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Discovering Biology in a Digital World

My thoughts on biology, teaching, life, and exploring the living world via the digital one. Only my opinions are represented by these postings, they do not represent the viewpoints of any funding agency or Geospiza, Inc.

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Sandra Porter I am a microbiologist and molecular biologist turned tenured biotech faculty turned bioinformatics scientist turned entrepreneur. My passion is developing instructional materials for 21st century biology (Geospiza Education).

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    MicrobeWorld Radio

    August 27, 2007

    What happens to graduates of high school biotech programs?

    Category: Science education

    Some of them work for Bayer.

    Read on »

    August 25, 2007

    Got DNA sequencing problems? Who ya gonna call?

    Category: Biotechnology

    Why the ABRF of course! I spend a fair amount time every summer giving workshops for college and high-school teachers on genomics and bioinformatics. One of the things that always surprises them, is the amount of lab work that's carried out by people working in shared, or core lab facilities. For example, if I was working at a research university...

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    August 24, 2007

    Digital Biology Friday: A helpful hint

    Category: Bioinformatics

    I 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....

    Read on »

    Godzilla, tuberculosis, and XDR-TB

    Category: Science education

    What's the connection?(image from Newton TAB blog) I have to admit, I don't know. But, I do know where you can find out. Dr. Gerard Cangelosi, from the Seattle Biomedical Research Institute, will be speaking about tuberculosis, godzilla, and XDR-TB, Monday night, 7 pm at the Pub at Ravenna Third Place as part of Science on Tap. tags: tuberculosis, informal...

    Read on »

    August 23, 2007

    Grants for kids to study beetles

    Category: Science education

    Charles Darwin was so fascinated by beetles he paid people to help him build his collection. The Coleopterists Society and the Smithsonian Institute want to help kids explore the wonders of beetles, too. They're providing grants for kids, in grades 7-12 to work on beetle biology. Applications are due by November 15, 2007....

    Read on »

    August 22, 2007

    Do biologists need to learn programming?

    Category: Science education

    I get asked this question often enough and now that's it's come up again, it seems that I might as well answer it once and for all and get it over with....

    Read on »

    SciVee: more beta than YouTube?

    Category: web resources

    or maybe seminars on parade? They're calling them PubCasts, but I don't think I'll be watching them in a pub. Seriously, SciVee is kind of cute, and has lots of potential down the road, and even has a few unintentional moments of humor right now, but.......

    Read on »

    August 21, 2007

    Is phred dead? Let's see the data

    Category: sequence analysis

    Calling all bases, how many are correct?

    Read on »

    August 20, 2007

    Careers in biotechnology, part VI. More opinions on bioinformatics in a software company

    Category: Bioinformatics

    Second opinions on bioinformatics careers and programming.

    Read on »

    August 17, 2007

    Digital Biology Friday: You make the call!

    Category: sequence analysis

    Developing "biological intuition" through case studies

    Read on »

    August 16, 2007

    Steven Colbert becomes intimately acquainted with his own DNA!

    Category: Humor

    Thanks 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?...

    Read on »

    August 15, 2007

    Will the real DNA sequence please stand up?

    Category: sequence analysis

    Sometimes 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...

    Read on »

    Jim Watson's genome on your computer, get it today!

    Category: sequence analysis

    Yes, 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...

    Read on »

    August 14, 2007

    What is the truth in DNA sequencing?

    Category: sequence analysis

    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...

    Read on »

    August 10, 2007

    Digital Biology Friday: Romantic DNA

    Category: molecular structures

    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...

    Read on »

    August 9, 2007

    Understanding software engineers: a guide for biologists

    Category: Humor

    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 reference from Silicon Glen. Although, maybe we biologists do have something in...

    Read on »

    August 8, 2007

    And we thought publishing was complicated in biology

    Category: Humor

    Biologist 1: How many physicists does it take to write a research paper?...

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    The X-ray method for pest control

    Category: Biology (Macroscopic )

    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 creatures of nightmares. During part of their lives, they live and travel as flies, and...

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    August 6, 2007

    Careers in biotechnology, part V. Bioinformatics in an academic lab

    Category: Bioinformatics

    Is an academics a dead-end if you're a programmer?

    Read on »

    August 5, 2007

    When your water starts tasting like dirt...

    Category: Chemistry & Biochemistry

    It could be geosmin....

    Read on »

    August 3, 2007

    Gene therapy with AAV: too risky for a cure?

    Category: viruses

    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...

    Read on »

    Digital Biology Friday: the answer to last week's puzzle

    Category: molecular structures

    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:...

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    August 2, 2007

    Summer time and the mosquitoes are biting

    Category: Microbiology

    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 sickness, insect control, malaria...

    Read on »

    August 1, 2007

    On the consequences of spending too much thinking about pubs and not enough time inside of them

    Category: Science culture

    Drug Monkey has an interesting take on an article that I wrote the other day about publishing in biology....

    Read on »

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