damurdock · HackerTrans

vor 10 Jahrendiscuss

I would recommend talking to a local genetic counselor. They may be able to find a genomics core that will fit your needs, and they will be able to help you interpret that data in a medically relevant way.

damurdock

vor 10 Jahrendiscuss

As a heads up, like the commenter on your blog mentioned, you can write to `/dev/rdisk?` to speed up your transfer. You can also view dd's progress by using pv (available in Homebrew) like: `pv /path/to/image.iso | sudo dd of=/dev/rdisk? bs=?M`

That aside, interesting article. All these new ultra-cheap computers are exciting.

damurdock

vor 10 Jahrendiscuss

FASTR specifically applies to research being published in peer-reviewed journals and specifically excludes:

>classified research, research resulting in works that generate revenue or royalties for authors (such as books) or patentable discoveries, to the extent necessary to protect a copyright or patent

damurdock

vor 10 Jahrendiscuss

damurdock

vor 10 Jahrendiscuss

How was the process of signing up for the PGP? I've been interested in doing it before, but wasn't sure if it would be a major hassle or more of an in-and-out of the doctor thing.

Also I'm impressed at the amount of data, I expected a few VCF files, not a ~60GB BAM.

damurdock

vor 10 Jahrendiscuss

We're still years off from sequencing at home for anyone other than dedicated biohackers. The MinION is really cool, but it's very much an advanced researcher's tool.

Honestly, if you're interested in having your genome sequenced/analyzed, I would suggest contacting a local genetic counselor and asking if they can find a sequencing core (or someone that does beadchips) that would agree to delete your data after analysis. They would also be able to discuss your data and the impact it has on your health with you, and provide referrals if more testing or diagnosis is needed.

damurdock

vor 10 Jahrendiscuss

I think they just care whether or not you're making money with the site period. As in, money that could potentially go towards a paid certificate.

damurdock

vor 11 Jahrendiscuss

Human Genome patents are no longer recognized in the US[0], but my understanding is that they were used to protect genetic tests and treatments. For example, Myriad Genomics held patents against the BRCA genes (which can indicate breast cancer risk) which they used to prevent competitors from creating BRCA-based panels.

[0]: https://www.genomeweb.com/clinical-genomics/us-supreme-court...

damurdock

vor 11 Jahrendiscuss

Human Genome patents are no longer recognized in the United States of America. https://www.genomeweb.com/clinical-genomics/us-supreme-court...

damurdock

vor 11 Jahrendiscuss

Pathogen identification is indeed a very exciting application for NGS. In case you're interested, here[0] is a paper about a tool called SURPI (Sequence-based Ultra-Rapid Pathogen Identification) which was designed for that purpose. Also, here[1] is a case report from the NEJM where SURPI was used to diagnose a patient with Neuroleptospirosis, which allowed him to be treated quickly and eventually recover. SURPI isn't the only horse in this game, of course, but I've worked with it before so it immediately came to mind.

[0]: "A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples" http://genome.cshlp.org/content/24/7/1180.long

[1]: "Actionable Diagnosis of Neuroleptospirosis by Next-Generation Sequencing" http://www.nejm.org/doi/full/10.1056/NEJMoa1401268

damurdock

vor 11 Jahrendiscuss

My family (rural SE US) uses Wildblue (now Exede) satellite internet. It works better than the dial-up alternative surely, but it falls flat in terms of speed, cost, reliability (you must maintain LOS, so rain, tree growth, and sometimes very thick cloud cover will kill it) and latency (~1000ms ping) compared to my mediocre cable plan. There is also a rolling 30-day bandwidth limit. Another common satellite provider is HughesNet, they have similar plans but do data limits differently IIRC. If satellite is your only choice, it's workable, but do check other options.

Another common rural option is a Wireless ISP (WISP), but they have limited coverage so it will entirely depend on where you are. Also check if DSL is available, it's not the most common thing but it can pop up in strange locations.

damurdock

vor 11 Jahrendiscuss

The whole "embedded programming is scary and impossible" sentiment seems to be pretty common these days. I mean, it's impressive, but well within the reach of an interested nation-state or even a skilled hobbyist like Sprite_tm.

It seems like the prevalence of modified router firmwares (and botnets based on them) should make it clear that firmware modification is A Thing That Happens(TM).

damurdock

vor 12 Jahrendiscuss

Digging through the github org a bit:

"The library builds and runs for the Xbox 360, PS3, PS4, nVidia Shield, iOS, Mac OSX, MacOS, Android, OpenWatcom for MSDOS, OpenWatcom for Windows, Visual Studio 2005, Visual Studio 2008, Visual Studio 2010, Visual Studio 2013, Codewarrior for Windows, Codeblocks 13.12 for Windows, Codeblocks 13.12 for MacOSX, OUYA, Nintendo Wii, Nintendo DSi and Linux." - Burgerlib[0]

I don't know why, but I find that immensely satisfying.

[0]: https://github.com/Olde-Skuul/burgerlib

damurdock

vor 12 Jahrendiscuss

Since someone already posted "Spandrels", I'll go with "How Not to be a Bioinformatician" by Manuel Corpas, Segun Fatumo, and Reinhard Schneider[0]. It's a humorous takedown of very common problems in Bioinformatics. I think the point comes across better when you say "if you do X, you are doing poorly" versus "don't do X if you want to do well". Plus, it's a little cathartic.

[0] http://www.scfbm.org/content/7/1/3

damurdock

vor 12 Jahrendiscuss

Does it run in standard VirtualBox?

damurdock

vor 12 Jahrendiscuss

    damurdock$ file /Applications/Google\ Chrome.app/Contents/MacOS/Google\ Chrome 
    /Applications/Google Chrome.app/Contents/MacOS/Google Chrome: Mach-O executable i386
    damurdock$ file /Volumes/Google\ Chrome/Google\ Chrome.app/Contents/MacOS/Google\ Chrome 
    /Volumes/Google Chrome/Google Chrome.app/Contents/MacOS/Google Chrome: Mach-O 64-bit executable x86_64

Top is my currently installed Chrome, bottom is freshly downloaded from Google. Looks like it's time to update!

damurdock

vor 12 Jahrendiscuss

Reddit's programmer subs are pretty nice, although they tend to be inactive for smaller languages/tools/topics.

Do people still use IRC? Where is active these days?

damurdock

vor 12 Jahrendiscuss

Mmm, homebrewed cider...

But seriously, I really like this idea. You should definitely PR this into Homebrew though.

damurdock

vor 12 Jahrendiscuss

Just a side note, there's a software called "Unchecky" that will automatically uncheck most "Free Toolbar!" installs.

But you're right, it's kind of staggering going from "sudo apt-get update && sudo apt-get upgrade" to Windows'... whatever.

Heck, even most programs in OSX will autoupdate, not to mention Homebrew and Homebrew-cask.

damurdock

vor 12 Jahrendiscuss

I'm reminded a bit of http://www.bvp.com/portfolio/antiportfolio, a collection of companies that applied to Bessemer Venture Partners for VC funds, were denied, and went on to make it big.

comments