Category Archives: SNPpets

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Friday SNPpets

This week’s SNPpets include a variety of things–some the usual hard science, some were clever strategies to engage in softer ways. We also had genomics diagnostics and a roadmap to the clinic. Genes and developmental delays. Animal models for mechanisms, not for target discovery. There was a fun #DNADay16 talk about the genetics of Wizarding, using Harry Potter characters as the pedigrees. Metagenomics pizza. Also this week, the first time I saw news first “reported on github”.


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 a range of tools and genomics studies, from microbial to planaria to salmon to humans, as usual–as well as some that are species-agnostic.  Also stuff that is aimed at drug targets and pharmacology, including the Open Targets project Target Validation Platform. There’s a new DNA privacy bill under discussion in the US that I found interesting. Also–next Monday April 25 is #DNADay! Participate in community outreach with a number of strategies.


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…


 

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Friday SNPpets

This week’s SNPpets includea number of things about costs. The costs of sequencing–scaling computation, but also an offer for a free Galaxy server. The other thing is the cost of maintaining resources. BioCyc notified users that it can’t get funded to make the resources available to the public anymore. Some projects seek votes or crowds for funding. Some orphan genomes sit around waiting for analysis. Alas. The other things include new tools or updates which apparently have funding currently. Best idea this week: a “Dear Abby” style place for patient questions on genomics.


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…


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Friday SNPpets

This week’s SNPpets include something unusual: bioinformatics software becoming a mainstream discussion. A recent NYT piece about Zika genomics included a Bandage software-based illustrations, and a subsequent explainer piece in SciAm covered it. Zika was big this week. Of course, we covered Bandage months ago…. A reprise and riff of Tardigate was good reading. Also this week: GBrowse for peanut, FireBrowse for the Broad, updates to GeneMania, Galaxy record hit, and the opposite of update: UCSC Genome Browser in ASCII. Impersonal genomics made me laugh.


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…


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Friday SNPpets

This week’s SNPpets include items just posted to bioRxiv–which is lately where I see all the really intriguing tools. Including the awesomely-named “Clusterflock”. In a popular related item, someone responds to the Biostar question, “why are there errors in bioinformatics software?”. We have bat and bean genomics. And conch and lobster DNA. There’s at least 2 efforts to coordinate/wrangle human public genomes. And more.


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…


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Friday SNPpets

fluorsThis week’s SNPpets include “The Internet of Living Things” with portable sequencers; a collection of Galaxy tours; challenges of clinical sequencing and diagnostics; more biocuration; new and updated tools as usual. Russ Altman’s annual favorite translational bioinformatics papers piece is always great fun. Most fun image in a while, though: phylogeny of fluorescent proteins, made with the proteins. Gotta see 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…


SNPpets_2

Friday SNPpets

This week’s SNPpets include the best MTA evah, my current new favorite name for a bioinformatics tool (Goldilocks), a project that will sequence every member of a species (Kakapo), a gnome, marijuana landraces, and more. PulseNet celebrates an anniversary–and proves itself to be a cost-effective and health improving resource. More good stuff–new tools and data, and a terrific effort by the MacArthur lab to support reproducibility. Check it out.


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…


 

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Friday SNPpets

This week’s SNPpets include new and updated resources, the CRISPR zoo,  jokes, and even a job opportunity. But if there’s one thing to read this week, it’s the last tweet. It’s a sad story of what went wrong with a young patient’s sequencing results. This week I was talking about how curation of quality information matters for patient treatments as we move further with personalized medicine. This illustrates exactly why.


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…


 

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Friday SNPpets

This week’s SNPpets include dog OCD genes, salmon SNPs, a tutorial on learning R from scratch, new ways to examine VCF files, 185 organisms RNA-seq data, and the news of the upcoming deprecation of GI numbers at NCBI. The two things that caught my attention the most this week, though, was the human knockout data, and coincidentally some interesting thoughts about how genetic counseling needs to be adapting to the volumes and types of information we are getting now. And the fact that a lot of it is coming from non-medical routes, like ancestry hobbyists. And 23andMe at Walgreens?


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’s SNPpets include a popular slide deck that illustrates roads that go to bioinformatics; questions of what to do with your own genome data (assuming you aren’t a PhD in bioinformatics); fast identification of bacterial strains with StrainSeeker; and the epigenomic landscape of prokaryotes;  the ancestors of cultivated peanuts sequenced; a cancer tool with proteomics coactivation pairs; very cool detailed visualization of tissue-level data that offers new insights; and microbiomes abound.


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…