Author Archives: Mary

Friday SNPpets

This week’s SNPpets include the highly topical human migration issues–those that weren’t prohibited by the White House, at least. Speaking of charged issues–the NAS releases the CRISPR-human editing report next week. Also this week–human food crop resources and papers. Quinoa! But one that’s truly key for science is the coffee genome, of course. I’ll bet a disproportionate amount of science world-wide relies on caffeinated grad students. Also: sequencing Filbert. Not the nut. I love crowd-funded genome projects. And I added a nice graphic of clinical mutations that could be useful in public outreach situations. I’m getting more and more interested in doing that.


SNPpets_2Welcome to our Friday feature link collection: SNPpets. 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. Here they are for your enjoyment…


Fired up! Blogging resumes soon.

Mayor Joe Curtatone, Mary Mangan, Oliver Sellers-Garcia, Russell Koty, Christine Andrews.

Mayor Joe Curtatone, Mary Mangan, Oliver Sellers-Garcia, Russell Koty, Christine Andrews.

If you were a regular reader of the blog, you may have noticed the post last summer about my blogging sabbatical. I had volunteered to be the “solar coach” for my community, helping my neighbors to learn more about the possibility of having solar power on their homes. It was a fantastic experience. I did a lot of the same kinds of outreach things that I have been doing in genomics for years: videos, talks, booths, and other educational materials.

I knew it would last past the summer, but I wasn’t sure how busy I would be. I was busy. The program deadline got extended into December. And just recently (I think) we finished up with most of the wrap-up stuff.

The outcome: we got 115 neighbors to sign up, for 568 kW of capacity in our community. And we exceeded our goal, which enabled us to get a 5 kW array to be awarded to a local non-profit organization in our community.

I’m really pleased with this. Since the US elections, it hasn’t been clear how much progress we can make on a green energy future, and in our approach to a changing climate. I don’t regret taking time to do that project, even if it was off the genomics path. It’s something I’ll be very proud to look back on.

Also since the election, we’ve been watching some of the impacts on science and genomics issues. Some of them are unsettling. It’s time to be watchful, and it’s time to speak up on various issues. And we can still celebrate interesting work in genomics, and new tools and new features to keep making progress with new knowledge. More to come.

Zimmer_gameofgenomes

Watch the “Game of Genomes” unfold

Ok, I know I said I was cutting back. But I think this is worth looking for soon. Carl Zimmer explores his own DNA.

Full story via STAT News: Sneak peek: The ‘Game of Genomes’ is coming

From the STAT Newsletter and story:

On Monday, July 11, STAT will publish the first part of a three-part series, “Game of Genomes,” about what I found….

Part two of the series will appear on Monday, July 18, and part three will appear on Monday, July 25

sun_panel_power_noun

Summer blogging sabbatical

Hi folks–just wanted to have a post available to let you know that we haven’t forgotten the blog. But we are going to have a summer blogging sabbatical. Between some vacation time, and a volunteer project I’m on with my city, we’ll be away from the computer for a bit of time, and not necessarily on top of breaking chatter and new tools as we usually try to keep up on for the regular weekly posts. There may be times when there’s something to talk about, and then we’ll post ad hoc.

sun_panel_power_nounThe volunteer project is actually a lot like what we do at OpenHelix, but on a different technology. I’m the “solar coach” for my city–I’m helping our residents learn about solar power for their homes via the Solarize Mass project. We’ll be having educational events, booths at farmer’s markets and festivals, blogging, hopefully an intro video, and I’ll be helping people to connect with information on reducing their greenhouse gas footprint via rooftop solar. So I’m using my transferrable skills in training materials, workshops and conference booths for the environment, rather than for genomics, for a little while. The really busy part of this project is the next couple of months as the project rolls out.

Summer blog traffic is usually lighter anyway.  But in the fall we’ll get back on the regular schedule.

Credit to The Noun Project for some handy graphics I’ll be using for my Solarize talks and blog posts! Check them out for helpful icons.

SNPpets_2

Friday SNPpets

This week’s SNPpets includes some info on the Brexit fallout, at least some good news as it affects EMBL-EBI. The genomes of foodborne illness are being wrangled. A note about HapMap retirement and data access. The PDB tour of proteins is really fun. I thought we were done with single genomes of an organism with a name (like Susie the orang or Cinnamon the cat), but we now have Santander the 1200 year-old olive tree. See also high-throughput screening in plants–and a fitbit for plants in the field. Software citation principles. Genome papers vs genome reports. GTEx resources at UCSC Genome Browser. Also–watch the Galaxy and GMOD meeting hashtags for great stuff.


SNPpets_2Welcome to our Friday feature link collection: SNPpets. 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. Here they are for your enjoyment…


support_MODs

Video Tip of the Week: FlyBase TV, and a letter of support for model organism communities

This week’s video tip was prompted by a couple of things. First, it was a tweet from FlyBase, about their video channel. It’s been a while since we’d done a FlyBase Tip of the Week, so that was enough of a reason.

But it also came just after I was thinking about the importance of the model organisms, based on the campaign by the model organism databases to save their funding. Here’s a tweet from the yeast genome database (SGD) with a plea:

But this letter cites yeast, flies, WormBase, ZFIN, MGI, RGD and Gene Ontology as well.

mergeI have a soft spot for model organisms, not only because of the tremendous amount of great biology they’ve provided. I was a postdoc at The Jackson Lab, and I am acutely aware of how crucial it is to have the depth of the species specialists involved in creating and maintaining the resources that are appropriate for their organism. But it’s more than just institutional knowledge and data, of course. It’s also the importance of the community of researchers working on that organism, supporting them and having their needs met in many ways with species-specific resources.

So this week’s tip highlights some features of the FlyBase tools, as a way to remind folks of the great work that’s going on at model organism databases (MODs).

Now, if you haven’t already done so, please consider signing on to the letter of support for these databases. You can read more about the issue over at the site, but briefly:

NHGRI/NIH has recently advanced a plan in which the MODs will be integrated into a single combined database, along with a 30% reduction in funding for each MOD (see also these Nature and Science news stories). While increased integration will present many advantages, the plan will result in a loss of critical organism-specific datasets. The funding cut will also cripple core functions such as high quality literature curation and genome annotation, degrading the utility of the MODs. Given the large number of scientists that this policy change would affect and the importance of their work, this is a matter of extreme concern.

I have always shouted about the importance of high-quality curation. It’s so undervalued, but it’s only more and more crucial now that we are getting so much sequence data and we need the best existing knowledge to help guide us through it. Now is not the time to cut back on curation.

So if you have valued MOD data and community sites, please consider signing on to the letter of support.

Quick links:

FlyBase:  http://flybase.org/

Support Model Organism Databases letter: http://www.genetics-gsa.org/MODSupport/

References:

Hayden, Erica Check. “Funding for model-organism databases in trouble.” Nature News. () DOI: 10.1038/nature.2016.20134

Kaiser, Jocelyn. “Funding for key data resources in jeopardy.” Science 351.6268 (2016): 14-14. DOI: 10.1126/science.351.6268.14

Attrill, Helen, et al. “FlyBase: establishing a Gene Group resource for Drosophila melanogaster.” Nucleic acids research (2015): gkv1046. DOI: 10.1093/nar/gkv1046

SNPpets_2

Friday SNPpets

This week’s SNPpets have lentils. I love lentils. But also zombies. And a baronet established by DNA sequencing. A need for some CRISPR edting. And the sudden retirement of HapMap. There’s also an attempt to save the model organisms from retirement or zombie-ness. Wormbase/Flybase/ZFIN et al need your signature. I wish signaures could save science from the Brexit as well. But I suspect that’s unlikely.


SNPpets_2Welcome to our Friday feature link collection: SNPpets. 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. Here they are for your enjoyment…


 

genonets_quickstart

Video Tip of the Week: Genonets, exploring genotype-phenotype relationships

Lately I’ve been keeping an eye on a lot of the tools that link individuals with sequence data, their phenotypes, and researchers/physicians who may either study or treat the associated medical issues (see MyGene2 most recently) . But there’s a lot of room upstream of these kinds of patient outcomes to explore genotypes and phenotypes. This week’s Video Tip of the Week is for Genonets, offering “Analysis and Visualization of Genotype Networks”, a tool that can help to explore these relationships for pre-clinical/research scenarios as well.

A recent paper explains the goals behind their tools, and they also have a series of videos on their web site to help you get going with Genonets. I’ll put the intro video here, but be sure to click over to their “Learn Genonets” page for a lot more. There’s also a text-based tutorial you can work through which is helpful.

You can also kick the tires a bit with a sample file that’s available from their search page. Just click the checkbox to load it up and try it out. And then be sure to explore those “deep dives” videos to go further.

Hat tip: 

Quick link:

Genonets: http://ieu-genonets.uzh.ch

Reference:

Khalid, F., Aguilar-Rodríguez, J., Wagner, A., & Payne, J. (2016). Genonets server—a web server for the construction, analysis and visualization of genotype networks Nucleic Acids Research DOI: 10.1093/nar/gkw313

SNPpets_2

Friday SNPpets

This week’s SNPpets have a pretty typical list of both new and updated sites and tools. The wheat genome (not gluten-free). A couple of key bits for folks who are scripting calls to NCBI (need to use https soon), or for folks in Asia who could use a UCSC Genome Browser mirror site closer to their location: http://genome-asia.ucsc.edu/. But my favorite thing this week was the best postdoc ad on twitter evah–see the snake one.


SNPpets_2Welcome to our Friday feature link collection: SNPpets. 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. Here they are for your enjoyment…


https://twitter.com/Sara_and_Snakes/status/742891484064546816

UCSC Genome Bioinformatics

Video Tip of the Week: UCSC Genome Browser Exon-only Mode

The team at UCSC Genome Browser continues to update their resources and offer new ways to find and visualize features of interest to researchers. One of the newer features is the “multi-region” option.  When it was first launched, I did a tip on how to use that, with some of the things that I noticed while I was testing it pre-launch. But now the folks at UCSC have their own video on the exon-only display that you might also find useful.

One of the things that is illustrated here is how the exon-only mode is handy to enhance your exploration of RNA-Seq data. It also uses a great ENCODE data set as an example, and if you haven’t been using that collection it’s a good reminder of the kinds of things you can find in that resource still. And this extensive data set shows how much easier it is to look at different isoforms in the data in this new exon-only mode.

So have a look at this display option if you haven’t before, especially how it can help you to see transcript differences. If you aren’t familiar with the ENCODE data that’s being used, you can also see our training on that which will help you to understand how to use that data and the filtering features that are also used in this video.

Special note: I have updated the UCSC Intro slides to include the new Gateway strategies as well. So download those slides for the latest look. 

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Disclosure: UCSC Genome Browser tutorials are freely available because UCSC sponsors us to do training and outreach on the UCSC Genome Browser.

Quick links:

UCSC Genome Browser: http://genome.ucsc.edu

UCSC Genome Browser training materials: http://openhelix.com/ucsc

ENCODE: http://www.openhelix.com/ENCODE2

References:

Speir, M., Zweig, A., Rosenbloom, K., Raney, B., Paten, B., Nejad, P., Lee, B., Learned, K., Karolchik, D., Hinrichs, A., Heitner, S., Harte, R., Haeussler, M., Guruvadoo, L., Fujita, P., Eisenhart, C., Diekhans, M., Clawson, H., Casper, J., Barber, G., Haussler, D., Kuhn, R., & Kent, W. (2016). The UCSC Genome Browser database: 2016 update Nucleic Acids Research, 44 (D1) DOI: 10.1093/nar/gkv1275

The ENCODE Project Consortium (2012). An integrated encyclopedia of DNA elements in the human genome Nature, 489 (7414), 57-74 DOI: 10.1038/nature11247