bioinformatics

getting the images was the hardest part

A lot of our colleagues are interested in bioinformatics and data science. While it is clear that bioinformatics is important, even essential, in modern biology research, there is the question about the levels of programming and computer skills needed for different jobs. I'm not going to answer that question here. Instead I'm going to focus on one end of the problem, that is, how is a bioinformatician similar to a data scientist? I'll illustrate the kinds of skills that are needed for this role by sharing my recent experience of how we moved the Discovering Biology in a Digital World (DWB ... Read more

Todd M. Smith [1,2], Sandra Porter [1,2], Linnea Fletcher [2,3]

1. Digital World Biology (DWB), 2. Bio-Link, 3. Austin Community College (ACC)

Students graduating from college in the 21st century need to be skilled in using a computer. Through several experiences including Austin Community College’s (ACC’s) interactions with industry, DWB’s experience, and combined participation in efforts such as the Network for Integrating Bioinformatics into Life Sciences Education (NIBLSE), it is clear students need to be more aware of how computing is used in the life sciences and the ... Read more

In our series on why $1000 genomes cost $2000, I raised the issue that the $1000 genome is a value based on simplistic calculations that do not account for the costs of confirming the results. Next, I discussed how errors are a natural occurrence of the many processing steps required to sequence DNA and why results need ... Read more

What do you call a biologist who uses bioinformatics tools to do research, but doesn't program?

You don't know?

Neither does anyone else.

The names we use
People who practice biology are known by many names, so many, that the number of names almost reflects the diversity of biology itself.

Sometimes we describe biologists by the subject they study. Thus, we have biologists from anatomists to zoologists, and everything in between: ... Read more

I often get questions about bioinformatics, bioinformatics jobs and career paths. Most of the questions reflect a general sense of confusion between creating bioinformatics resources and using them. Bioinformatics is unique in this sense. No one confuses writing a package like Photoshop with being a photographer, yet for some odd reason, people seem to expect this of biologists. In the same respect, even the programmers and database administrators who work in bioinformatics, are unfairly assumed to have had graduate level training in biology.

In many ways, it's easiest to ... Read more

Last spring, I gave my first hands-on workshop in working with Next Generation Sequencing data at the Eighth Annual UT-ORNL-KBRIN Bioinformatics Summit at Fall Creek Falls State Park in Tennessee. The proceedings from that conference are now on-line at BMC Bioinformatics and it's fun to look back and reflect on all that I learned at the conference and all that's happened since.

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I'm a big of learning from data. There are many things we can learn about swine flu and other kinds of flu by using public databases.

In digital biology activity 1, we learned about the kinds of creatures that can get flu. Personally, I'm a little skeptical about the blowfly, but...

Now, you might wonder, what kinds of flu do these different creatures get? Are they all getting H1N1, or do they get different variations? What are H and N anyway?

We can discuss all of these, but for now, lets see what kinds of flu strains infect different kinds of creatures.

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Genome sequences from California and Texas isolates of the H1N1 swine flu are already available for exploration at the NCBI. Let's do a bit of digital biology and see what we can learn.

Activity 1. What kinds of animals get the flu?

For the past few years we've been worrying about avian (bird). Now, we're hearing about swine (pig) flu.

All of this news might you wonder just who gets the flu besides pigs, birds, and humans. We can find out by looking at the data.

Over the past few years, researchers have been sequencing ... Read more

I don't usually publish press releases, but I'm making an exception for this one, since your's truly is one of the Co-PI's. If you're a teacher within commuting distance of Seattle, the schedule and sign up information is here.

NSF AWARDS $1.3 MILLION TO NWABR FOR BIOINFORMATICS EDUCATION

Innovative Technology Experiences for Students and Teachers (ITEST) brings the understanding of how biology and information technology interact to teachers and their students

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In which we search for Elvis, using blastp, and find out how old we would have to be to see Elvis in a Las Vegas club.

Introduction

Once you're acquainted with proteins, amino acids, and the kinds of bonds that hold proteins together, we can talk about using this information to evaluate the similarity between protein sequences. We can easily imagine that if two protein sequences are identical, then those proteins would have the same kind of activity. But what about proteins that are similar in some regions, and not others, or proteins that ... Read more