Tag Archives: nih

Video Tip of the Week: NIH 3D Print Exchange

The other day I was joking about how I was 3D-printing a baby sweater–the old way, with yarn and knitting needles. And I also mentioned that I assumed my niece-in-law was 3D-printing the baby separately. I’ve been musing (and reading) about 3D printing a lot lately–sometimes the plastic model part, sometimes the bioprinting of tissues part. So when I came across this new NIH 3D Print Exchange information, it seemed worthy of highlighting.

Although I haven’t had access to a 3D printer setup yet (although I’m planning to take a course soon at the local Artisan Asylum), I’ve been seeing quite a bit of chatter about it. Some folks are designing gel combs (rather than paying ridiculous catalog prices). Some folks print skulls and other bones. There is so much opportunity for a wide range of helpful scientific applications across many fields that it seems an introduction to this topic would be wise for a lot of folks.

So when someone pointed me to the 3D printing initiative at NIH, I was hooked. The public announcement and site launch was in mid-June, according to their blog and press release. I was catching up by reading other items on their site, including some press coverage that provides context for this and other government initiatives on 3D printing. Make Magazine’s piece “The Scramble To Build Thingiverse.gov is On!” notes that the Smithsonian and NASA also have projects underway. But for me, molecules in 3D are what I’m most interested in, so I’ll focus on this NIH version below.

An intro video provides an overview of the kinds of things that will be available on their site. But there’s also a YouTube channel with more.

At the site now you will find a number of ways to get started. At the “Share” navigation area you will find already there is a section for custom lab gear, anatomical stuff, and biological structures and even some organisms. So if you have models to share, you can load ‘em up. With the “Create” space you can quickly generate some items with a handy quick start feature. Because I’m fascinated with the beautiful structures of hemolysins (have you seen these things?) I picked one out, entered a PDB ID, and within a half hour I was notified that the printable model was available to me–and you can see it here. But you can build your own from scratch as well, of course. There are other tutorials that will help you get some foundations in place.

Hemolysin 3D printable modelOr you can look around–from the “Discover” page you can browse or search for examples of models people have done. At this time, there are 347 (including the one I just did yesterday). But there will be more. I want to get mine printed up, and then see some other proteins too.

Ok, so it’s not like I made a kidney or something (although we know that day is coming). Being able to think about the 3D printing process, file types, and various options are probably worth noodling on. Getting your feet wet with a little protein structure or organelle might be a good way to get started. Check it out, and start thinking in other dimensions.

Quick links:

NIH 3D Print Exchange: http://3dprint.nih.gov/

Hemolysin for image: http://www.pdb.org/pdb/explore/explore.do?structureId=3B07

Model Generated for hemolysin from PDB record: http://3dprint.nih.gov/discover/3dpx-000579

Murphy S.V. (2014). 3D bioprinting of tissues and organs, Nature Biotechnology, 32 (8) 773-785. DOI: http://dx.doi.org/10.1038/nbt.2958

[update]Tip of the Week: A Lapse in Appropriations, Some Affects on Research

nsfclosed[to keep abreast of the effect on research, this from is a good article from Science Careers, see below for more links and information]. Forgive me as I create a lapse in our weekly tips and instead give one ‘insider’s’ view of the shutdown (or lapse in appropriations in official parlance). This most definitely not a full understanding of how the government shutdown will effect you as a researcher, educator or student, but hopefully will give you an idea.

As many readers know, I am currently on a temporary leave from OpenHelix to work at the National Science Foundation. Though on leave, I still write Tips (among other activities) for the blog. My turn was today. Unfortunately, yesterday the government shut down and though it did, it took a lot of the day to prepare for an ‘orderly shutdown.’  We were given a large portion of the day to shut down operations. That was an intense time of emails, calls and preparations. We had to leave the office by 1:30pm. (unfortunately for me my home computer seized up in it’s own version of a shutdown the day before). So that you, our readers, may get an idea of the affect of the shutdown on NSF and research in general, allow me to relate my experience and some of the affects the shutdown will have on research and possibly you.

My work at NSF (and AAAS), for the most part, entails working on programs to broaden participation in science education. Among other activities, I organize working meetings to explore the research in the topic and develop and run a science engagement project for refugee youth.

As part of the shutdown, NSF shut it’s doors. This is pretty much a complete shut down. All NSF employees were told they had till 1:30pm to complete an “orderly shutdown” of all activities. For me this included emailing all the PIs and educators attending a meeting next week here at NSF about computer science education for those with disabilities and others that I am working with on other projects. By federal rules, no NSF employee, fellow or other staff is allowed to access email, respond to communications, work on any and all NSF-related activities, travel to conferences or meetings or otherwise conduct any business. The violation of this is a large fine.

What does that mean for those who have funding or dealings with NSF? If you have no immediate work or need to contact an NSF employee, than the effect will be minimal if the shutdown is short. If you need to submit a grant proposal, talk to a grant officer or have an NSF meeting to attend or any other business with NSF within the next few days (or as long as the shutdown lasts) you will be unable to do so. All activities have ceased. If there is an NSF meeting that takes place during the shutdown, it is canceled.

For example, I have been planning and organizing a meeting here at NSF for educators in computer science for persons with disabilities. It has entailed everything from getting rooms settled to setting agendas to choosing reviewers to procuring ASL interpreters and translating documents into Braille. If the shutdown continues into next week, that meeting will be canceled  and all attendees will be unable to come. So, in my case, if the shutdown lasted into the next week, this even would be canceled, the researchers and educators (about 20) attending will have to cancel their flights and plans and all arrangements will be for naught. Obviously this will have some costs from lost flights and plans, but it will also mean that hundreds of man hours of past work will be wasted.

If you have a current award, there should be little impact in the short term, but no new solicitations will be made, grants will not be allowed to be submitted, etc. As the homepage now says:

No new funding opportunities (program descriptions, announcements or solicitations) will be issuedFastLane proposal preparation and submission will be unavailable.Grants.gov may be up and running, however, since FastLane will not be operating, proposal downloads from Grants.govwill not take place. Therefore proposals will not be checked for compliance with NSF proposal preparation requirements or processed until normal operations are allowed to resume.”

The National Institutes of Health will also shutdown though the impact will be somewhat different. Since NIH is a research institution in addition to be a granting one (NSF is a granting institution), all research at NIH will cease. Universities will feel little short term affect as one of the three granting cycles just completed. That said, October 5th is the next round of deadlines and if the shut down continues past that date, no grant applications will be accepted. A short shutdown will only delay the processing of those grants for up to a month, the longer the delay the more exponentially delayed the process will become because of backlogs.

There are other effects on the shutdown on researchers also. Visa sponsorships or requests from visiting scientists will not be issued during the shutdown and some activities will be postponed or cease. Another example from my own work is the science engagement program I run for refugee youth. Though not funded through NSF, it is something I do under my fellowship and thus I am not allowed to work on it. THis means the program will be halted until further notice and the students will not be able to participate in the activities they’ve been very excited to do.

So, let’s reiterate the top 10 effects on research the shutdown will have:

10. NSF, NIH and other agency websites and information will be unavailable or affected. Many databases such as PubMed will not be updated or maintained.
9. Visas for visiting scientists to the US or scientists collaborating overseas will not be processed.
8. Payments of student loans and stipends might be slowed or otherwise affected in the long term.
7. NIH, NSF and other agency-hosted meetings and discussions will cease.
6. New grants proposals will not be accepted, processed or reviewed.
5. Contractors and businesses that rely on NSF, NIH and other research and granting institutions will receive no business and payments will be delayed.
4. Government employed researchers, grant officers and staff (at NIH and NSF among other agencies) will not be paid.
3. Government employed researchers, grant officers and staff will not be allowed to work or contribute to any and all meetings, work-related activities or communications.
2. Research at NIH (and some other agencies such as Energy’s ARPA-E) will cease.

and the number one affect (at least in the sadness factor)
1. Children with cancer will be turn away at NIH.

Do you know of an effect missed here? Comment!

An article from ThinkProgress about some other effects on science and research including other agencies such as NOAA, etc.

A long Reddit discussion from scientists  (with some good pointers and not-so-good stories) about the effects.

Don’t worry, the lapse in a video tip will not be long as the shutdown. I have a lot of time today :D , so will be doing one for later.

Video Tip of the Week: Biological Sequence Analysis I @ NIH

Well, more than a tip, a lecture. We haven’t done a tip today, we are in grant application process (time limiting) and this is an excellent video we’d like for more to see. Mary posted the first lecture, The Genomic Landscape circa 2012, in a series given at NIH. As the course description mentions, “The lectures are geared at the level of first year graduate students, are practical in nature, and are intended for a diverse audience.” Having watch the first and seeing most of this second, I’d say this is for 1st year graduate students and research scientists who are delving more into genomics and bioinformatics. You can view the course syllabus here and learn more about the course and topics.

Today, the second lecture in the series is up on GenomeTV and the lecture list entitled “Biological Sequence Analysis I”:

In this video he goes through the basics of sequence alignment, discussing such topics as similarity vs. homology, global vs. local alignments, scoring matrices, blast and blah. The introduction is pretty straightforward and excellent for those just starting out and for review for those of us who know these concepts but need refreshing.

It’s 90 minutes long, and worth every minute.

Quick Links:

Course page http://www.genome.gov/12514288

Direct link to YouTube for this lecture: http://www.youtube.com/watch?v=Ud_6VpX5AgI


Green, E., Guyer, M., Green, E., Guyer, M., Manolio, T., & Peterson, J. (2011). Charting a course for genomic medicine from base pairs to bedside Nature, 470 (7333), 204-213 DOI: 10.1038/nature09764

National Institutes of Health subscribes to OpenHelix training portal

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.

At NIH? You’ve got tutorials!

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.

Friday SNPpets

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” :D (cute, huh?). So without further ado…


nr_Bassett-DachshundI 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 :D).

Open Access Publishing

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.

Race and Genetics: The Future of Personalized Medicine

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.

Lists of Lists. Whoa. You've got mail.

email.jpg 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.