D-genies Github

[Giorgio Aguilar]

Just wanted to share this in case this is of interest or of any help to anyone here. (My family member had PD, I am not currently diagnosed with it; I'd been gathering info on his behalf here in the past.)Recently I watched a podcast with Bryan Johnson, a billionaire who is aiming to reverse his biological age ... a biohacker. Controversial figure, but he's very systematic and dedicated in his approach. Basically he says he lets the data speak for itself in determining his diet, supplements, exercise, to try to stave off effects of aging.

I myself have tried many supplements ... very trial and error ... but in the spirit of "let the data speak," I finally decided to use data from a 23andme genetic test I'd taken years ago and just got a nutrigenomic test done (Nutrahacker; there are others).

I found I have MTHFR variants and slow COMT, among other things, and neurotransmitter levels, ability for liver to detox, glucose metabolism, etc., etc. Certain supplements were recommended, some were contraindicated to help influence genetic expression positively. Found I was taking some things I should actively avoid. It was eye opening. One can say a supplement or food is healthy, but it may really depend on genotype.

Anyway, such testing might be a helpful point of reference. One can upload raw data from 23andme or Ancestry, etc. Genetic Genie doesn't give suppement recommendations but it offers metabolic and detox profile reports (free for now).

Also-- If you're eligible, the PD GENEration will analyze your genome for Parkinson's variants for free. The under-$300 consumer genetic tests do not sequence one of the important PD genes (GBA) correctly, but the PD GENEration project does.

For the GBA gene, if you have a whole genome sequence (WGS) like Dante or Nebula, you can try running your data through Gauchian. Gauchian is a GitHub program that uses statistics to try to correctly identify GBA mutations.

Excellent, thanks so much for these details in this very informative reply. I'm in Canada and I gather the PD GENEration is only in the U.S. However, I was starting to consider any possible covered genetic testing/counselling for PD where I am in Canada and found two local hospitals that do this, if I'm eligible, but I need to be referred by my doctor. And I was considering WGS but prefer free testing if available.

I think you're better off with the official targeted tests if they are covered. 30x WGS can't read the GBA gene correctly-- during processing , many of the GBA gene fragments are mapped to the GBAP1 gene and vice versa. The genes are nearly identical, but they have different functions.

Researchers have addressed the WGS problem in this paper: nature.com/articles/s42003-..., and they developed a python program called Gauchian: github.com/Illumina/Gauchian. If you are tech savvy you can run your BAM or CRAM file through Gauchian, and it will analyze your GBA and GBAP1 genes, and try to determine the "true" values. But a targeted test is going to be more accurate.

thanks for the info. i checked my bam file from sequencing.com. had to convert it (1->chr1) and add an index with samtools. everything negative, just: CN(GBA+GBAP1):4 gensurf, do you know what it means?

For some of my files I had erroneous results from Gauchian when I accidentally tagged the wrong genome build. I knew something was wrong because the .json showed SNPs with "0,0" instead of expected values like "0,28". So be sure to check that everything looks normal there.

I have recently started learning Markdown for use with documentation, and need to print out a few of my Markdown pages. I would like to use a command-line, Terminal, etc. utility that allows me to convert Github-flavored Markdown to PDF. It needs to have proper syntax highlighting and should not look horrible. Thanks for any help.

Take a look at pandoc. It does have syntax highlighting. It might require you making (minor) changes to your document since it has its own flavour of markdown and I don't know how closely it matches the GitHub flavour.

There's an online converter available at
This provides syntax highlighting out of the box and is the simplest solution I've seen so far. It also correctly handles other features specific to GFM e.g. tables.

I'm still looking for a command-line solution which produces results this high-quality [Update: I came up with a pandoc command which uses CSS for formatting, and looks pretty good: pandoc -f gfm -t html5 --metadata pagetitle="test.md" --css github.css test.md -o test.pdf--see my other answer here now!], but:

My preferred technique, because it looks so good, is to use the Markdown Viewer plugin in Chrome. It works really well, and looks surprisingly similar to GitHub markdown! Just open your markdown file in Chrome with this plugin installed and activated, then use the menus to print and save as a PDF right from Chrome.

The above markdown file produces this output directly in my Chrome browser when viewed with the Markdown Viewer plugin installed and on. Notice it has language-aware syntax highlighting for code blocks, nice-looking, greyed code backgrounds, and reasonable column widths for output content.

It supports themes too. See the "GitHub" theme is selected here, for instance. Just click the little m plugin icon in the top right of your Chrome browser to choose Markdown Viewer settings you want:

Contrast this to the output from grip, which I think doesn't look nearly as good. grip doesn't have syntax highlighting for code blocks, greyed background for code, nor reasonable column widths for the output content. On a wide monitor, it takes up the whole width.

NB: neither of mentioned here and on the Internet solutions worked for me: 1) browser-based solutions (i.e. grip) are adding excess info, like page numbers, which I didn't manage to remove, 2) pandoc convertage to pdf is broken, for me it generates an empty table (perhaps because of unicode, and yes, I configured it to use xetex), 3) site based solutions (i.e. gitprint.com) are also adding redundant things, like github-like margins, whereas I need just a simple table I generated with awk!

The Flipper can only generate a limited number of codes in a time period. When the codes are more complex or if you have to try the same code on multiple frequencies(MHz) it will take longer to brute force the code.

Flipper Sub gigahertz radio is capable of 300MHz to 928MHz but some frequencies are locked out for legal reasons based on the country you are in. Check what frequencies are legal in your country because those are the ones you need to focus on.

A weird thing happened when I tried the bruteforce on the garage door. The subghz command I have from copying my actual garage remote says CAME 12bit 433.92mhz, but I tried all the codes and none of them worked. Just on a whim I tried the 868.35 and strangely that did work, though it seems to have sent two signals because the door started to open and then immediately stopped.

The subghz command I have from copying my actual garage remote says CAME 12bit 433.92mhz, but I tried all the codes and none of them worked. Just on a whim I tried the 868.35 and strangely that did work,

It might make the transmitters and receivers easier to produce. An IF mixer could double the frequency. The antenna would not need to be changed because the same antenna would be resonant on both frequencies. Then only software would need to be changed to turn the IF mixer on or off. A simple 1 or 0 in code would be enough.

We have our CB band way down in the 26MHz range. That gives it very different properties. It can skip if the weather is right and go 1000miles easily although in normal conditions 6 miles is more common unless you have a very high antenna.

I was wrong. The thing that worked was the sub that is called CAME_bruteforce_all.sub
But as mentioned, it sends, I think, two signals, so it opens the door but then stops again after a second or so.

Try the 433mhz subs from that gdrive, if it is bitshift 12 bit retro it should work (the 16bit ask one) , otherwise you would want to try a application that is able to do this , there are multiple githubs that offer these applications specifically for things like this including multiple CAME implementations.

Well, the way I was envisioning it was that facilitation would kind of be pull-based, teams ask for a facilitator (and block on the existence of a facilitator) for threads they feel will get contentious. Most threads don't need facilitators. Facilitators can also be called in when stuff has unexpectedly gotten contentious -- this form of defusing has worked in the past -- but ideally it's more proactive than that. Facilitators can also assign themselves to threads they are interested in -- usually threads they feel they have very little opinion on, but are on a topic they wish to see progress on. We can also treat this somewhat like an ops position with early metrics informing facilitators what's going on (@anp has a bunch of ideas on this)

When I was talking to folks there was a lot of interest in filling in this role at least partially -- I feel that a large chunk (if not a majority?) of the community doesn't have strong opinions about most bits of contention on discussions, but often does want to see these things go through and would like to help cut through the bickering smooth the discussion so that it can progress. This role can be designed without a hard time commitment, too, making it easier to be a part of.

That's what I immediately thought of, too : maybe something along the lines of reddit. That's one automatic way to scale well [EDIT] way to help with scaling, but of course the facilitators idea is great. Just my 2 (or 5 or 50) cents.

Because it makes tangents easy and relatively harmless, it also makes tangents more common. Even when it's possible to distinguish the garbage from the gold without having to literally read the entire thing, it still makes the reading experience marginally less pleasant.

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