Author Archives: Mary

Friday SNPpets

This week’s tips contain quite a range of things, from patent battles to drying tardigrades (probably somebody patented this?). I put in the goat genome again because I like goats. We have precision medicine, and mutants asking to not be discriminated against. Some interesting tools this week too.


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…


Friday SNPpets

This week we find that all biology is computational biology. And that coding is missing. And I loved the knitted example of chromosomes–knitting is code. Also, some new misuse of data, and new appropriate uses. Get a fungus mug. Patients are going to be getting data, but nobody in the public knows about it. It’s a secret.


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…


check that one for embedded tweet too

Friday SNPpets

This week I gave a pub talk on the UCSC Genome Browser. It was the first time I’d tried a more general-public version of this. It was huge fun. And it was great timing to have this example of 5000+ samples from autism families to make the case about how hard it is to visualize all this data we are getting. But I also talked about microbes. I even mentioned to goat genome. The benefits and the trip-wires of misuse of personalized data were covered. We touched on restoration of extinct species. So it was a lot like this post, actually…. But I didn’t have the threat to GINA until today. Alas–I would like to have included that. I can’t believe we’re back there.


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…


Friday SNPpets

This week’s list of interesting tidbits is a mix of the promise and the peril. So much data, so much drama on how to move forward with it. But, as our focus is largely software tools, there are some useful tools as well. It’s not obvious from the tweet, but the “Evolving Health Care” article has a nice list of tools at the end.

So, off we go!


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…


Friday SNPpets

This week’s SNPpets include 2 weeks of tidbits. I was at the AAAS meeting last week. It’s not the best meeting for software–but I find myself currently seeking the thoughts of wise people in science communication and science policy on the state of play in the US. I went to so many CRISPR talks, Fake News talks, and media interface talks that I was really CRISPRed out. FYI: you can get a really reduced registration if you will volunteer to do poster judging for a morning. And it’s great to support the students that way. So I did that. A nice experience too.

And the rally in Copley was terrific. Resist.


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…


 

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…