Tag Archives: microbiome

SNPpets_2

Friday SNPpets

This week was big on #CRISPR stuff. That drama about the off-target alterations, and the pushback, consumed much oxygen. But there’s plenty of the usual stuff too–new software, personalized medicine marches on, DTC genetic testing issues, new samples from ancient sources. Best thing: the script to convert fastq to emojis.

Oh–I’m off next week because I’ll be on the road without much chance to capture the tweets with my butterfly net.


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…


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…


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…


Video Tip of the Week: Microbiome Resources From JGI


Just over a month ago an issue of Nature had two articles from the Human Microbiome Project Consortium – you may have seen them, or noticed the Friday SNPets items we had on them. I promised myself that I’d read the articles (which I did), and that I’d visit my old friends the IMG (Integrated Microbial Genomes) & IMG/M (IMG with Microbiome Samples) to see what is new at these powerful microbial genome resources. In today’s tip I decided to take you along on my visit with me, because I found that IMG now has a resource dedicated to the analysis of genomes related to the Human Microbiome Project called the Integrated Microbial Genomes-Human Microbiome Project, or IMG/HMP. We visit both IMG/M (briefly) and the IMG/HMP in today’s tip.

When I referred to IMG as an old friend, I really do feel that way – our tutorial on IMG* was one of my first projects for OpenHelix. I was new, and IMG was new, having been released in March of 2005, only a few months before I created our tutorial (on their June 2005 release, if I am remembering correctly). They have grown into such an extensive, powerful resource. To give you an idea of how fast they have grown & developed, our current IMG tutorial is version 12 and I’ll be working on version 13 as soon as I finish updating our SGD tutorial. When we first created our IMG/M tutorial*, metagenomes were a relatively new concept and the resource included a total of 24 microbiome samples – now it has over 1000!

But enough with the nostalgia, let’s get to the resources! :) IMG/M integrates metagenome data with isolate microbial genome sequences from the integrated microbial genome (IMG) system to enable the analysis of phylogenetic composition and functional or metabolic potential of the aggregate genomes (metagenomes) in microbial communities (microbiomes). Genomes generated as part of the Human Microbiome Project (HMP) are included into IMG/M from RefSeq via IMG. IMG/M resources allow users analyze metagenomes, genomes, genes and functions by making lists of items and then manipulating them in “analysis carts”. Metagenomes can also be analyzed using the tools provided from their ‘Metagenome Details’ page. These options are explained in much more detail than I can cover here in the IMG/M reference that I site below. I also link to the most recent IMG publication, since an understanding of it is essential to understand any IMG/M-based resource.

* OpenHelix tutorial for this resource available for individual purchase or through a subscription.

Quick Links:
Integrated Microbial Genomes (IMG): http://img.jgi.doe.gov/cgi-bin/pub/main.cgi

Integrated Microbial Genomes with Microbiomes (IMG/M): http://img.jgi.doe.gov/cgi-bin/m/main.cgi

Integrated Microbial Genomes-Human Microbiome Project (IMG/HMP): http://www.hmpdacc-resources.org/imgm_hmp/

OpenHelix Introductory Tutorial on IMG: http://www.openhelix.com/cgi/tutorialInfo.cgi?id=54

OpenHelix Introductory Tutorial on IMG/M: http://www.openhelix.com/cgi/tutorialInfo.cgi?id=24

References:
Victor M. Markowitz, I-Min A. Chen, Ken Chu, Ernest Szeto, Krishna Palaniappan, Yuri Grechkin, Anna Ratner, Biju Jacob, Amrita Pati, Marcel Huntemann, Konstantinos Liolios, Ioanna Pagani, Iain Anderson, Konstantinos Mavromatis, Natalia N. Ivanova, & Nikos C. Kyrpides (2012).
IMG/M: the integrated metagenome data management and comparative analysis system Nucl. Acids Res. , 40 DOI: 10.1093/nar/gkr975

Victor M. Markowitz1, I-Min A. Chen, Krishna Palaniappan, Ken Chu, Ernest Szeto, Yuri Grechkin, Anna Ratner, Biju Jacob, Jinghua Huang, Peter Williams, Marcel Huntemann, Iain Anderson, Konstantinos Mavromatis, Natalia N. Ivanova, & Nikos C. Kyrpides (2012). IMG: the integrated microbial genomes database and comparative analysis system Nucl. Acids Res., 40 DOI: 10.1093/nar/gkr1044

Friday SNPpets

Welcome 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…

Metagenomes in Nature

Nature had a nice feature on metagenomics last week and another on the Human microbiome metagenomics. You’ll need to have a subscription to access those :(, but the gist of the latter news feature is the possibilities of Human microbiome research, pros and cons and the projects out there. There are a lot. In order of amount of funding they are:

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