The OpenHelix Blog

I’d like to point out the new NCBI Education page. There is a lot there that you might want to check out. NCBI will be, starting this fall, offering a series of two-day training courses they are calling Discovery Workshops. Two years ago they ended the NCBI Field Guide workshops, so this seems to be a welcome change.

There are also webinars. Our research suggests that webinars are not particularly popular, so I’m curious how these turn out. There are also ‘how-to’ guides, documentation, community, teacher resources. It’s quite a nice site with lots of things to check out.

I’d also like to point out the “recommended links” section. There are lots of links to additional educational resources like the Cold Spring Harbor’s Dolan DNA Learning Center and much more. And, incidentally , a link to our own free tutorials which was very nice to see. You might want to check those out, we have over 10 including PDB, SGKB, UCSC Genome Browser, Galaxy, several model organism databases, and more.

Speaking of outreach, I just saw a tweet from the NSF reminding me that tomorrow is the culmination of National Lab Day!

From the press release:

The National Science Foundation has launched a Web-based resource for scientists seeking guidance on how to effectively interact with K-12 teachers as part of National Lab Day, a grassroots effort to invigorate science education.

National Lab Day is a volunteer effort designed to form local “communities of support” around science, technology, engineering and mathematics (STEM) teachers and to connect them with STEM professionals who will share their expertise as well as their excitement and passion for their disciplines.

Point those teachers and kids to these resources.  Scientists–volunteer for projects.  Let’s get ‘em trained up in science. We’re gonna need ‘em. I wish I had heard about the volunteer opportunities earlier. But it looks like some of them are still ongoing, as this isn’t supposed to be limited to one specific day.  Maybe there’s something there…

That was the word I got back from a kid who was assembling a plastic model of a virus that was donated to his science class. I also got this fabulous diagram of a plant cell from another kid. There were some funny and sweet thank you notes in the mail for me as one of the donors to the project. The project was called “Fill Our Display Case” and you can see the kids building the models in the photos over there.

A friend on another blog has been running a weekly project to find worthy science classroom projects on the Donor’s Choice site, and try to raise funds for these classes. A lot of people complain about science education today–but don’t know what to do about it, and she’s found a way to make a difference directly to teachers who want to change it up.

Some people use the holidays as a time to focus their giving to meritorius projects and causes.  If you are considering holiday donations please think about the Donor’s Choice projects.  You get to pick projects you like, and you can see the delight of the teachers and kids who benefit.  It just struck me what a great way it is to find science educators who need support, and directly touch the lives of kids with science!  And now I have very nice artwork to hang in my office

Anyone who has either used or helped to create a database of biological information has probably come across ontological terms. In today’s tip I feature a great resource devoted to promoting the creation and proper use of ontologies. The resource is the The National Center for Biomedical Ontology, and allows users to learn about ontologies, find and use ontologies that are already in existence, and even to add newly developed ontologies to the resource so others might use them.

Ontologies are basically organized sets of controlled vocabulary terms that are applied in a uniform manor across diverse collections of information. They are important because of their ability to make abstract biological terms computer searchable. They also aid in the interpretation of biological information by researchers because each term includes a definition of how and when it should be applied to biological information. In this tip I briefly touch on finding ontologies, and on the educational resources available from the NCBO and BioPortal web sites.

Being summer, a strangely slow connection and some other factors, I am embedding a talk from Doug Ramsey (posted on SciVee) on the GEBA project at JGI (instead of doing a tip myself . The GEBA project recognizes that many, if not most, of the bacterial and archaeal genomes that have been sequenced to date have some relevance to human disease or other human interest. This of course is reasonable, but it also leads to big gaps in our knowledge of bacterial evolution and genomics, knowledge that would help us better understand those genomes that we find relevant and knowledge that in and of itself can be quite interesting and potentially useful. View the talk to learn more about this project to sequence 100 phylogenetically diverse bacterial and Archaeal genomes.
I’m also posting this as an introduction to JGI’s Adopt a Genome project. This project allows student groups to adopt and study a bacteria in the GEBA project and hopefully add to our knowledge and annotations of the genome while learning. The students can then annotate the adopted genome by using IMG-ACT.

So, yesterday was the 200th anniversary of Darwin’s birth. Lots of festivities and NPR stories surrounding that day including a few announcements like UCSC announcing their v200th browser code a day early so as to coincide (they couldn’t resist the coincidence ). Another announcement that was apropos was the announcement that researchers at the Max Planck Institute for Evolutionary Anthropology have finished the draft sequence of the Neanderthal genome. Since only about 63% of the genome is actually covered (3.7 billion bps covered of the 3.2 billion bp genome, with duplications), when one announces a “draft” can be a bit arbitrary, so the 200th anniversary of the of the man who wrote “The Descent of Man, and selection in relation to Sex” is as good a time as any. And we are learning a few things like, Neanderthal’s might have had the physical ability for language, but couldn’t stand milk as adults (didn’t agree with their digestion). It is expected a draft and research will be published at the end of this year. We’ll report on that of course, and link to any browsers they might be setting up . Ancient genomes are teaching us some things.

Speaking of which, the Exploratorium, an excellent science museum in my fair city, has a great exhibit (on site and online) on the ‘how we know things’ and how science works. This exhibit is specifically on the origins of humans and Neanderthal DNA and the research at Max Planck figures prominently.

A recent paper (couple weeks ago) in PLoS Biology from Hingamp et al. had me intrigued. Entitled Metagenome Annotation Using a Distributed Grid of Undergraduate Students, the lecturers put together a system to teach bioinformatics to undergraduates that uses new unannotated sequences from metagenome projects. As stated in the announcement,

This method asks students to randomly pick and analyze unknown metagenomic DNA fragments from a real research sequence stockpile. The student’s mission, using Internet tools only, is to figure out from which organism the DNA comes from, and what biological function it might have. As well as gaining confidence and proficiency in bioinformatics, students experience the authentic research process of weighing the arguments, establishing prediction reliability, building hypotheses, and maintaining rigorous disourse.

The lecturers have put together  a teaching-annotation procedure in a publicly accessible “annotation environment” they call “Annotathon.” This web interface walks the student through the annotation process in a procedure as you see in the figure here. Since you can join and use this interface, I thought I’d give it a test drive.

From the Boston Globe I was led to a local blogger, who brought my attention to the Nerd Girls. Apparently this is a local group of engineering students who are trying to make engineering “cool” for girls. I’m not sure I’m psyched on luring them as chemical engineers for make-up, but if that’s what gets some smart young woman interested in the field, so be it. So far we aren’t doing that well with our current outreach strategies.

So have a look at the Nerd Girls. I think their confidence is great, and the social networking approach is worthwhile. Kudos to IEEE for their support of this. But mostly congrats to the Nerd Girls for the courage and the effort.

We are here at the science blogging conference this morning. It starts in 30 minutes. I’m looking forward to attending several sessions. First one im attending is on “open science” or how the Internet has changed science. I just wrote a post about that . The next session I’m going to will be on teaching science online. Then there is the making your blog more interactive. Last are the general sessions. I’ll report on them all later. Right now I’m testing out my iPhone blog posting interface

EDIT by Mary: I’m watching this conference remotely on UStream.tv from this link: http://ustream.tv/channel/waynesuttontv

You have some non-biologist colleagues (attorney? manager? programmer?) you need to get up to speed, or you need to brush up on some concepts yourself? A good place to start is this list from John Wilkins (Evolving Thoughts). It is a list of links to blog post across the blogosphere that explain and expound on various basic concepts in science. The list for the life sciences ranges from basic evolution to clade to biomes to linkage disequilibrium to a lot else. It includes a list of lectures from Bora Zivkovic at Blog Around the Clock in basic biology. Additionally, make sure to read the comments to the first link, commenter contributed a lot of their own. A wealth of information out there in the blogosphere.