Category Archives: General Science

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:

Protip: check the genome of your cell line. HeLa cells are “strikingly aberrant”

This is a paper I’ve been waiting for: the analysis of the HeLa genome. I was aware of a lot of issues with the cell lines and missing or duplicated regions from the ENCODE data that was coming along some time ago: Mining the “big data” is…fascinating. And necessary.

People may be familiar with HeLa cells even if they aren’t in biomedical research because of the great book by Rebecca Skloot: The Immortal Life of Henrietta Lacks which explored the history of these cells and the woman whose terrible cancer led to their existence.

But there were many discussions over the years about how different these cells are from actual tissues, and concerns over how representative they are for actual human research issues. Here are some:

So a new paper has been published that explores this–and it’s at the top of my reading list for later today.

Here’s the paper itself: http://www.g3journal.org/content/early/2013/03/11/g3.113.005777.abstract 

Hat tip Ward Plunet via twitter:
RT @WardPlunet: Havoc in biology’s most-used human cell line: Genome of HeLa cells sequenced for the first time http://t.co/VVpZmiwIiX .

Update: A piece from one of the paper’s authors:

Reference:

Landry JJM, Pyl1 PT, Rausch T, Zichner T, Tekkedil MM, Stütz AM, Jauch A, Aiyar RS, Pau G, Delhomme N, Gagneur J, Korbel JO, Huber W, & Steinmetz LM (2013). The Genomic and Transcriptomic Landscape of a HeLa Cell Line G3 : 10.1534/g3.113.005777

“The Revisionaries” and the Texas Textbook Massacre

I wrote about this film when I saw it at a local festival, but I wanted to alert you (well, the US readers) that it’s going to be shown on PBS soon.

It will be on the Independent Lens show. More here, trailer, etc: http://www.pbs.org/independentlens/revisionaries/

Check your local listings here: http://www.itvs.org/television?film=revisionaries and set your DVR. You have to see how this played out, and watch out for it in your own community.

Here’s the original trailer:

The Revisionaries Trailer from Naked Edge Films on Vimeo.

Hat tip Scott Johnson on G+: https://plus.google.com/u/0/111312280150673387587/posts/TDwJFUT1FoW

Rare photo of me in the wild….

Of downtown Boston, at Tufts Medical Center, singing the praises of IMG and the Integrated Microbial Genomes resources.

I love workshops that only require a trip on the Orange Line.

Today we were doing the World Tour of Genomics Resources. Tomorrow it is UCSC Genome Browser (intro + advanced), and Thursday ENCODE. So if you want to workshop vicariously you can check out all of our tutorials on those. The slides, handouts, and exercises are all over there for you to download if you’d like.

As much as I love the online training and webinars and all, you really do get important information about the needs of folks in the room that you just don’t really get from the intertubz, and I do like to do the material live.