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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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    Bioinformatics:

    A vaccine against lung cancer?

    A potential link between lung cancer and human papilloma virus may make parents even more glad about vaccinating their children with Gardasil®. Not only are the children protected against viruses that commonly cause cervical cancer, they may be protected against some forms of lung cancer as well. The April 25th version of Nature News reports (1) that two viruses, HPV...

    Comparing mutant and wild type structures

    How to compare mutant and normal protein structures.

    The wonders of webinars

    One of my favorite web 2.0 technologies is the webinar. When you work at a company and not a University, with constant seminars, it gets a bit harder to hop on a bus and travel across town to learn about new things. Webinars are a good way to fill that gap. I grab my coffee cup, put on my headphones,...

    Mapping polymorphisms in 16S ribosomal RNA

    In the class that I'm teaching, we found that several PCR products, amplified from the 16S ribosomal RNA genes from bacterial isolates, contain a mixed base in one or more positions. We picked samples where the mixed bases were located in high quality regions of the sequence (Q >40), and determined that the mixed bases mostly likely come from different...

    Digital Biology Friday: A DNA sequencing data puzzle

    Can you solve this puzzle?

    Google Docs has pivot tables!

    Goodbye desktop, we're off to see the web. Both my students and I have been challenged this semester by the diversity of computer platforms, software versions, and unexpected bugs. Naturally, I turned to the world and my readers for help and suggestions. Some readers have suggested we could solve everything by using Linux. Others have convincingly demonstrated that Open Office...

    Dinosaur DNA discovered in GenBank

    Is it real or is it April Fools?...

    A beginner's guide to making a phylogenetic tree

    I made this video (below the fold) to illustrate the steps involved in making a phylogenetic tree. The basic steps are to: Build a data set Align the sequences Make a tree In the class that I'm teaching, we're making these trees in order to compare sequences from our metagenomics experiment with the multiple copies of 16S ribosomal RNA (rRNA)...

    How to use Cn3D

    A video tutorial on molecular structures.

    DNA sequencing errors hit home

    One of my colleagues has a two part series on FinchTalk (starting today) that discusses uncertainty in measurement and what that uncertainty means for the present and Next Generation DNA sequencing technologies. I've been running into this uncertainty myself lately....

    Exploring OpenOffice: what did we learn?, part I

    I think all of us; me, the students the OO advocates, a thoughtful group of commenters, some instructors; I think many of us learned some things that we didn't anticipate the other day and got some interesting glimpses into the ways that other people view and interact with their computers. Some of the people who participated in the challenge found...

    A Bustard is not just a bird

    It's a Solexa data directory. I've held off on blogging about Next Generation Sequencing here, but now that one of my colleagues has started blogging about it, it seems like a good time to write a little about FinchTalk, our company blog. We've decided that we can serve an educational role for people who are interested in Next Generation DNA...

    The OpenOffice challenge: can you do what needs to be done?

    Okay OpenOffice fans, show me what you can do. Earlier this week, I wrote about my challenges with a bug in Microsoft Excel that only appears on Windows computers. Since I use a Mac, I didn't know about the bug when I wrote the assignment and I only found out about it after all but one of my students turned...

    Google Maps meets bacterial genomes

    I read about this in Bio-IT World and had to go check it out. It's called the Genome Projector and it has to be the coolest genome browser I've ever seen. They have 320 bacterial genomes to play with. Naturally, I chose our friend E. coli. The little red pins in the picture below mark the positions of ribosomal RNA...

    Linux is amusing, but this is why I teach with Excel

    The other day, I wrote that I wanted to make things easier for my students by using the kinds of software that they were likely to have on their computers and the kinds that they are likely to see in the business and biotech world when they graduate from college. More than one person told me that I should have...

    The NASA Earth Observing System and dealing with all that data

    The NASA Earth Observing System is an incredible resource for both science and education. One of the amazing things about it is all the different kinds and quantities of data are assembled together into pictures that even grade school kids can immediately comprehend. How do they do it? Each of the EOS satellites delivers a terabyte or more of data...

    An unexpected challenge with teaching on-line

    Three (or more) operating systems times three (or more) versions of software with bugs unique to one or systems (that I don't have) means too many systems for me to manage teaching. Thank the FSM they're not using Linux, too. (Let me see that would be Ubuntu Linux, RedHat Linux, Debian Linux, Yellow Dog Linux, Vine, Turbo, Slackware, etc.. It...

    Digital Biology Friday: A microbiology blast puzzler

    Here's a fun puzzler for you to figure out. The blast graph is here:...

    Bacterial metagenomics on the JHU campus: analyzing the data, part IV

    Do different kinds of biomes (forest vs. creek) support different kinds of bacteria? Or do we find the same amounts of each genus wherever we look? Those are the questions that we'll answer in this last video. We're going to use pivot tables and count all the genera that live in each biome. Then, we'll make pie graphs so that...

    Bacterial metagenomics on the JHU campus: analyzing the data, part III

    This is third video in our series on analyzing the DNA sequences that came from bacteria on the JHU campus. In this video, we use a pivot table to count all the different types of bacteria that students found in 2004 and we make a pie graph to visualize the different numbers of each genus....

    Bacterial metagenomics on the JHU campus: analyzing the data, part II

    What do you do after you've used DNA sequencing to identify the bacteria, viruses, or other organisms in the environment? What's the next step? This four part video series covers those next steps. In this part, we learn that a surprisingly large portion of bioinformatics, or any type of informatics is concerned with fixing data entry errors and spelling mistakes....

    Bacterial metagenomics on the JHU campus: analyzing the data, part I

    For the past few years, I've been collaborating with a friend, Dr. Rebecca Pearlman, who teaches introductory biology at the Johns Hopkins University. Her students isolate bacteria from different environments on campus, use PCR to amplify the 16S ribosomal RNA genes, send the samples to the JHU core lab for sequencing, and use blastn to identify what they found. Every...

    How do I love thee SQL? Let me COUNT the ways. Number 1...

    I love the way you show me secret things. All I do is type: Select * from name_of_a_table And you share everything with me. Without you, my vision is obscured, and all I see is the display on the page. In fact, this was the push that finally made me decide to learn SQL....

    A quick introduction to BLAST

    A quick video introduction to BLAST.

    Where do you go to learn SQL? I go to the zoo

    A long standing debate in my field is whether or not biologists, who work with computers, need to learn how to program. I usually say "no." Let the programmers program, the biologists interpret the results, and let everyone can benefit from each other's expertise. Well, I've changed my mind in one respect. Most biologists need to work with some kind...

    Hunting for huntingtin, part II: In which we're reminded that database searches are experiments

    In which we're reminded that database searches are experiments, too. One of the trickiest things with bioinformatics experiments is repeating them. This challenge isn't related to the validity of the original results, the challenge is that, unless you made your own database and kept it in the same state, the database that you'll be using at a later time, sometimes...

    Hunting for huntingtin, part I

    How do you go about researching a genetic disease? This multi-part series explores how digital resources can be used to learn about Huntingtin's disease. Reposted and updated from the original DigitalBio. A bit of background Alice's Restaurant is a movie with an unforgettable song that mostly revolves around Arlo Guthrie hanging out with his friends. Somewhere in the movie, the...

    Digital Biology Friday: Free to evolve? - the answer

    Last week I posted an image with two molecules (below the fold), one protein and one nucleic acid, and asked you about the probability of finding similar molecules in different species. You gave me some interesting answers....

    No more mystery meat!

    If you like ham and bacon, you might be interested in this. GenomeWeb reports that researchers at the University of Barcelona have developed an assay that tests 46 SNPs and can be used to trace the origin of your pork dinner. According to GenomeWeb, the test identifies both the breed and origin of the animal. The university and the company...

    Did she or didn't she? Genetic testing and virgin birth

    If we suspected a virgin birth, how could we prove it?

    Interpreting DNA sequencing data: answers to the quiz

    Which read(s): 1. contain either a SNP (a single nucleotide polymorphism) or a position where different members of a multi-gene family have a different base? C 2. doesn't have any DNA? B 3. is a PCR product? A, B, and C.  All of three reads were obtained by sequencing PCR products, generated with the same set of primers. The quality...

    Interpreting DNA sequencing data: what can you get from quality scores?

    Kind of like reading tea leaves, but more meaningful.

    Digital Biology Friday: Animal Mitochondria and Evolution, part II

    You too, can compare chimp and human DNA.

    Match the trace with the sample

    Can you do it? This is what bioinformatics technicians or data analysts do in diagnostic labs.

    High school students uncover their past through their DNA

    Students at Soldan International High School are participating in an amazing experiment and breaking ground that most science teachers fear to tread. Soldan students, along with hundreds of thousands of other people, are participating in the National Geographic's Genographic Project. Through this project, students send in cheek swabs, DNA is isolated from the cheek cells, and genetic markers are used...

    Digital Biology Friday: Animal Mitochondria and Evolution Revisited

    An evolution activity for the classroom.

    Digging up the dirt on campus bacteria: how do we know if we have good data?

    Metagenomics is a field where people interrogate the living world by isolating and sequencing nucleic acids. Since all living things have DNA, and viruses have either DNA or RNA, we can identify who's around by looking at bits of their genome. Researchers are using this approach to find the culprit that's killing the honeybees. We're also trying to find out...

    Metagenomics, biomes, and dirt: separating good data from bad

    Sequencing the dirt: see how it's done

    Playing in the dirt: metagenomics on the JHU campus

    We have lots of DNA samples from bacteria that were isolated from dirt. Now it's time to our own metagenomics project and figure out what they are. Our class project is on a much smaller scale than the honeybee metagenomics project that I wrote about yesterday, but we're using many of the same principles....

    Metagenomics and the mystery of the dying bees

    Dying bees and DNA sequencing

    Making discoveries in the open: doing digital biology with the class

    Would you like to have some fun playing with chromatograms and helping our class identify bacteria in the dirt?...

    Computers vs. the science class: IT 1, Instructor 0

    It's hard to teach bioinformatics when schools work so hard to keep us from using computers....

    Fall bioinformatics class: welcome students!

    Welcome 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...

    The real cost of J. C. Venter's genome

    A 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?...

    Digital Biology Friday: What sequences do you believe?

    During 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...

    Genetic Variation I: What is a SNP?

    If 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...

    Watson's genome, Venter's genome, what's the difference?

    "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....

    Digital Biology Friday: A helpful hint

    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....

    Is phred dead? Let's see the data

    Calling all bases, how many are correct?

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

    Second opinions on bioinformatics careers and programming.

    Digital Biology Friday: You make the call!

    Developing "biological intuition" through case studies

    Will the real DNA sequence please stand up?

    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...

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

    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...

    What is the truth in DNA sequencing?

    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...

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

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

    Careers in biotechnology, part IV: the tip of the informatics iceberg

    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...

    Conventions, authorship, and fields of study

    What happens when authors play by different rules?

    Careers in biotechnology, part III: Life in a bioinformatics software company

    What do people do in bioinformatics software companies?

    Bug hunting is a BLAST

    Software testing and the scientific method.

    Kudos to my commenters!

    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...

    Careers in biotechnology, part II bioinformatics

    Where does bioinformatics fit in the biotech food chain?

    Teaching with the new BLAST

    Some things I like, some were surprises.

    It's still a DNA puzzle, but this is the answer

    This DNA is nonpareil.

    Updates to the BLAST for beginners tutorial

    BLAST has gotten harder.

    A DNA puzzle

    It's a pair of bases, but something's not quite right.

    Gadget Lust

    Viewing chromatogram trace files on iPhone.

    What if Garrison Keillor did bionformatics?

    What happens when a biologist tries to talk to the IT group?

    Using Bioinformatics to Study Evolution: Animating PCR

    The best PCR animations on the web

    "A college education is not job training"

    Answers to a commenter who bemoans bioinformatics education.

    To bioinformatics students everywhere: advice from the pros

    Know your biology! I get asked often about the type of bioinformatics training that students should get and whether it should be a special course or not. And I answer that I think teaching bioinformatics in the absence of biology is like teaching Microsoft Word in the absence of writing. There isn't much point. tags: bioinformatics, education So I was...

    Digital Biology Friday: hot plants and viruses, the finale

    Could a protein from a virus help plants handle global warming?

    Finding scientific papers for free: contributions from our readers

    Suggestions from librarians and scientists.

    Using Bioinformatics to Study Evolution: reading assignments

    Assigned readings on BLAST and phylogenetics.

    Using Bioinformatics to Study Evolution, intro

    An introduction to our Alaskan NSF Chautauqua course and a pre-course assignment. I don't know how well this will work, but I thought it might be interesting this year to experiment with blogging about our course and sharing some of our experiences with the rest of the world. Here's your chance readers, if you'd like to do some of the...

    Digital Biology Friday: hot plants and viruses V

    Through the Related Structures tab and what I found there.

    Finding scientific papers for free, one more experiment

    One last experiment with PubMed (for now).

    Finding scientific papers for free, part III: my new favorite method

    Instructions for using my new favorite method.

    Finding scientific papers for free, part II: comparing methods

    We do an informatics experiment with PubMed to compare different search techniques.

    Finding scientific papers for free, part I

    The trials of an English physician.

    Digital Biology Friday: hot plants and viruses, part IV

    How does grass grow in the hot, inhospitable soils of Yellowstone National Park?

    Biotechnology Education in Viriginia

    Do you want to learn how to use some cool biotechnology and bioinformatics methods in your college or high school class? If you're on the East coast, the best place to go is the Fralin Biotechnology Conference at Virignia Tech, July 18-21st. (Yes, it's the same Virgina Tech, and that's why I waited to post this announcement). There's something for...

    Bears, moose, and bioinformatics are all happening in Alaska

    tags: moose, bioinformatics class, willows, plant genes PZ's morning post about a bear killing a moose in someone's yard (they do live in Alaska, after all), reminded me that it's time to make an announcement about our upcoming course. No, no, no! We're not going to kill any moose on the premises. We're going to learn about the moose and...

    A great interview with Joe Felsenstein

    If you've ever looked at an evolutionary tree, contemplated phylogeny, cladistics, or the like, you're probably aware that Joe Felsenstein is one of the leaders of the pack....

    2007 Bio-Link Summer Fellows Workshop

    It must be spring. Summer course announcements are popping up everywhere and this site is no exception. Last Friday, I posted an announcement about our summer bioinformatics course in Alaska, June 27-29th. This week, I have a couple more conferences to announce. Naturally, I'll be at both of them, leading hands-on workshops for college and high school teachers in using...

    Bioinformatics in Alaska: Of course it's a course, of course, of course

    Registration has opened a bit late this year, but it's always tricky when large programs change hands. The Chautauqua Short Course program for College Teachers is no different. In fact, as far as I know, we may still be waiting for the National Science Foundation to make a final decision on funding. Still, summer is rapidly approaching and I know...

    Hot plants and viruses, part III: An inordinate fondness for hypothetical proteins

    How do plants grow at 65°C?

    MeSH part I. Where can you find the meaning of "life"?

    The best place for biology words.

    What are hypothetical and putative proteins?

    "Beware the Jabberwock, my son! The jaws that bite, the claws that catch! Beware the Jubjub bird, and shun The frumious Bandersnatch!" - from Jabberwocky, by Lewis Carroll I'm certain that if we ever sequenced DNA from the frumious Bandersnatch it would match hypothetical and putative proteins....

    Hot plants and viruses: the story continues

    Yesterday, both Joshua and I wrote about grasses that grow in the unusually hot soil at Yellowstone National Park. Now, I knew that hot springs bacteria can tolerate high temperatures, but I was really surprised to learn that plants could....

    Sequencing a Genome, part VII: Want to win $10 million dollars?

    How to win the X PRIZE in genomics In October, 2006, the X PRIZE foundation announced that second X prize would focus on genomics. The first team to successfully sequence 100 human genomes in 10 days will win $10 million dollars. And I would venture to guess, that the winning team would also win in the IP (intellectual property) game...

    Biology as a second language: what is a vector?

    Defining a biology term for scientists in other disciplines.

    Sequencing a Genome, part VI: Chimeras are not just funny-looking animals

    Chimeras invade the sequencing lab!

    Sequencing a Genome, part V: checking out the library

    Send in the clones, but only the random ones.

    Basics: How do you sequence a genome? Part IV. How many reads does it take?

    "How deep is the ocean? How high is the sky?"

    Basics: How do you sequence a genome? part III, reads and chromats

    In which we define reads, chromatograms, and shotgun sequencing.

    Basics: How do you sequence a genome, part II

    Some background on the strategies: mapping vs. shotgun

    Bioinformatics teaching tip #1: Remember Julia Child!

    No more live BLAST searches during lectures!

    Basics: How do you sequence a genome?

    Ask Dr. Science: yes, I do take requests.

    What is a gene? My definition is better

    In the effort to help us define a few basic concepts, PZ started out by giving us a nice simple definition of a gene, but as he, rightly noted: I tell you right now that if I asked a half dozen different biologists to help me out with this, they'd rip into it and add a thousand qualifiers, and it...

    Bioinformatics for biotech students: my favorite computer programs

    The bioinformatics classes that I teach use web services and web sites as much as possible, but I still find that it's helpful to have programs on our classroom computers. Here is a list of my favorite desktop programs for those of you who might want to add some bioinformatics activities to your biology courses....

    Snow Day!

    I was frantically getting ready for class when I happened to glance out the window. What did I see? Big fluffy white flakes rapidly falling from above. You can't say we weren't warned. The newspapers have been predicting snow since Monday. It's just, well, unusual. And Seattle is never prepared to deal with it. Even the kids aren't looking too...

    My equipment wish-list for teaching bioinformatics

    There's nothing like the first day of class to make you appreciate the difference between the equipment you end up using at schools and the equipment that you get to use on the job. For the month of January, I'm teaching a night class in bioinformatics at a local community college. We're introducing lots of web-based programs, and databases, and...

    Welcome Bioinformatics Students!

    It's the first day of our bioinformatics class.

    Did you publish a scientific mistake? Blame the software!

    When computers first entered the mainstream, it was common to hear them getting blamed for everything. Did you miss a bank statement? that darned computer! Miss a phone call? - again the computer! The latest issue of Science had a new twist on this old story. Now, instead of a researcher failing to take responsibility for doing sloppy science, we're...

    Oh sure, blame it on the bacteria!

    Bacteria can cause other epidemics, why not obesity? Is there a relationship between our body weight and our bacterial inhabitants?...

    The science behind Benghazi

    Who infected the children with HIV: Using the data to solve the puzzle.

    There's no place like "ome"

    A quick guide for the omically challenged.