Approval for Open Impute

Hello, my name is Kevin Arvai, posting a review request for Open Impute, which is applying for project approval on Open Humans. This project adds a data source by performing genome imputation on members’ existing genomic data sources.

The genome imputation pipeline runs on a server hosted by Open Humans, but I have access to it. When the pipeline finishes and the new data source has been uploaded, all of the member’s data is deleted from the server programmatically.

Should this project be visible and available for all Open Humans members to join?

Please vote Approve or Deny , and/or comment.

Quick links

Project info

  • Title : Open Impute
  • Managed by: Kevin Arvai
  • Description: The goal of Imputer is to provide users with a more comprehensive picture of their genome. Direct to consumer genetics companies, like 23andMe, only genotype a small fraction of the genome. Researchers are finding new genetic locations associated with traits and diseases at a rapid pace. Users might be interested in knowing their genotype status for these new associations, but the locations may be in regions that direct to consumer tests are not genotyping. Imputer leverages the vast amount of genotype data made available by 1000 genomes project to provide Open Humans users with genotype estimates at additional locations in their genome.
  • Project website:
  • Connections: 0 members
  • Requested sources 23andMe Upload, AncestryDNA Upload, FamilyTreeDNA integration, Gencove, Genome/Exome Upload, Harvard Personal Genome Project, and openSNP
  • Data added: member.imputed.vcf.bz2

i’m :+1: to approve after these minor changes:

  • update Django to 2.1.5 (there are a couple of minor vulnerabilities in 2.1.1)
  • check other packages for vulnerabilities; I think running this would suffice:

Thanks for reviewing @beau much appreciated!
Suggestions have been incorporated and a test pipeline is running now.

With the merge of all of the security updates:

I also approve of this project!

I’m so excited to see this project @arvkevi!

I want to be impartial though and apply the standards I tend to apply to projects… please forgive me in advance! :pray:

  1. Information about the project

    • :question::question: who manages it? I don’t think @arvkevi’s name is anywhere on the site itself, although it’s on the activity page in
    • :white_check_mark: what will it do? The about page does a great job explaining imputation! :smiley:
    • :question: what is in the data it has access to? arguably redundant with permissions in Open Humans, but maybe nice to have a brief statement like “will request access to your genetic data in Open Humans (e.g. 23andMe)”.
    • :question::question: security, privacy, and data management? – you don’t need to do overkill here, but I think it’s currently not addressed? it’s important to explain some general info about data management & sharing. You might want to create a brief “terms of use” page, I have a brief “terms” page for Genevieve. (Note that a terms page can also protect someone running a site with a “disclaimers” section! :wink: )
  2. Summary info on the front page – while an about page is probably appropriate for a complete description, most people don’t bother looking there. I think the website’s front page should make sure to hit highlights of info mandated by project guidelines (but not too wordy) & direct someone to an “about” page to read details. In particular, “who is running it”, and “what it will do”. (e.g. I think Bastian’s Rescuetime project does a nice job with brief info highlights.)

  3. name consistency? In Open Humans, it’s Open Impute. The logo/badge/icon says Imputer. The URL is openimpute. The website says " Genotype Imputation for Open Humans" and “the Open Humans genotype imputation app”. (Note - the last one might lead someone to think Open Humans staff manage the project directly? users could get confused and report bugs to the wrong people, etc.) I like “Open Impute” or “Imputer” – both great! but maybe more consistency, some people are easily confused :stuck_out_tongue:

Hopefully this is all easy stuff, it’s just wording… feel free to ask for suggestions if you’re having writer’s block :slight_smile:


Thanks Mad, very helpful feedback, I’ve addressed the suggestions.
New terms of use page:

Thanks @arvkevi! This looks good to me.

And thanks to @Benc and @beau for their reviews as well :smiley:

I don’t see any further feedback, so I’m going to mark this project as approved. :+1: