Author Archives: phi1ipp

1000 genotypings, and 3 years of openSNP!

In 2011, someone asked me how many genotypes I personally would expect users to upload, and if I remember correctly, I said 30. That was quite the understatement: Just a few days ago on the 30th of May, openSNP received its 1000th genotyping!

On this happy occasion we thank the users and participants for their trust in the project and their continued support and interest.

Since 2011, people have used openSNP in research, art, and their own projects, have written additional software to interact with openSNP’s API, written great comments, and much more. We have published a paper on openSNP a few months ago, which is for most of us the first publication in our careers.

openSNP has come a long way, here are the first three commits from June 2011, with Basti’s oldest on the bottom:

commits

That was nearly exactly 3 years ago! Since then we’ve (among other things) learned to write proper commit messages.

So what does the future hold for openSNP?

  1. A better server: We recently received a grant from Bayer HealthCare so we can move to bigger servers, so that the site should load and react much faster. Maybe we can even start hosting bigger datasets?
  2. Pre-given phenotypings: One of the biggest problems with openSNP’s data is the high amount of variation in phenotypes entered by users: researchers who want to work with the data still have some manual cleaning to do. We’ve prepared a set of phenotypes for which users can only choose their variation; this should greatly improve the speed with which researchers can start working on the data.
  3. Faster parsing: we’ve replaced the Ruby-based genotyping parser by a 99% complete implementation written in Go. So far, it’s much much faster, but still only marginally tested.
  4. A variety of smaller things: A stats-page, bug-fixes, genosets, etc. – have a look at the Issues page here.

We thank you for your continued support and interest, and here’s to many more years! If you know of any other project that uses openSNP data, feel free to post it in the comments!

Now included: FitBit-data (plus minor design changes)

Hi there,

Basti has been hard at work linking the Fitbit-API to openSNP – if you’re a customer of Fitbit, you can now connect your Fitbit-data with your openSNP-profile to give researchers around the world an even better picture of how your genes interact with your health.

The new Fitbit-phenotype-overview – still kind of empty!

Why this data?

There are several SNPs associated with an increased risk of developing obesity, SNPedia has a very good overview here. For example, some variations are involved in how early your body starts to store fat, or how strong your appetite is.

Carrying these variants, however, does not mean that there’s nothing you can do about your weight – there are some studies showing that regular exercise helps alleviate these effects (see here, for example). This is where the Fitbit-data comes in – it gives researchers a detailed overview of your movement-patterns, the status of your body-weight and your sleep patterns. Using this data scientists can then perform association-studies by comparing weight and activity-data to known and unknown SNPs linked to obesity. You can also link your sleep-data (if you are tracking it) – this enables research into the genetics behind some sleep disorders.

Another reason why it’s great to collect data through a technical device instead through surveys it that all data which comes through the Fitbit-API is normalized into standardized units. This makes it much easier to compare the data, as you don’t have to convert between units (metric & imperial system) or have to work around spelling mistakes etc., while it also allows to circumvent the cognitive biases we all have while answering questions about ourselves. And of course it’s also is more convenient for you, because you don’t have to update your BMI and activity-pages manually, as we automatically will get your latest Fitbit-data. This means there is one profile less you have to worry about!

As a bonus, the level of detail in this data is a level researchers usually can’t reach due to time and financial constraints.

Basti’s page

How to link your data

Linking a Fitbit-account to openSNP is a matter of just a few clicks – once you’re logged in, click on My Account, then on Settings and under the Fitbit-tab you’ll be able to go through the procedure. Alternatively, here’s the direct link to the page. Of course, you can specify which data is going to be shared with openSNP – we don’t automatically take all of it, because that wouldn’t be very nice of us. After you’ve approved that you want to link Fitbit and openSNP you will get redirected to a page where you can choose which categories should be shared and mirrored on openSNP. And yes, you have to submit the form which selects which categories you want to share, until you’ve done so we will not grab any data.

Note that: a) the data at openSNP is automatically updated with new data from Fitbit along with all the data you have put into Fitbit so far and b) you can always unlink your Fitbit account from openSNP, this also deletes your Fitbit-data on our end, in the settings.

This is where we hid the bodies the link

For researchers

If you’re interested in this data, it’s from now on available in all data-dumps in CSV-format for easy parsing (available on the genotypes-page, or directly here). Please note that the CSV lists 0 (that is zero) for missing data-points.

Slight re-design

We’ve also slightly updated the design of openSNP to the newest Bootstrap-version. You shouldn’t have been affected by that (except in the way that things now look a bit nicer. For example take a look at the SNP-pages which now show pie charts for the allele & genotype-frequencies) , but if you find anything wrong, please tell us in the comments or at info@opensnp.org!

Thanks for reading and have a wonderful weekend,

the openSNP-team

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Milestone reached: 200 genotypings!

We’re happy to announce that openSNP has reached the magnificent number of 200 open genotypings! It’s great that you guys support open science so much, we didn’t think to reach this number so fast. openSNP has been growing constantly, here are some interesting stats:

Here’s the amount of data downloaded from openSNP.org every day over the last 6 months, with the days on the x-axis and the traffic in megabytes on the y-axis:

Image

As you can see, the amount of data jumps around wildly – that’s because the data-dump with all genotypings is fairly large, and there are lots of days in there where no-one downloaded any genotypings, and some days where a lot of people download data – nothing much in between!

And for fun, here’s the amount of daily attacks on the server (usually automated scripts that look for open administrator-interfaces)

Image
What happened there in May? Two articles were released on openSNP and Basti and Fabian held two talks (at the SIGINT and at the re:publica), so that increased positive and negative attention.

Some things that are coming soon:

- picture-uploads for phenotypes

It would be great if users could upload pictures of their phenotypes and variations, for example, the shape of their heads or the form and color of their eyes. We’re currently working on this, might take a while longer.

- more secure backend

In light of the recent attacks on linkedin, last.fm and others we’ve switched the password-storing system from salted SHA512 to salted bcrypt-hashes. If you’re interested in how that works, check out this article, Keeping passwords safe by staying up to date.
We’re currently testing how well the implementation works but it’s looking good, coming very soon. You’ll probably not notice any changes.

- a couple more talks

We’ve submitted some more applications to talk at different conferences but haven’t heard back from any. If we go and hold a talk somewhere, we’ll link to the videos!

Thank you for your interest & help and time, we couldn’t have done it without you!

The openSNP-team

Replies to all genotyping-applications have been sent

It took us some time to read through all your great applications and it was a hard task to decide which applications we should consider for the free genotypings. After heavy discussions and bargaining we had two things: a list of successful applications and a short list of applicants that would get a 23andme-kit if there would be a DNADay-discount with 23andMe this year.

By now all applicants should have received an email from us which either brings the good or bad news. If you haven’t received an email you should take a look into your spam-folder (look for a message from info@opensnp.org). A handful of applicants either had some typo in their address or have closed down the account they used to register for the application. If you haven’t heard from us at all this might be the reason.  In this case, please contact us again and tell us your old or original e-mail-address.

For everybody on the shortlist: Unfortunately 23andMe doesn’t offer discounts this year, so we can’t consider your applications. We’re really sorry about this as we really would like to genotype all of you. Drop us an email if you want to get notified about a potential follow up free-genotyping. We’re still trying to get some funding for this.

Please give us your postal address if your application was successful. We need it to order you a spit kit.

Thanks again to everybody who participated.

Cheers,
the openSNP-team

The WissensWert contest vote is now open!

Hello everyone!
The Mendeley/PLoS Binary Battle is now over, so it’s time for the next one  – the WissensWert-Contest (page is in German) by the German Wikimedia-Foundation.

They have pledged up to 7000€ for ideas that promote open knowledge and open science – naturally, we had to apply!

What we’re trying to do with the money (if we win) is to give out free genotypings to people who can’t afford them, but still want to participate in the research. We could give out up to 35 genotypings with the money. Of course, just because we give anyone the money to get genotyped doesn’t mean that they have to publish it – we can’t force you to reveal potentially damaging information about you.

To win this contest we need your voteyou can vote here, the page is in German but you only have to activate the radio-button for project “02-Open (Citizen) Science durch mehr öffentlich verfügbare Genotypisierungen” (that’s us, translation: “Open (Citizen) Science through more openly available genotypings”) and then press the submit-button on the bottom of the page. You don’t necessarily have to supply any of the additional information (which seems to be for their statistics), but if you speak or write German I’m sure they would appreciate the input!

We’re thrilled to have won the Mendeley/PLoS Binary Battle and we’re sure we couldn’t have done it without you guys. Thanks for your votes & your continuing support!

The openSNP-team

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