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, but they end up in fouth author hell - always the fourth author on hundreds of papers - ... Read more
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 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. ... Read more
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 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 ... Read more
What do people do in bioinformatics software companies?
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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 company disappeared from ... Read more
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 to learn how much of the scientific method goes into testing software and doing digital biology.
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What happens when the scientific method ... Read more
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 work in the biotech industry, while I work with people who slave away building the picks and shovels (picture a Greta Garbo sigh, for dramatic effect ... Read more
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.
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Well no, I said, and added that I'd never heard of a bioinformatics technician before and I really didn't know what they would do. I thought that the people most likely to use our activities on-the-job would be research ... Read more
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 very good at illustrating evolutionary relationships on a molecular level.
A few months ago, the NCBI changed the web interface for doing BLAST searches at their site. I ... Read more
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.
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.
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Because of these changes, and because I'm giving a workshop for teachers on BLAST at the Fralin Biotechnology Conference in Blacksburg, VA, next week, it seemed like a good time to update our animated ... Read more
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.