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Mike the Mad Biologist
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- August 31, 2010
- 11:02 AM
- 922 views
The Price of Sequencing Versus the Cost
by Mike in Mike the Mad Biologist
So, Nature Reviews Genetics has an article, "Computational solutions to large-scale data management and analysis", which claims the following in the abstract (italics mine):
Today we can generate hundreds of gigabases of DNA and RNA sequencing data in a week for less than US$5,000. The astonishing rate of data generation by these low-cost, high-throughput technologies in genomics is being matched by that of other technologies, such as real-time imaging and mass spectrometry-based flow cytometry. Success in the life sciences will depend on our ability to properly interpret the large-scale, high-dimensional data sets that are generated by these technologies, which in turn requires us to adopt advances in informatics. Here we discuss how we can master the different types of computational environments that exist -- such as cloud and heterogeneous computing -- to successfully tackle our big data problems.
I've dealt with cloud computing before, but what I want to address is the $5,000 for hundreds of gigabases (that's hundreds of billions of bases; the human genome is about 3 gigbases, times two cuz we're stupid diploids).
So is that $5,000 figure correct?
Yes.
If... Read the rest of this post... | Read the comments on this post...... Read more »
Schadt EE, Linderman MD, Sorenson J, Lee L, & Nolan GP. (2010) Computational solutions to large-scale data management and analysis. Nature reviews. Genetics, 11(9), 647-57. PMID: 20717155
- August 10, 2010
- 11:13 AM
- 858 views
Some Thoughts About the Statistics of the Human Microbiome
by Mike in Mike the Mad Biologist
Reporting on the human microbiome--the microorganisms that live on and in us--is quite the rage these days. As someone who is involved in NIH's Human Microbiome Project, it's a pretty exciting time because the size and scale of the data we're able to generate is unprecedented.
This also means we have to figure out how to not only generate, but also analyze these data. One of the kinds of data we generate are 16S rRNA sequences, which are found in all bacteria and can be used as a 'barcode' to identify and quantify the bacteria in a community without having to culture each species. A recent paper which has received some coverage compared the gut microbiomes (actually, the bacteria found in stool) of children who eat a Western diet with those raised in Burkina Faso who had a fiber-rich diet. The authors found that the two populations had very different compositions of bacteria based on the frequencies--and that last word will become very important--of different bacteria phyla.
While it's an interesting paper, I didn't like how the authors assessed statistically significant differences at all. Read the rest of this post... | Read the comments on this post...... Read more »
De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, Collini S, Pieraccini G, & Lionetti P. (2010) Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proceedings of the National Academy of Sciences of the United States of America. PMID: 20679230
- July 22, 2010
- 10:20 AM
- 792 views
Dogs and Adaption to Humans
by Mike in Mike the Mad Biologist
In a good post about puppy mills, Amanda Marcotte made a good point about domesticated versus undomesticated pets (italics mine):
This would probably mean that people couldn't get exotic pets, and that isn't really the sort of thing that would keep me up at night, either. I understand the urge to have something like a pet ferret, but like with smoking, it's an understandable urge that probably is best not indulged. Cats and dogs evolved to be our pets and want nothing more than to be our pets, thus they are the best choices for pets. They may not love every second of being a pet---going to the vet comes to mind as a moment they don't love---but on the whole, what they want is to be a pet. If you've ever adopted a cat that was feral but is well-socialized, you're probably familiar with how true this is. Even though my cat Molly only spent perhaps the first two months of her life as a feral kitten, she is clearly still haunted by the memory. When we had a backyard, I would let them hang out there under supervision, and while Dusty (who was never feral) was simply happy to go out, Molly wouldn't go out unless I left the door open for her so that she could be assured that she could run back into the condo at any second. She was that afraid of ever going back to non-pet status again. If you want a pet, cats and dogs want to be your pet. It's the simplest relationship in the world, and I see no reason to complicate it by insisting that the humble cats and dogs are too boring to be your pet. Read the rest of this post... | Read the comments on this post...... Read more »
UDELL, M., DOREY, N., & WYNNE, C. (2008) Wolves outperform dogs in following human social cues. Animal Behaviour, 76(6), 1767-1773. DOI: 10.1016/j.anbehav.2008.07.028
Gácsi M, Györi B, Virányi Z, Kubinyi E, Range F, Belényi B, & Miklósi A. (2009) Explaining dog wolf differences in utilizing human pointing gestures: selection for synergistic shifts in the development of some social skills. PloS one, 4(8). PMID: 19714197
- July 13, 2010
- 10:35 AM
- 932 views
MR-CoNS: A Reservoir of Resistance for MRSA?
by Mike in Mike the Mad Biologist
No, MR-CoNS isn't some kind of crazy new conservative, it stands for methicillin resistant coagulase-negative staphylococci. CoNS are relatives of the bacterium Staphylococcus aureus (the 'SA' in MRSA), and are common human commensals--they typically live on us and in us without causing disease.
One of the important things, from a health perspective, about CoNS is that many are resistant to methicillin (methicillin resistance is the "MR" in MRSA). In fact, the resistance mechanism, known as the SCCmec gene cassette, is similar to those found in MRSA (SCCmec is a class of similar, yet genetically distinct genetic elements).
A recent paper looked for CoNS in patients admitted to a French hospital. The findings are disturbing: Read the rest of this post... | Read the comments on this post...... Read more »
Barbier, F., Ruppé, E., Hernandez, D., Lebeaux, D., Francois, P., Felix, B., Desprez, A., Maiga, A., Woerther, P., Gaillard, K.... (2010) Methicillin‐Resistant Coagulase‐Negative Staphylococci in the Community: High Homology of SCCmec IVa between and Major Clones of Methicillin‐Resistant . The Journal of Infectious Diseases, 202(2), 270-281. DOI: 10.1086/653483
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