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  • Mar 14 15:34
    gedankenstuecke closed #537
  • Mar 14 15:34
    gedankenstuecke commented #537
  • Mar 14 10:00
    joannearcilla opened #537
  • Feb 06 14:35
    tsujigiri synchronize #536
  • Feb 06 14:35

    tsujigiri on setup-github-action

    Update paperclip gem (compare)

  • Feb 05 16:46
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    tsujigiri on setup-github-action

    WIP (compare)

  • Feb 05 16:41
    tsujigiri synchronize #536
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    tsujigiri on setup-github-action

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  • Feb 05 16:28
    tsujigiri synchronize #536
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    tsujigiri synchronize #536
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    tsujigiri synchronize #536
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    tsujigiri synchronize #536
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    tsujigiri synchronize #536
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
sk75
@sk75
Is it possible or is this available .. I'm looking for SNP data that represent a family over a few generations. Is it readily available as one download. Or how can I search and make up a set of SNPs. Any help is appreciated, apologies if this is not the right question for here, and if the question does not make much sense as I just am starting to get interested in this.
Sharif Islam
@sharifX
I recently downloaded opensnp dataset. I need to store the genotype_frequency data for each rsid. This was not in the download. Is there a way to get this data downloaded (without calling the JSON endpoint)?
Bastian Greshake Tzovaras
@gedankenstuecke
@sharifX sorry for the delay in answering, it was grant writing season in France! Unfortunately there’s no easy way to get the frequencies for each rsid without downloading the whole data set and calculating them yourself at this point
VittorioAccomazzi
@VittorioAccomazzi

@sharifX @gedankenstuecke I faced a similar problem with my 23andme data. So I wrote an application for it, which display the frequency for the MT and Y Chromosomes (I’m interested mostly in genealogy). It is a web app, and processes the data is your browser:
https://vittorioaccomazzi.github.io/snpsandme/
The application displays the frequency of each rsid using the dbSNP and then sorts them.It also provides link and number of publications. So it allows to explore your genome easily, with the support of dbSNP.

The source code is on github. 🖐 Feedback is welcome !

Bastian Greshake Tzovaras
@gedankenstuecke
@VittorioAccomazzi thanks for sharing! For me it ends up with a blank page and the JS console throws an error in GA4React :)
VittorioAccomazzi
@VittorioAccomazzi
@gedankenstuecke which browser are you using ? If you don't mind I would like to understand what is happening. I validated on Chrome, Edge and Safari
Bastian Greshake Tzovaras
@gedankenstuecke
I tried in both Chrome and Firefox
VittorioAccomazzi
@VittorioAccomazzi
@gedankenstuecke the error reported by GA4React says "ga4manager.tsx:182 Uncaught (in promise) Error: GA4React Timeout" followed by "at ga4manager.tsx:182" ?
Bastian Greshake Tzovaras
@gedankenstuecke
Yep
VittorioAccomazzi
@VittorioAccomazzi
@gedankenstuecke Thank you. I increased the timeout. I appreciate if you can retry and let me know: https://vittorioaccomazzi.github.io/snpsandme/ .Hopefully it will work this time. In any case in this video you can see how the application works : https://www.youtube.com/watch?v=lUS8Q2-EbyY . In short the application displays the SNPs of the Y and MT chromosome and sort them by frequency. For each SNP it reports the number of publication and links to dbSNP, so you can navigate quickly your genome.