Three posters presented at AAAS2015

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Here are the three posters I am presenting at AAAS2015, or better said, I am presenting the first GEP poster, and the two others are student posters. Whew! It was a bit stressful last week, but it is nice that it is done. Poster session this afternoon, 2/14. Happy Valentine’s Day!

Three posters presented at AAAS2015.

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Once I am done with the applications and posters…

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Barral allGEP AAAS poster draft

The state of my AAAS poster, January 24 6.27 AM.

I cannot wait to be done with the three essays, three posters, and one merit letter. They are all due during the first two weeks of February, and as a good procrastinator, I have left them all to the last minute (and because I had a bunch of other deadlines before). In fact, things are better than usual! I already started working on one essay, two posters, and the letter.

And, things are better also because the only one that requires creativity is the merit letter. And by creativity I mean, in the literature sense. A merit letter has to be in a beautifully written and convincing prose. Obviously, content is essential, but presentation matters. In a way, beauty reflects content, I believe Hegel said, and in this case it reflects craftsmanship, attention to detail, and also how important this particular item is for us. While I don’t consider myself a good writer, over my lifetimeI I have created some decent pieces of writing. The exosome review I published in a relatively obscure journal ten years ago is still being downloaded, and it is one I am very proud of. It took forever to get started, but once I came to the first sentence (it was sitting in silence looking at one of San Diego’s canyons), all went quickly. For the merit letter, I already have the thread that will string together my accomplishments, so the “only” thing that I need is to sit down and write it.

The other essays are not really literary essays- I just need to show that I have the background and experience to be successful for that particular training program. As I mentioned in one of my previous postings, my administration has been asking for monthly lists of activities, providing us with an effective and detailed log of scholarly and outreach achievements.

Posters are a different beast. Two of them are student posters, but I started them so the students can putz around with the results. For mine, the challenge is to adapt a number of very scientifically oriented verbiage to AAAS’s (I expect) more general audience. My poster is about the Genomics Education Partnership, of which I have blogged extensively. The structure and modus operandi of GEP allows sharing of presentations so we are not really starting from scratch, but I would like to lighten up the informative load to make the poster stand out and make it more attractive. Here is a problem, though…I do not want to look too “flashy.” So I am struggling with the background. I really like the one I have now, but I may need to step back and change it to a more conservative color. I tried putting Drosophila flies as a background, but that was too busy. Dear Readers, what do you think? I am open to suggestions. Of course, my coauthors will have the last say, but it would be nice to have feedback.

Now, I started saying “once I am done.” Yes. There is an exciting completely new research project I am involved with now, that has to do with microbes, plastic, and the ocean. I can’t wait to get started in earnest.

But I need to be done with three essays, three posters, and one merit letter first…

“No rest for the wicked…

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and the righteous don’t need it!”

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Washington University in St. Louis

With those words ended Sally Elgin’s presentation last night kicking off the GEP workshop. After few hours of sleep, getting up at 4 am,and flying to St. Louis, my brain foggily registered that some very intense days were in front of the group. However, it is such an exciting possibility, especially by the combination of learning some cutting edge research techniques at such a prestigious university, together with a group of educators coming from a variety of schools, mostly small liberal arts colleges, community colleges, and like myself, a private non-profit. Even after such a short time we discussed similar issues: few resources, lots of courses to teach, a a strong desire to share with our students the experience and joy of research.

I am writing this at the breakfast table, in a hurry- we are heading for a full day of computer work with annotation, so I am not sure how much and how quickly I will be able to write. But for now, visit the course material page, from where most of the materials we will be using are.

Will be back soon!

Prepping for Bioinformatics: basics

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Picture showing my foot very close to the edge of the Grand Canyon

Thrill of the edge: the North Rim of the Grand Canyon and me

In a post last January I shared how excited I was to become a participant in the Genome Education Partnership project. In less then 2 weeks I am bound to St. Louis, Missouri, to learn about bioinformatics (BI) as a project for crowdsourced research in education. I hope to document a bit my transition from a very superficial knowledge of BI to a deeper one, hopefully one adding a new dimension not only to my teaching, but also research.

My interest in BI came from my student’s interest in an obscure microbe and its even more obscure metabolic pathway. It has been a recurring pattern in my life that some of the most interesting things I learned (bringing me new avenues) came in a mysterious serendipitous way. So once he expressed his interest in having me as a thesis advisor (last Fall), I bought a basic BI book, started following people doing BI on Twitter, and filing articles away on Mendeley and Endnote. However, it was not until some days ago that I found enough space in my brain to actually start reading.

To clarify: if you know BI, you probably won’t find this interesting. On the other hand, I know that a lot of people do not learn certain things because they look intimidating, so they don’t even try. For years I avoided BI because I thought I could be a perfectly happy biologist without delving too deep into it…but the way things are shaping up, the next generation of biologist will need it. And as an educator of biologist, I should be teaching it then. Ergo, I need to learn more about it.

Back to the workshop materials: we were instructed to read the short article by Webber and Ponting for the definitions of the “-ogy” words, such as homology, analogy, orthology, paralogy, and xenology. While it is easy to say: orthologs arise from speciation, and paralogs from gene duplication; additional events such as deletion, duplications, conversions, and horizontal gene transfers (causing xenology) can make the picture quite complicated.  Sequence identity does not mean homology, although statistics (such as an E value lower than 103 ,provided by BLAST) and certain structural features strongly suggest homology.

Next, we were asked to work our way through some materials in the GEP website, such as BLAST tutorials, and introduction to Consed. I feel ok with Blast, although I will review the tutorials, but my next big leap will be to learn about finishing and sequence improvement.

Not today though.

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