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  • Sep 22 03:07
    apriha commented #533
  • Sep 21 14:52

    gedankenstuecke on master

    Add link to `snps` library (#53… (compare)

  • Sep 21 14:52
    gedankenstuecke closed #533
  • Sep 21 14:52
    gedankenstuecke commented #533
  • Sep 21 04:58
    apriha opened #533
  • Sep 21 04:52
    Travis apriha/snpr@38f66d2 (add-link-to-snps) passed (1)
  • Jul 28 08:49

    tsujigiri on update-rack

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  • Jul 28 08:49

    tsujigiri on master

    Update rails (#532) (compare)

  • Jul 28 08:49
    tsujigiri closed #532
  • Jul 28 08:21
    tsujigiri opened #532
  • Jul 28 08:20
    Travis openSNP/snpr@8c512ff (update-rack) passed (2327)
  • Jul 28 08:17

    tsujigiri on update-rack

    Update rails (compare)

  • Jul 28 07:13

    tsujigiri on bundler

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  • Jul 28 07:13

    tsujigiri on master

    Bump json from 2.1.0 to 2.3.0 (… (compare)

  • Jul 28 07:13
    tsujigiri closed #531
  • Jul 27 19:42
    Travis openSNP/snpr@67b983c (dependabot/bundler/json-2.3.0) passed (2324)
  • Jul 27 19:38
    dependabot[bot] labeled #531
  • Jul 27 19:38
    dependabot[bot] opened #531
  • Jul 27 19:38

    dependabot[bot] on bundler

    Bump json from 2.1.0 to 2.3.0 … (compare)

  • Jun 25 14:50

    philippbayer on bundler

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Bastian Greshake Tzovaras
@gedankenstuecke
thanks @sinarueeger, doing the update right now :)
and fixed :)
Sina Rüeger
@sinarueeger
Thanks @gedankenstuecke for the quick fix!
Amborella
@Amborella
Hi! I'm new here and not an expert on genetics but if you look at the page for SNP rs187238 it says the genotype frequency for CC is 54%, CG is 39% and GG is 7%. However the article this info is based on here seems to say that GG has frequency 54% and CC has frequency 7%. Am I misinterpreting something or is it the wrong way around on the website? Thanks!
Bastian Greshake Tzovaras
@gedankenstuecke

hey @Amborella! That’s well spotted. This is most likely the result of how 23andMe reports their SNPs. 23andMe and most other genotyping companies report the variations all based on the +/forward strand of the DNA. But dbSNP and many publications etc. give variants based on the orientation of the gene.

In the case you highlight the IL18 gene is on the -/reverse strand of the DNA (see https://www.snpedia.com/index.php/Rs187238), so one needs to take the complement of the reported 23andMe allele to be in line with that notation, which flips the Gs & Cs around in this case.

Hope that makes sense! :)

Amborella
@Amborella
Hi Bastian! Thanks for the quick reply. I sort of understand what you are talking about. Just to confirm if I took a genetic test and got CC as my genotype what would it correspond to in openSNP? Thanks!
Also according to what it says on openSNP 7% of the population (those with genotype GG by the notation on the page) have increased risk for SCD due to hypertension while according to the original paper 54% of people had this risk (those with genotype GG going by the notation in the original paper). Should the complement be taken somewhere here as well?
Bastian Greshake Tzovaras
@gedankenstuecke
in openSNP it will also be noted down as CC. But if you look at dbSNP, SNPedia or any other source that takes orientation into account you need to check if the variant of interest is on the minus strand
So if you are CC in 23andme (and by extension in openSNP), then this translates to being GG in the paper you are looking at
and then i think all the numberes make sense, no? 7% CC in openSNP means we have 7% GG in the notation of the paper?
Amborella
@Amborella
Thanks for the reply. If you look at the Links to SNPedia bit on the page it says: "rs187238 G/G Hypertension increases risk 3.75x for sudden cardiac death". On openSNP it says 7% of people have this genotype while the paper says 54% do.
From your reply I get the impression that it is not possible to just go from the genotype frequency on openSNP to the Links to SNPedia to work out what percentage of population is susceptible to the increased risk without checking if the variant is on the negative strand. Can you confirm if that is correct?
Bastian Greshake Tzovaras
@gedankenstuecke
yes, and the snpedia page gives that informatio
so for rs187238 SNPedia says that GG on the minus strand gives the elevated risk, which the paper says is found in 54% of the population. As it’s on the minus strand we have to look at the CC in openSNP and can see that 54% of openSNP members have that variant too, no?
Amborella
@Amborella
Great, thanks a lot. That makes it much clearer!
Also as an aside how do you tell if a SNP is on the negative strand from SNPedia? Is it the - in -137G or something else?
Bastian Greshake Tzovaras
@gedankenstuecke
in the box on the right hand side the first item is “orientation minus"
Amborella
@Amborella
Got it. Thanks!
Philipp Bayer
@philippbayer
nice, i just resubmitted a paper on Amborella pangenomics
Amborella
@Amborella
Yeah, I think Amborella is amazing. Strongly considering taking a holiday in New Caledonia sometime in the next few years just so I can get myself a pot of the stuff and bring it back. Although I'm more interested in it from the rare plant side of things than the genetics side.
Bastian Greshake Tzovaras
@gedankenstuecke
All the best for the resubmission!
Sina Rüeger
@sinarueeger
Hi, for some reason the SSL certificate expired again, could you update that?
Philipp Bayer
@philippbayer
sorry about that, fixing it right now
done!
Sina Rüeger
@sinarueeger
many thanks!
Philipp Bayer
@philippbayer
@gedankenstuecke @tsujigiri i've just added a bash script to /root/run-letsencrypt.sh and added that to crontab, let's see whether that works :PP
the current cert expires Sunday, 22 November 2020. if it works right then next thursday (tomrorow) we'll have a later cert.
Helge Rausch
@tsujigiri
I already added a CRON job earlier. Doesn't seem to work... :laughing:
Helge Rausch
@tsujigiri
0 0 * * * root /usr/local/bin/renew_ssl_cert.sh
Bastian Greshake Tzovaras
@gedankenstuecke
😂
Is it because something needs to be run as app instead of root for the containers?
Philipp Bayer
@philippbayer
is yours running within the container? mine's running on the host OS
Bastian Greshake Tzovaras
@gedankenstuecke
Yeah, but I remember that there used to be some issue if you tried to do things inside the host OS if the stuff was owned by the container
Helge Rausch
@tsujigiri
Yes, it's running inside the container.
From the logs it seems to be running, but there is no output, good or bad...
I changed it to 0 0 * * * root /usr/local/bin/renew_ssl_cert.sh > /var/log/renew_ssl_cert.log 2>&1 now, let's see...
Helge Rausch
@tsujigiri
Plenty of time to renew, exiting.
I remember seeing this the last time I checked. I'll change the Dockerfile to permanently log the output, so we see what happens over time...
Bastian Greshake Tzovaras
@gedankenstuecke
Great, thanks!
Philipp Bayer
@philippbayer
thanks :) I see my bad script is commented out, good so they don't clash
Philipp Bayer
@philippbayer
the ssl cert is still until the 22. november
Helge Rausch
@tsujigiri
When I run it, it still says Plenty of time to renew, exiting. No sure when it decides its close enough. There is also openSNP/opensnp.org-docker#18 still open.
Philipp Bayer
@philippbayer
thanks, merged!
yes normally when we run it manually we're too late ^^
Philipp Bayer
@philippbayer
hmmmm cert still expires 22.11.2020
i.e., the old one
Helge Rausch
@tsujigiri
I think it allows renewal one month before expiration, at the earliest. Maybe even less.
Chill! :smile:
Maybe we should subscribe to the notification emails? https://letsencrypt.org/docs/expiration-emails/
Bastian Greshake Tzovaras
@gedankenstuecke
that sounds good, at least we get an early warning if the cronjob fails :D