The OpenHelix Blog

NIH scientists and staff can now efficiently and effectively learn to use bioinformatics and genomics resources with the extensive tutorial suite catalog from OpenHelix.

Bellevue, WA (PRWEB) April 19, 2010 — The National Institutes of Health Library (www.nihlibrary.nih.gov) has purchased a subscription toOpenHelix (www.openhelix.com) giving NIH scientists and staff access to over 90 tutorial suites on bioinformatics and genomic resources.

With OpenHelix tutorials, NIH now offers their employees a quick and effective way to learn about the most powerful and popular genomics and bioinformatics databases and resources. These tutorials cover many types of resources including protein databases, bioinformatics analysis tools, model organism databases, SNP databases, comparative genomics, pathway and interaction resources and much more.

The online narrated tutorials, which run in just about any browser, can be viewed from beginning to end or navigated using chapters and forward and backward sliders. The approximately 60 minute tutorials highlight and explain the features and functionality needed to start using the resources effectively. The tutorial can be used by new users to introduce them to a resource, or by previous users to view new features and functionality, or simply as a reference tool to understand specific features.

In addition to the tutorial, users also have access to useful training materials including the animated PowerPoint slides used as a basis for the tutorial, suggested script for the slides, slide handouts, and exercises. This can save a tremendous amount of time and effort for teachers and professors creating classroom content.

“It is difficult, and certainly cost prohibitive, for research institutions themselves to create and provide training on the many critical genomic resources available.” said Scott Lathe, Chief Executive Officer of OpenHelix, “NIH uses the OpenHelix subscription to provide an efficient and effective training solution for their researchers.”

About the National Institutes of Health
Composed of 27 Institutes and Centers, the NIH provides leadership and financial support to researchers in every state and throughout the world.

For more than a century, the National Institutes of Health has played an important role in improving the health of the nation. The NIH traces its roots to 1887 with the creation of the Laboratory of Hygiene at the Marine Hospital in Staten Island, NY.

NIH is the steward of medical and behavioral research for the Nation. Its mission is science in pursuit of fundamental knowledge about the nature and behavior of living systems and the application of that knowledge to extend healthy life and reduce the burdens of illness and disability.

About OpenHelix
OpenHelix, LLC, (www.openhelix.com) provides a bioinformatics and genomics search and training portal, giving researchers one place to find and learn how to use resources and databases on the web. The OpenHelix Search portal searches hundreds of resources, tutorial suites and other material to direct researchers to the most relevant resources and OpenHelix training materials for their needs.

Researchers and institutions can save time, budget and staff resources by leveraging a subscription to nearly 100 online tutorial suites available through the portal. More efficient use of the most relevant resources means quicker and more effective research.

Hey folks–if you are working in the NIH system, at any of the campuses, you should now have full access to all of the OpenHelix tutorials.  NIH has taken a subscription to them, and from the NIH Library page you can get the link to OpenHelix.

Or you can go here directly: http://www.openhelix.com/

Once you get there, you have to register once, but then have access to everything.  We think we have all the right IP addresses–but if you think you ought to have access and don’t seem to be in once you’ve registered, let us know. Movies, slides, exercises–all yours to use.

You now have access to the full set of nearly 100 tutorials. Use the search, or browse the lists or categories.

OpenHelix in the news: NIH Taps OpenHelix for ‘Omics Resource Tutorials

Our press release about that: National Institutes of Health subscribes to OpenHelix training portal

PS: we love feedback–feel free to tell us what you think, or would like to see in there, or if you have access issues.

We are going to try a new Friday feature. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. We are going to start posting them in a Friday feature of a list of snippets of information we call “SNPpets” (cute, huh?). So without further ado…

• Nick Loman (of the blog Pathogens: Genes and Genomes) has put together this very handy map of 2nd gen sequencers around the world. Two quick points: a) That’s a lot of data being generated! b) Boston seems to be an epicenter of 2nd gen sequencing. Hat tip: Genetic Future [Trey]
• NIH announces a Genetic Testing Registry. “a public database that researchers, consumers, health care providers, and others can search for information submitted voluntarily by genetic test providers.” [Trey]
• Henry Louis Gates Jr. discovers his Irish roots using personal genomics in “Who’s your Irish Daddy?” (I post this one because I’ve been thinking a lot about ancestry and genetics lately. Will become a post at some point). [Trey]
• NYT discusses consumer genomics.  Conclusion: not ready for prime time.  [Mary]
• Another day, another genome: Sea Hare!  Woot!  {I think….what’s a sea hare?} Anyway, UCSC Genome Browser, now with sea hare!  [Mary]
• This paper was teh buzz of the #bioinformatics tweet-o-sphere the other day: Extracting biology from high-dimensional biological data by John Quackenbush. [Mary]
• Please fill out the ENCODE survey at the UCSC Genome Browser.  Go to a gateway page and you’ll see the highlighted link to take the survey. [Mary]
• The newly signed health care bill has been getting a lot of attention of course, and it seems there are some boons to the biomedical field  both for personalized medicine and increased funding for biomedical research.[Trey]
• NIH extends PubMed database back another year to 1947. [Trey]

I had a Basset Hound growing up. His name was Useless, Useless S. Grunt. Well, actually it was formally Ulysses S. Grant because the US Kennel Club wouldn’t accept Useless S. Grunt as a name as they felt it was too demeaning. Not sure if they felt it was demeaning to the dog or to the president, but that’s neither here nor there is it?

So,you ask, what made me think of that long-passed sweet dog that tripped over it’s too-long ears with it’s too-short legs? It turns out that they found out what genetic cause there was for those short legs in Basset Hounds (and Dachshunds and other breeds).

As NHGRI’s press release states:

In a study published in the advance online edition of the journal Science, the researchers led by NHGRI’s Elaine Ostrander, Ph.D., examined DNA samples from 835 dogs, including 95 with short legs. Their survey of more than 40,000 markers of DNA variation uncovered a genetic signature exclusive to short-legged breeds. Through follow-up DNA sequencing and computational analyses, the researchers determined the dogs’ disproportionately short limbs can be traced to one mutational event in the canine genome – a DNA insertion – that occurred early in the evolution of domestic dogs.

The insertion turns out to be a retrogene, which of course I also find interesting in that I studied retrotransposable elements. Reverse transcriptase has this habit of reverse transcribing RNA into DNA which can get reinserted back into the genome (hence processed pseudogenes of course).

The study is interesting for two reasons (other than because I had a Basset Hound and studied the evolution of retroelements , it gives us a further clue into evolutionary events that lead to large changes in morphology and the role of retrotranscription and it gives us a clue into possible human conditions.

For more about dog genome, you can read our several posts about the dog genome, go to NCBI’s dog genome home site (or UCSC or Ensembl and other browsers) and read the paper (needs a subscription of course, it’s in Science). It’s an interesting read so far (I want to find some time to read it more fully, perhaps Useless doesn’t live up to his name.. he didn’t really even then ).

If you haven’t already seen it, open-access publishing either just made a jump backward or forward. The not-so-open access Springer publisher bought Biomed Central, the open access publisher recently. Open access publishing took a huge leap with the passage of a law last year that requires NIH-funded research to be open access and deposited in PubMed central within 12 months of publication. The law hasn’t not met resistence though. Perhaps Springer saw the writing on the wall, so to speak, and decided that buying BioMed Central was a good move in a world were open-access publishing seems to be gaining ground. Or…?  According the BioMed Central FAQ about the buy, BioMed Central publishing will remain 100% open access.

From Kaisernetwork.org, this web seminar on Wednesday 8/20 1ET (tomorrow):

View a live webcast of the Kaiser Family Foundation’s series, Today’s Topics In Health Disparities, which will discuss the potential of race-based medical solutions for improving healthcare and reducing racial/ethnic health disparities. The webcast will take a closer look at efforts to study the interaction between race, genetics and health.

Panelists will discuss the efforts underway to develop medications to treat diseases that disproportionately affect certain racial and ethnic groups, as well as the benefits and drawbacks of using genetic markers for race in medical decisions. Other topics covered include which genetic factors are being used to personalize medicine and what pharmaceutical companies are doing to target the drugs and treatments they offer to certain groups.

Details about the technology and setup are here: Today’s Topics In Health Disparities – Race and Genetics: The Future of Personalized Medicine

I’m not sure how research-oriented it will be. But if you are interested in the future directions of personal genomics this is an area that might be worth learning more about. A new focus at NIH includes the NICGHD, that we talked about here.

I’m on a lot of mailing lists. We are trying to keep up with software updates on a whole bunch of tools and sites–all of which have their own system, of course. Of course there are a number of science ones–not only bioinformatics/genomics–that we need to be on top of. Then there are the industry news and networking ones–stuff in the industry that I need to follow.

It almost seems too much to show you this, if you are drowning in similar collections of mail. But it really may be useful to find the right group among all the possible ones at the NIH, if you are trying to keep an eye out for announcements in this time of challenging budgets, for example. It may be of use to stay on top of certain project areas. The other day when I was signing up for a new mailing list at NIH I came across this site, called the Lists of Lists. It appears to have a caboodle of mailing lists around the NIH in one collection. I’m not sure it contains all of them–I think there are a couple I’m on that I don’t see. But if you funding area or research topic is represented, it might be worth joining up for announcements or discussions.

The Office of Technology administers the Small Business Innovation Research (SBIR) Program and the Small Business Technology Transfer (STTR) Program to provide funding to small and fledgling biotechnology and genomics businesses. These programs are currently scheduled to sunset in September, but this week an extension is being considered that would take the programs through September 2012, according to the article I just saw in the GenomeWeb News email that I just received. You can read more about the program here.

Now you may be wondering “Who Cares?”…

At OpenHelix, we certainly appreciate DNA! So we wanted to join in the festivities on DNA Day–this year the party is April 25, just about a week from today.

DNA Day commemorates the completion* of the human genome sequencing project. Annually there are special events, teaching and learning opportunities, and sometimes cupcakes**.

We are going to have something to offer, but we aren’t telling what just yet. Be sure to come back on Friday April 25th to see what we have available here. In the meantime, you might enjoy hearing Francis Collins talk about DNA Day. Did you know there will be a national chat room on that day? Or you might consider signing on to the COGE board: the Community of Genetic Educators. There are other ways to get involved–I know the American Society of Human Genetics organizes around this as well.

DNA Day at the NIH: http://www.genome.gov/20519692

ASHG Genetics Education and Outreach: http://genednet.org/pages/k12_mentor.shtml

*yeah, I know. But that’s the way it is told.

**maybe that’s just me. Down the street from me they make the best cupcakes in the world.

NIH announced NICGHD last month. This center’s priority:

“… will be to understand how we can use the tools of genomics to address some of the issues we see with health disparities,” Rotimi said. “The availability of tremendous expertise and the remarkable research infrastructure at NIH will make our research activities more robust and will allow us to tackle questions in ways that were not feasible in the past.”

This is good development. Recent research highlights this disparity

I look forward to see the ways genomics tools can address this. There is more information about this in a recently published book, “Unequal Treatment: Confronting Racial and Ethnic Disparities in Health Care” and podcast with the same name.