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Thread: Automated Global25 nMonte entirely from the web

  1. #1
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    Lightbulb Automated Global25 nMonte entirely from the web

    I have put together the nMonte runner entirely from the web, so you do not need to setup R or manage the coordinate files yourself. Just select the outgroups and the samples, then press the button.

    The web app is free, but has some restrictions to avoid blowing up the server. I am raising funds for a better server that can handle more outgroups and samples for many users. If you are interested in contributing, let me know. It will still be free for all (until my funds run out lol).

    http://185.144.156.77:3000/

    Give it a try. Any feedback is appreciated.
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    To include your G25 coordinates and/or sponsorship support - email: Hidden Content
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    LukaszM's Eurogenes K36 PCA: Hidden Content | Hidden Content

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  3. #2
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    R1a > M198 > YP 1337

    Poland
    Maybe add info who is author of nMonte (huibregts) algorhitm and who created Global25 dataset (Generalissimo).


    Is it correct? For every Polish sample it is the same. If we change on Beaker _Netherland or Yamnaya _Samara also. Should be like 1/4 (1/3) BB to 3/4 (2/3) Yamna but maybe I'm wrong...




    Nevertheless very interesting tool. Maybe possibility of using as outgroups single samples besides averages would be useful?
    Last edited by lukaszM; 07-20-2018 at 11:49 PM.

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    Quote Originally Posted by lukaszM View Post
    Maybe add info who is author of nMonte (huibregts) algorhitm and who created Global25 dataset (Generalissimo).


    Is it correct? For every Polish sample it is the same. If we change on Beaker _Netherland or Yamnaya _Samara also. Should be like 1/4 (1/3) BB to 3/4 (2/3) Yamna but maybe I'm wrong...




    Nevertheless very interesting tool. Maybe possibility of using as outgroups single samples besides averages would be useful?
    Good catch. I thought I had the credits. Thanks, will add that.
    Hidden Content
    Global25 Web Runner - Scaled - Hidden Content | Hidden Content | Hidden Content
    Global25 Web Runner - Unscaled - Hidden Content | Hidden Content | Hidden Content
    To include your G25 coordinates and/or sponsorship support - email: Hidden Content
    Hidden Content
    LukaszM's Eurogenes K36 PCA: Hidden Content | Hidden Content

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    Also, is there an up to date spreadsheet that I can use? The g25 spreadsheet I had is a couple of months old. If Davidski has added more, I need to incorporate those.

    Per Lukasz's suggestion, I will work on averaging the samples so that you don't have to run each one to get a sense of fit across a group.

    Edit - I read Lukasz wrong. He wants the ability to run individual samples as outgroups. That is easy and quick to add, technically, but I need to see server implications. The outgroups files will increase substantially. Good feature though.
    Last edited by poi; 07-21-2018 at 12:52 AM.
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    Global25 Web Runner - Unscaled - Hidden Content | Hidden Content | Hidden Content
    To include your G25 coordinates and/or sponsorship support - email: Hidden Content
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    LukaszM's Eurogenes K36 PCA: Hidden Content | Hidden Content

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    Technically how it works? Website is connected to R instance on server? Or it works without R? This is Linux server?

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    How do I pay for sponsorship levels and when I've paid how does it tell I'm not a guest user?
    Last edited by firemonkey; 07-21-2018 at 11:01 AM.
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    Quote Originally Posted by lukaszM View Post
    Technically how it works? Website is connected to R instance on server? Or it works without R? This is Linux server?
    Nothing magical about this at all. All it does is automate what we do when we're running nmonte manually.Everything is still R-based. I might move it out of R and see if there is a performance improvement, but that requires some time. The server is Linux(Ubuntu) although the code can run anywhere R can be installed.

    Quote Originally Posted by firemonkey View Post
    How do I pay for sponsorship levels and when I've paid how does it tell I'm not a guest user?
    Email me at pantam1981@gmail.com and I will send my paypal info to you. I don't want to put a direct paypal link as this website is not a business. After that, there will be a separate link(with a key) for each contributing user. If I raise enough, I will set up a separate server for contributing members so that things run a bit faster.

    Sponsor Level 1: $5. Upto 4 outgroups for upto 3 samples/coordinates. Allow upto 1 custom sample's coordinate.
    Sponsor Level 2: $9. Level 1 plus upto 5 outgroups and 10 samples. Allow upto 5 custom samples' coordinates.
    Sponsor Level 3: $19. Level 2 plus upto 6 outgroups and 20 samples. Allow upto 20 custom samples' coordinates. Allow upto 6 custom outgroups' coordinates.
    Sponsor Level 4: $29. Level 3 plus upto 7 outgroups and 50 samples. No restrictions on custom coordinates.
    Sponsor Level 5: $49. Level 4 plus enable automatically running of all possible combinations from the selected outgroups. For example: 7 outgroups can automatically run 99 nmonte models, using various combinations, for each sample/coordinate. nMonte results are automatically saved for future references or for further analyses.
    Hidden Content
    Global25 Web Runner - Scaled - Hidden Content | Hidden Content | Hidden Content
    Global25 Web Runner - Unscaled - Hidden Content | Hidden Content | Hidden Content
    To include your G25 coordinates and/or sponsorship support - email: Hidden Content
    Hidden Content
    LukaszM's Eurogenes K36 PCA: Hidden Content | Hidden Content

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    I want to give @huibregts and @davidski sponsor level access to the tool since my tool would not be possible without their work. PM me or email me pantam1981 @ gmail.com

    I am fixing the credits section.
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    Global25 Web Runner - Unscaled - Hidden Content | Hidden Content | Hidden Content
    To include your G25 coordinates and/or sponsorship support - email: Hidden Content
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    LukaszM's Eurogenes K36 PCA: Hidden Content | Hidden Content

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    If anyone wants their G25 coordinates included in the tool itself (so that you can compare yourself against others), let me know. Also, this tool currently only supports Scaled coordinates.
    Hidden Content
    Global25 Web Runner - Scaled - Hidden Content | Hidden Content | Hidden Content
    Global25 Web Runner - Unscaled - Hidden Content | Hidden Content | Hidden Content
    To include your G25 coordinates and/or sponsorship support - email: Hidden Content
    Hidden Content
    LukaszM's Eurogenes K36 PCA: Hidden Content | Hidden Content

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    Quote Originally Posted by poi View Post
    If anyone wants their G25 coordinates included in the tool itself (so that you can compare yourself against others), let me know. Also, this tool currently only supports Scaled coordinates.
    Absolutely! For sponsors (I plan to) or all? And via email or here in your thread?
    My 23andMe kit into Eurogenes K36 then oracle (thanks to lukaszM):

    nMonte restricted: Ireland 48.05, SW-England 20.95, Finnish East 20.05, Russian Tver 3.70, Latvian 3.15, Mari 1.90, Lithuanian 1.30, French Basque 0.90, Orcadian 0.00

    nMonte full: Ireland 45.70, Finnish East 20.05, SW-England 20.05, Russian Tver 4.10, Orcadian 3.05, Latvian 2.45, Mari 1.95, Lithuanian 1.45, French Basque 1.00, W-England 0.15, Belarusian East 0.05

    Maternal uncle: R1b-U152

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