Tag Archives: personalized medicine

SNPpets_2

Friday SNPpets

This week’s SNPpets have a range of resources–from food crops to public health to personal genomics. Really, it’s touching everything we do now. A resource filling a gap–digenic diseases–was new to me: DIDA.  A nice collection of miRNA resources. And a popular item about NGS can go “horribly wrong”. An awesome FAQ. The final JABBA award. There’s a lot more too–great week for fascinating reads.


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/ACGT_blog/status/696816305945632768

SNPpets_2

Friday SNPpets

This week’s SNPpets explore the past and the future. There’s the effect of climate on human population movements. And a correction to another ancestry paper. We have retro bioinformatics hardware. The creator of the ribbon protein diagrams appears. Top stories from last year, and from this year (so far). And Neil DeGrasse Tyson and Anne Wojcicki on a “future without disease” (oh, please–but that was the headline writer’s fault, the interview isn’t that pollyanna-ish). There’s also the future of genetic discrimination and GINA. And future disease outbreak tools. Have a look.


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 cover a range of issues. Attempting to community-curate bioinformatics tools, a new paper on UCSC Genome Browser‘s features, iPlant now reborn as CyVerse, errors in databases, personalized diagnosis from the UK 100000 Genomes project and the re-launch of their PanelApp, and some new plant tools: AgroPortal and 30 plants going into OrothoDB. Also, read those thesis submissions carefully. There may be an easter egg.


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…


Thanks for joining us

Video Tips of the Week, Annual Review 2015. Part II

As you may know, we’ve been doing these video tips-of-the-week for eight years now. We have completed or collected around 400 little tidbit introductions to various resources through this past year, 2015. At first we had to do all of our own video intros, but as the movie technology became more accessible and more teams made their own, we were able to find a lot more that were done by the resource providers themselves. So we began to collect those as well. At the end of the year we’ve established a sort of holiday tradition: we are doing a summary post to collect them all. If you have missed any of them it’s a great way to have a quick look at what might be useful to your work.

You can see past years’ tips here: 2008 I, 2008 II, 2009 I, 2009 II, 2010 I, 2010 II, 2011 I, 2011 II, 2012 I, 2012 II, 2013 I, 2013 II, 2014 I, 2014 II, 2015 I.

July
July 1: MorphoGraphX, morphogenesis in 4D
July 8: PhenomeCentral
July 15: Introduction to the UCSC Genome Browser
July 22: PathWhiz for graphical appeal and computational readability
July 29: PathWhiz for Pathways, Part II

August
August 5: Araport, Arabidopsis Portal
August 12: World Tour of Genomics Resources, part II
August 19: gene.iobio for genome and variation browsing
August 26: Human Metabolome Database, HMDB

September
September 2: ENCODE Data Coordination Center, phase 3
September 9: UCSC features for ENCODE data utilization
September 16: BANDAGE for visualization of de novo assembly graphs
September 23: UCSC Xena System for functional and cancer genomics
September 30: Global Biotic Interactions database, GloBI

October
October 7: Weave, Web-based Analysis and Visualization Environment
October 14: 100,000 Genomes Project
October 21: PanelApp, from the 100000 Genomes Project
October 28: New Reactome Pathway Portal 3.0

November
November 4: RNACentral, wrangling non-coding RNA for simplifying access
November 11: UCSC Table Browser and Custom Tracks
November 18: Explore Gene Pages at NCBI with Variation and Expression Information
November 25: iDigBio for access to historical specimens and more

December
December 2: KBase, DOE’s Systems Biology Knowledgebase
December 9: Send UCSC Genome Browser sequence to external tools
December 16: Plant Reactome at Gramene
December 23: Video Tips of the Week, Annual Review 2015 (part 1)
December 30: [this post]

SNPpets_2

Friday SNPpets

This week’s SNPpets offer both science and humor. I think people get a little punchy around the holidays/end of semester. There’s software for assembly, a bioinformatics network for African topics, bioethics of gene editing, cancer and personalized medicine,  Dilbert comments on big data and health, interesting tools for open- and evidence-based medicine, microbiome concepts and a metagenomic journey. Most curious thing this week: the mouse poem constructed entirely from paper titles.


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 range of things, from Pardis Sabeti’s recovery from a serious accident to tardigrade genome drama. There are new databases and tools such as the GMO sequence tracker in the EU, to new uses of tools such as Docker, to explore. Reports of a serious BLAST bug. A look at common spreadsheet formatting mistakes and some solutions. It’s not a gene-editing moratorium. 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…


SummitGeneEdit

What’s the Answer? (Dare we edit the human race?) #GeneEditSummit

SummitGeneEditThis week’s question is a biggie. And there’s no answer yet. But that is the topic of the National Academies big event this week, International Summit on Human Gene Editing. I have been glued to this for the whole time and didn’t spend much time looking for questions this week. And I’ll be watching the final day today. You can find the agenda and livestream at that link now, and the recordings will be available later.

A very good summary of the meeting so far came from STAT News today, and that’s where I got the title. So the closest thing you’ll get to an answer right now is that. And you will see that mostly there are just more questions at this point. Hat tip to Tim Caufield.

In that STAT piece, you will also see the reference to Sarah Gray’s powerful moment. It’s less than a minute, but it had me weeping at my desk. I had already heard Sarah and her son’s story on Radiolab. Hat tip to Michelle Meyer for that connection after Sarah’s comment:

In case you missed it, it’s hard to link to exactly where it is in the videos. It doesn’t have a way to get you to a spot like Youtube. So I’ve taken the clip out here. You can link to the full video collection at the National Academies site here. Go to Day 1, Part 3, 2:01:30 for the part with her comment for the best version. I just offer this short screengrab clip because I think that reading her comment doesn’t have the same impact and you should see it. Take a minute.

In case you can’t watch the video, the quote from STAT:

She implored the meeting, “If you have the skills and the knowledge to eliminate these diseases, then frickin’ do it!”

I have nothing to add to that, except to say I stand with Sarah.

Quick links:

Summit site: http://www.nationalacademies.org/gene-editing/Gene-Edit-Summit/index.htm

Agenda document:  http://www.nationalacademies.org/cs/groups/genesite/documents/webpage/gene_168809.pdf

Reference on the summit:
Reardon, S. (2015). Human-genome editing summit to sample global attitudes Nature DOI: 10.1038/nature.2015.18879

SNPpets_2

Friday SNPpets

This week’s SNPpets include transcription factor binding site evolution–with their secret partners transposable elements; PrecisionFDA coming along; bad habits of bioinformaticians; new synthetic biology tools and rock star status; consumer reluctance to share their health data; Russian genomes on the way. And more, including the XKCD on DNA in case you missed it.


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 lot of back-and-forth on the artist formerly known as personal genomics (now personalized medicine). We got the EU mucking up access, we have privacy issues unearthed, we have the cost of variant calling–and the uncounted cost of other analyses. But we also have the importance of genome sharing. There’s a follow-up story on the kid who was the “first child saved by genome sequencing”. Also some cool research on “essential” human genes. New databases or updates, as usual (dbGaP is one I need to go deeper on). 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…


 

SNPpets_2

Friday SNPpets

This week’s SNPpets include bringing pharmacogenomics to the clinic, de novo assembly with long reads, a good example of using BioGPS, iDNA (it’s not what you think), places for women in science, law enforcement poking around consumer genomics sites, analysis of consumer sites, a neuroscience vs genetics smackdown begins, a new pathway tool, and a new citation metric. 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…


http://questiongene.com/baming-with-bacteriophage/ [need tweet here]