Author Archives: Mary

SNPpets_2

Friday SNPpets

This week, DNA was indicted and decades later led to a conviction. Genomes of birch trees and shape-shifting butterflies. And the most interesting stuff to me is non-human, but dbSNP will stop accepting non-human species info. Sigh. Well, I do think alternative splicing is interesting too, and we have some of that this week. Human gene editing, tumors, and various types of personalized genomics were out and about this week as well. It’s not that I dislike humans (all the time), but I’m sort of agnostic on species.


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…


SNPpets_2

Friday SNPpets

This week is a pretty eclectic set of things. Ancestry and African Americans, oral history of genomics researchers, tools for various types of analyses, and another genome that created a caffeine pathway that’s so crucial to me. The most unusual item is probably that Microbiome board game. We live in interesting times.


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 has a duplication event–I was on the road to the March for Science last week, and wasn’t able to post the SNPpets. But I stood for plant science at the march (see photo below). It was raining cats and dogs–and this week the snips also include cat and dog microbiomes. It has the peep genome. And monuments to barley. We touch on humans a bit 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…


https://twitter.com/IHStreet/status/857411838723715072

Newly updated Quick Reference Card

Video Tip of the Week: UCSC Genome Browser in the Cloud (GBIC)

Newly updated Quick Reference CardFor all the years we’ve been out doing training on the UCSC Genome Browser tools, we could watch the evolution of the needs of the researchers and the corresponding features of the UCSC Genome Browser site. At first, people just needed access to the public data. But then they needed ways to add their own data to the public data context and share the views. UCSC gave us custom tracks, and they gave us browser sessions. Woot!

Increasingly, the data sets got bigger and more complex and custom tracks couldn’t handle the volume. UCSC delivered track hubs. Woot!

Some people were telling us that they had patient data that they couldn’t load on to the UCSC site because of privacy and legal issues. Then UCSC delivered GBIB–Genome Browser in a Box. You could download a local copy of the browser and use your own data behind your firewall.

All of these strategies continue to help users combine their own data with the public data and visualize what they want to show. But there’s also another way now–GBIC, Genome Browser in the Cloud. This week’s tip shows you the video the team created to help people to understand what the GBIC can do. There’s additional information about the features that you can see on their announcement, via the mailing list. But just quickly, here’s the nutgraf:

Until now, genomics research groups working with sensitive medical data were largely limited to using local Genome Browser installations to maintain confidentiality, complicating data-sharing among collaborators. Today, the Genome Browser group of the UC Santa Cruz Genomics Institute announced they have changed that by launching a new product, Genome Browser in the Cloud (GBiC). GBiC introduces new freedom to collaborate by allowing rapid Browser installation, in a UNIX-based cloud or UNIX-virtualized cloud.

And here you can have a look at how it works.

In addition, we’ve recently updated our popular Quick Reference Cards, and we added the note that the GBIC can be used to help people work with their own data. You can download those cards, or get some printed ones, from our website. These cards have had to keep evolving over the years to keep up with all the important features that UCSC adds regularly.

Try out the GBIC with your own data. And they are always looking for feedback on how it suits your needs, or other things you might need. Help them evolve.

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

Reference:
Tyner C, Barber GP, Casper J, Clawson H, Diekhans M, Eisenhart C, Fischer CM, Gibson D, Navarro Gonzalez J, Guruvadoo L, Haeussler M, Heitner S, Hinrichs AS, Karolchik D, Lee BT, Lee CM, Nejad P, Raney BJ, Rosenbloom KR, Speir ML, Villarreal C, Vivian J, Zweig AS, Haussler D, Kuhn RM, and Kent WJ. The UCSC Genome Browser database: 2017 update. Nucleic Acids Res. 2016 Nov 29;. PMID: 27899642; PMC: PMC5210591.

Friday SNPpets

This week was includes quite a range of species–from maize to mammoths to microbiome samples around the world. Also time travel–genome assembly in ancient samples. There’s also helpful stuff on the role of genetic counselors, and a guide on when researchers should enjoy chocolate (which may be relevant to some of you this Easter weekend).


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 was a busy and diverse week. From Bioinformatics as an Amusement Park, to the very serious FDA approval of 23andMe’s reports. From Lenski’s April Fool’s post to cancer databases. From diagnosing children with genomics details, to CRISPR sci-fi. We live in interesting times. But at least now we will be able to see everybody citing everybody else.


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…


Video Tip of the Week: Neandertal Inheritance and Consequences

Ok, it’s been a while since this was a regular feature. But I am still finding that I want to show some videos of science topics and software tools sometimes. So it may not be a regular feature, but I will be highlighting some videos that seem interesting to me for various reasons.

This video struck me because I recently gave a talk about the information from ancestral genomes and the influence of the DNA on us today (as well as how we visualize that). They use software that we’ve talked about before, PolyPhen and SIFT, in this analysis. And it would have been handy to have this as a resources to give out to the audience members, who were general public folks in a pub. I am impressed that a research team did this additional step of explaining their research in this way.

Reference:

Dannemann, M., Prüfer, K., Wagner, A., & Kelso, J. (2017). Functional implications of Neandertal introgression in modern humans Genome Biology 18:61. DOI: 10.1186/s13059-017-1181-7

Friday SNPpets

This week’s tips offer some software, including a pre-print from one of my favorite groups–the folks who do great visualizations of sets. I have talked about UpSet before, but now there’s an R package for it. Speaking of great visuals, check out the sponge-microbe symbiosis. And 10 legume genomes. Cannabis as a gateway to plant genomics. And a story of entrepreneurship, and how it ends.

And for kicks, there’s a video that I helped to script-edit that’s been popular: Are GMOs Good or Bad?


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 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