What 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 several of those stars blink out, one by one. The card disappeared, too. Maybe we got tired of marking off the companies as they went, maybe we just lost the card when we moved to our present office. No matter. Over time, the bioinformatics universe got a little smaller and colder each time another…