jm + genomics   6

Crumlin hospital sent DNA off without consent
a company called WuXi NextCODE owning the genome data for a large part of Ireland's population is very cyberpunk
wuxi-nextcode  genomics  genomes  data-privacy  privacy  crumlin-hospital  genes  ireland  gdpr 
25 days ago by jm
Building a Regex Search Engine for DNA | Hacker News
The original post is pretty mediocre -- a search engine which handles a corpus of "thousands" of plasmids from "a scientist's personal library", and which doesn't handle fuzzy matches? I think that's called grep -- but the HN comments are good
grep  regular-expressions  hacker-news  strings  dna  genomics  search  elasticsearch 
april 2016 by jm
The impact of Docker containers on the performance of genomic pipelines [PeerJ]
In this paper, we have assessed the impact of Docker containers technology on the performance of genomic pipelines, showing that container “virtualization” has a negligible overhead on pipeline performance when it is composed of medium/long running tasks, which is the most common scenario in computational genomic pipelines.

Interestingly for these tasks the observed standard deviation is smaller when running with Docker. This suggests that the execution with containers is more “homogeneous,” presumably due to the isolation provided by the container environment.

The performance degradation is more significant for pipelines where most of the tasks have a fine or very fine granularity (a few seconds or milliseconds). In this case, the container instantiation time, though small, cannot be ignored and produces a perceptible loss of performance.
performance  docker  ops  genomics  papers 
november 2015 by jm
Can we have medical privacy, cloud computing and genomics all at the same time?
Today sees the publication of a report I [Ross Anderson] helped to write for the Nuffield Bioethics Council on what happens to medical ethics in a world of cloud-based medical records and pervasive genomics.

As the information we gave to our doctors in private to help them treat us is now collected and treated as an industrial raw material, there has been scandal after scandal. From failures of anonymisation through unethical sales to the care.data catastrophe, things just seem to get worse. Where is it all going, and what must a medical data user do to behave ethically?

We put forward four principles. First, respect persons; do not treat their confidential data like were coal or bauxite. Second, respect established human-rights and data-protection law, rather than trying to find ways round it. Third, consult people who’ll be affected or who have morally relevant interests. And fourth, tell them what you’ve done – including errors and security breaches.
ethics  medicine  health  data  care.data  privacy  healthcare  ross-anderson  genomics  data-protection  human-rights 
february 2015 by jm
How I decoded the human genome - Salon.com
classic long-read article from John Sundman: 'We are becoming the masters of our own DNA. But does that give us the right to decide that my children should never have been born?' part two at http://www.salon.com/2003/10/22/genome_two/
human  genome  genomics  eugenics  politics  life  john-sundman  disability  health  dna  medicine  salon  long-reads  children 
may 2013 by jm

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