gabeiscoding

7 ms·

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by gabeiscoding 2mo ago
From WBEZ Chicago, it's This American Life. I'm Ira Glass. Stay with us.
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by gabeiscoding 1y ago
I sunk a lot of time trying to get perfect 1-bit font rendering running under Docker (Debian Linux), but could not get it match the precision of the Mac default Arial font rendering. I have a side-by-side rasterized image showing the differ
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by gabeiscoding 1y ago
Feel free to ask me any questions. I put enough documentation in here to make this an easy to copy with your own hardware.
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Show HN: E-Paper Family 2 Day Calendar(github.com)
6 points by gabeiscoding 1y ago|2 comments
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by gabeiscoding 4y ago
I felt a loss when the On the Metal podcast series wrapped up. I figured these Oxide guys now have too much real work to do, they won’t be able to keep up this podcast, even if it is the best tech podcast I’ve listened to. Bryan is an unbea
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by gabeiscoding 6y ago
I created a desktop GUI tool [0] that used multiple cores for seam carving images of your choice. Including masking parts of image to keep or remove. The backend code parallelizing the work is from the CAIRE project. It was ages ago, and ha
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by gabeiscoding 7y ago
Cool to see this popping up again. It always impresses if you haven't seen it before and is a cool algorithm to work through. The original paper was discussed on slashdot and back at that time I was inspired to build a little GUI aroun
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by gabeiscoding 8y ago
The author of this post wrote klib/khash, and uses it in his very popular cpu-intensive bioinformatics programs such as bwa (short read alignment against the human ref genome). I've been learning rust recently. As a learning exerc
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Comparing rust HashMap to the clever C lib used in bioinformatic tools(github.com)
3 points by gabeiscoding 8y ago|0 comments
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by gabeiscoding 9y ago
A much better source for those with an interest in the science is Chris Mason's slides from his recent talk[1] at genetics conference (AGBT) about this that he shared on twitter[2]. He's a great speaker, and a cool guy and tackles
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by gabeiscoding 9y ago
I wrote a GUI for another seam carving library back in 2009[1], and it looks like although in archive mode, you can still access the source as well as the windows / mac binaries. Just tested it and it still works! Not as fancy as photo
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Direct to Consumer Whole Genome Sequencing with Health/Wellness App(kickstarter.com)
1 points by gabeiscoding 10y ago|0 comments
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by gabeiscoding 11y ago
Looks great, but I can't comment more as I haven't used it. It looks to be solving the same problems as DNAnexus, Seven Bridges, BaseSpace etc as a way to wrap open source tools in more user-friendly ways. But it's orchestrat
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by gabeiscoding 11y ago
While I think it's great to have Google putting their weight behind standardization efforts like Global Alliance for Genomic Health (GA4GH), I really don't get the need to replace VCF and BAM files with API calls. Ultimately, the
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by gabeiscoding 11y ago
They are correct in calling out Illumina's de-facto monopoly rents they are extracting on the market, but sadly I don't share their wildly optimistic view that we are eminent for technological disruption that will re-start the pri
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by gabeiscoding 12y ago
So, what do you want? Just RStudio? Or do you want more utilities that work together and run locally? (i.e. repeatable workflows in project bundles of scripts + data + saved notebook logs etc).
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by gabeiscoding 12y ago
Could you please share some of the 'retrocomputing' podcasts you listen to as well as the app to manage your subscriptions? Sounds fantastic and something I would love to check out.
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I Just Built a New Columnar File Format for Big Data Genomics(blog.goldenhelix.com)
1 points by gabeiscoding 13y ago|0 comments
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by gabeiscoding 14y ago
Nope. It was a Pilot and they are not sure about doing more exomes. From my last chat with Brian Naughton (their lead informatics guy) about this, it sounds like they are planning on doing more sequencing in the future. But it could be whol
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by gabeiscoding 14y ago
Ahh the efficiency argument. The trick is, academics often have excess manpower capacity in the form of grad students and post-docs. Even though personell is usually one of the highest expenses on any given grant, they often don't look at w
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by gabeiscoding 14y ago
They key is 23andMe was not using bleeding-edge nightly builds but official "upgrade-recommended" releases. GATK currently has no concept of a "stable" branch of their repo (Appistry is going to provide quarterly releases in the future, whi
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by gabeiscoding 14y ago
On your first point, my post detailed that 23andMe confirmed it was a GATK bug that introduced the bogus variants and the bug was fixed in the next minor release of the software. There are comments on the post from members of 23andMe and th
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by gabeiscoding 14y ago
If you're interested in Next Generation Sequencing (the new "technology" OP referred to to replace microarrays), I wrote a 3-part series on my blog: "A Hitchhikers Guide to Next Generation Sequencing" Part1: http://blog.goldenhelix.com/?p=
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by gabeiscoding 14y ago
I live in this field, as a computer scientist learning the biology, and trying to make a living with a bootstrapped company. I wrote a post about why GATK - one of the most popular bioinformatic tools in Next Generation Sequencing should no
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by gabeiscoding 14y ago
Very cool, but I fired up an emacs session and hit Ctrl+N to start scrolling through a file.... doh!
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by gabeiscoding 15y ago
Excellent book BTW, would recommend it to anyone interested in the history of not just computing but what we think of as UI/UX. It's almost depressing to see the same problems we keep (re-)solving have had great minds beating on them for qu
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by gabeiscoding 15y ago
My Google offer experience: I turned down a offer from Google last spring. Long story, but my reasons can be summed up as having a more challenging opportunity in a leadership position at a small company versus having to enter the "engineer
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by gabeiscoding 16y ago
Very interesting and ambitious project. A few notes when testing it: - Uses PyQt/RPy and bundles it's own R instance, but the R instance is quite old and people don't usually like having two entire R installs (twice the maintenance of their
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by gabeiscoding 16y ago
I do for my team. As a small business that sells commercial software, I am totally not opposed to paying for good software. I've been watching Fogbugz for a while. Our previous solution was Trac + Subversion for about 5 years and it served
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by gabeiscoding 16y ago
I got this exact same question in a Google on-site interview. It was one of those warm-ups :) It does require someone to think like a C programmer: handling buffers directly, in-place modification and using NULL terminators to end strings t

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