Category Archives: General Science

OpenHelix server move, a bit of downtime Nov 6

Supposedly we are getting a new more energy-efficient server–that’s good news!

Just a quick note to say that our site will be down for some scheduled maintenance at our hosting company for a little while on Wednesday November 6 in the US, Nov 7 in the EU. So if you need to download any slides, do it right now while you are thinking of it….

The server downtime is supposed to be at 2am CET, which is 8pm ET/5pm PT in the US. Or for other locations try this Event Announcer table. We are told it is scheduled for 4 hours, might be less.

If there are any surprises we’ll post that to twitter. Our account there is: @OpenHelix. http://twitter.com/OpenHelix.

 

 

 

 

[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.

The Perfect 46 ≠ Son of GATTACA. Really. I saw it.

Recently when I saw the announcement for the upcoming film The Perfect 46 in an early screening at the Consumer Genetics Conference, I was worried, I admit it. There are plenty of ways that stories about genetic testing and resulting “perfection” can go off the rails. And I say that as someone who has remaining reservations about unresolved issues on this front–privacy, quality, and misuse of information among those concerns. But I also didn’t want to see something that suggested we were creating some kind of dystopian genetic future loaded with global corporate and government conspiracies and such fictions.

So here’s good news: this film is not the Mutant Son of GATTACA.

The film that I’ll describe briefly here (without spoilers) was an early cut–this may not be the final form that goes out (heh, much like this field, actually). And it was in a conference ballroom (with no popcorn) and less-than-ideal projection. But I was really interested in the content and the overall portrayal of the science anyway, not the artistic details, so that’s what I’ll focus on.

The premise of the story is that people in many states now have access to their whole genome sequence data which is stored by the government somehow. Because of this existing data, a company comes in that offers a special type of analysis–it will tell you if you and your partner are good genetic matches and your likelihood of having “perfect” children. biologists_dateThis service is voluntary–and they stress this several times. That was the key to my tolerance on this story. They were not matching random lab specimens together to make a super-genetic-army or Nobel-winners or anything like that. It really was much more reflective of what people can actually do right now in an early, preliminary way (such as 23andMe And Planning For A Healthy Future Together). Of course, there has always been the similar risk of biologists dating too…

And there are real-life examples of partnership matching based on genetics happening right now. In some Jewish communities, a rabbi will perform genetic testing of potential partners: A Community’s Twist on Genetic Tests. And Cyprus has dramatically reduced the incidence of beta thalassemia by testing couples for several decades now. China (with the additional layer of complexity of 1-child rules) is now implementing testing like Cyprus (1). So the foundations are not far-fetched (compared to the space travel assignments in GATTACA, for example).

So this heady start-up company drama rolls along, and happy couples with healthy children result. But things change. And to avoid spoiling the story, I don’t want to go into what happened. But let’s also say it’s not that far-fetched to imagine biotech start-up mental health meltdowns, among other outcomes for the clients. I will only note that as someone who has tested software in this field, version 2.0 gave me chills. And have parents sued for wrong results of testing and other “wrongful birth” situations that created huge anxiety and financial issues for them? Mm hmm.

Various perspectives are provided from people who are gung-ho for this service, to people who are somewhat reluctant to know what their genes might portend, to some who use the word “eugenics”. Some of this is done for dramatic effect of course. But none of them were out of the realm of discussion that already goes on in this arena. Lee Silver (who is associated with GenePeeks) was in front of me during the movie, and stayed with us at the end for a bit of discussion with the director, and he said he has had people raise this issue with him.

The screening room was full of people with intimate knowledge of this field. And there was not one giggle about goofy science, not one groan of horror over some extreme aspect, or any real discomfort that I could tell. I’ve been in screenings with scientists where that wasn’t the case, and I was listening for it. Although Lee did want the director to check the math on a couple of things.

Will the film irritate some practitioners in this field? No doubt. But it seemed to me that all of the issues raised were fair shots at this topic. And there was a real attempt to get the underlying science right to a plausible degree.

So I enjoyed it. It was like looking at a news report some years out–like those ones Carl Zimmer’s been talking about on the Retro Report. And I’m still thinking about it. So it made its point.

Good job Brett Ryan Bonowicz and your team. (PS: I’m sorry I worried you with my earlier post.) And I want to say how much I admire Brett for bringing this rough cut to this audience at the Consumer Genetics Conference. It was the lion’s den–this group could have been really harsh (they aren’t shy) and they are the main target of this movie. It was pretty brave to deliver it directly to them like this. And I think it went pretty well.

Fun trivia fact the director gave is in the chatter afterwards: the actor who plays the CEO of the company, Whit Hertford, also played the young kid in Jurassic Park who argues about velociraptors. Heh.

Film companion site: The Perfect 46 http://www.theperfect46.com/

This is a small, independent film and I have no idea if it will find wider release at some point–I hope it will find its way to some festivals. They did this with some funding from an IndieGoGo campaign, actually. If you want to know a bit more about the film and the goals you can hear Brett talk about it over there in a short video, and you can reach the team by clicking the “Buy” link on the movie companion page to get to their Facebook page. There was some coverage of it at the MIT Technology Review.

EDIT: and just to make the case, someone commented over at the MIT review with this assessment:

perfect46_comment

Update 2: I had to attach this to this post for future reference: Personal-genetics firm denies pursuit of designer babies in patent filing. Yeah, 23andMe.

Reference:
(1) Hvistendahl M. (2013). China Heads Off Deadly Blood Disorder, Science, 340 (6133) 677-678. DOI:

Tip of the Week: Gemini, exploration of genetic variation

You Tube:

This week’s tip of the week is on Gemini which is the acronym for “GENome MINing.” Unlike most of the tips we give every week, this one is a software package. But, it is does use and integrate with many internet databases such as dbSNP, ENCODE, UCSC, ClinVar and KEGG. It’s also a freely available, open source tool and quite a useful software package that gives the researcher the ability to create quite complex queries based on genotypes, inheritance patterns, etc.  The above 12 minute clip is a talk given at a conference that gives a introduction of the science behind the tool.

The abstract from the recent paper from the developers gives a good introduction concerning the functionality of the tool:

Modern DNA sequencing technologies enable geneticists to rapidly identify genetic variation among many human genomes. However, isolating the minority of variants underlying disease remains an important, yet formidable challenge for medical genetics. We have developed GEMINI (GEnome MINIng), a flexible software package for exploring all forms of human genetic variation. Unlike existing tools, GEMINI integrates genetic variation with a diverse and adaptable set of genome annotations (e.g., dbSNP, ENCODE, UCSC, ClinVar, KEGG) into a unified database to facilitate interpretation and data exploration. Whereas other methods provide an inflexible set of variant filters or prioritization methods, GEMINI allows researchers to compose complex queries based on sample genotypes, inheritance patterns, and both pre-installed and custom genome annotations. GEMINI also provides methods for ad hoc queries and data exploration, a simple programming interface for custom analyses that leverage the underlying database, and both command line and graphical tools for common analyses. We demonstrate GEMINI’s utility for exploring variation in personal genomes and family based genetic studies, and illustrate its ability to scale to studies involving thousands of human samples. GEMINI is designed for reproducibility and flexibility and our goal is to provide researchers with a standard framework for medical genomics.

If you’d like to learn more, there is some pretty good documentation of the software package here.

While I’m at it, and totally unrelated except it’s human genomics, there is this slideshare presentation of the ‘current’ state of personal genomics. Current is in quotes because the slideshare is actually from 3 years ago, but there is a lot of good information in there. Anyone know of a more up-to-date slide set or extensive intro to the current state of personal genomics science similar to this?

 

Relevent Links:

GEMINI Software package
dbSNP
ENCODE
UCSC Genome Browser
ClinVar
KEGG

(tutorials are linked below for those tools in bold above)

Relevant Reference:

Paila U, Chapman BA, Kirchner R, & Quinlan AR (2013). GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations. PLoS computational biology, 9 (7) PMID: 23874191

GenoCAD training action shot

Recently we had a training at WashU on the GenoCAD tools that I mentioned before–the ones that are currently the “most viewed” item on figshare: computer-assisted design tools for synthetic biology. And the Peccoud lab has posted a brief report on that session on their blog, with photo of me doing the training:

GenoCAD tutorial at Washington University in St Louis

It was a great opportunity to workshop the new training materials (which you can access over there). We are now making a few tweaks to make the sessions even smoother, and we’ll have the recorded versions up soon.

There’s an opportunity to get this training coming up at the end of July at Tulane if you are there–contact the Peccoud lab for details on that one from their blog.

The GenoCAD site: http://www.genocad.org/

Edit: two opportunities for more GenoCAD training came across twitter yesterday with more details. Just wanted to add them here.

Official Launch of the new Database of Genomic Variants (DGV)

The Database of Genomic Variants (DGV) has been working on a new site for a while. It’s been available as a beta site to get used to it and kick the tires, but now it’s ready for prime time. They are retiring the existing site and moving to the new version.

As a public service announcement, I’ll paste the text of their email notice here. We’ll update our tutorial soon–we like to give new sites a bit of time to work out the bugs, but then we’ll rework our materials as soon as we can.

++++++++++++++

Hello!

We would like to announce the official launch of the new Database of
Genomic Variants! The latest release includes a number of updates and
corrections to the current data, and this completes the transition
from the original (http://projects.tcag.ca/variation) and the Beta
version (http://dgvbeta.tcag.ca/dgv/app/home) to the new Database of
Genomic Variants (http://dgv.tcag.ca/dgv/app/home ).

We will now host only one version of the database, and the original
site will be retired. We will continue to provide a track of the
original DGV data in the genome browser (gbrowse) which will be
searchable and include details from the original variant details
page. Any links from third party sites and software which use the
“VariationID” to point to the original DGV genome browser or
variant details page will be automatically redirected to the
corresponding entry in our new database. This will ensure that all
data (new and old) will be fully available to users.

We will work with the various partners and websites that provide
links to the original data to update the content to reflect the
information available in the new site.

With this final update, we have included a total of 53 studies,
representing all of the fully curated and accessioned versions of the
original studies, in addition to 10 new datasets. There are a number
of changes to the content and format, and we have summarized these in
the newsletter, which is available at
http://dgv.tcag.ca/dgv/docs/201306-DGV_Newsletter.pdf

We have provided additional details in our FAQ and Training Resources
pages including an updated tutorial which can be found at
http://dgv.tcag.ca/dgv/docs/DGV_User_Tutorial.pdf

As always, we appreciate your feedback, and if you have any questions
or concerns please contct us at dgv-contact@sickkids.ca for help and
assistance.

Best regards,

The DGV development team

The Database of Genomic Variants

Tip of the Week: Prezi and other nonlinear presentation methods


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Though not specifically about genomics, today’s tip of the week will hopefully help you find alternative methods for presenting science that might at times work better than a straight linear slidshow presentation. I have a quick intro above to Prezi, but also see Prezi site for Prezi presentations about Prezi use. Prezi (and other similar programs) are not for every presentation, but it does offer an alternative for some times of presentations that would work better in a less linear presentation style than a slide show (wikipedia article). At least it can be a nice change after a slew of slide presentations.. something to grab the audiences’ attention. Of course, like with slide shows you don’t want to get their attention because it’s a bad presentation.

What is a Prezi? (or similar method). Basically, a prezi is somewhere between a slide show and a white board. It’s a canvas that zoomable. That gives it some advantages (and disadvantages) that slide shows don’t have. First, look at some of the best Prezis of 2012 (as decided by Prezi :) to get an idea of what can be done. Here is one on the 2008 election results.

Prezi’s are sharable in the cloud (or private, or semi-private) and you can work in groups to edit them. Also, you can present them online or download a file that allows you to present it without an internet connection. I’ve found that the file has worked for me regardless of OS or computer.

Prezi is free if all you want to do is create, edit and share presentations, but if you want to create private presentations or use your own logo, etc.. it will cost anywhere from 5-13 dollars a month.

There are alternatives to Prezi that are free or open source. I personally like Prezi best, it has the most features and simple to use, but there are some others that are good. My favorite of the alternatives is Impress.js (downloaded software) and the editor Impressionist (can do 3d!). So if you like the idea of a Prezi-like presentation but want a more open alternative, that might be one to try.

Who’s your daddy?

A new article in Slate describes a case of non-paternity unearthed as a result of a 23andme scan.

Who’s Your Daddy?

The perils of personal genomics.

By

I expect a bit of chatter from the genoscenti. I’ll collect responses below if I see them. I agree that the actual studies of non-paternity show values that are all over the map. But I suspect that there are going to be a lot of people affected by this who didn’t see it coming. And many of those stories will be quiet and private, and won’t be widely known. Some will turn into Jerry Springer, perhaps.

But I know of cases where this has already had serious impact, like the woman who was thrown out of her tribe as a result of her DNA test. This is a very heated topic in some circles: Tribal Enrollment and Genetic Testing Resources.

Interesting times.

All I could think of was this: