Category Archives: General

#thedress, ethics for participant-lead research, research hack days

It’s been a little less than a year since we reached out to you. Right now our ± yearly newsletter is going out and there’s some things that might interest you as well: Since the last newsletter openSNP has grown in size quite drastically. Our database now holding over 1700 data sets! Thanks to everyone who made this possible! And today we have a couple of topics to present:

#THEDRESS

You might have followed the media buzz around #TheDress, the viral phenomenon that started around the end of February. It lead to one of the new big questions of our time: Is the dress black & blue or is it white & gold? Lots of scientific explanations have been put forward and of course, genetics has also been thrown in the mix in order to explain why people so vehemently disagree about it.  

23andMe recently started to investigate this question amongst their user base and thanks to Michael Whitehead you can now also contribute on openSNP. So if you want to participate in research about the genetics of #TheDress you can enter this phenotype.

Mike briefly spoke to us about his motivation to dive into the topic:

“We know that there are numerous elements of colour vision that are influenced by genetics. Red/green colour blindness is the most famous, but there are a variety of heritable colour-blindness phenotypes, as well as tetrachromats who can see a richer pallette of colours than the rest of us. It is therefore conceivable that variation in our perception of the dress is influenced by underlying variation in our genes.”

23andMe already has some first results in, but having an open data source for this would still be fun. So please, help us out. So far it looks like team blue/black is taking the lead.

RESEARCH HACKDAYS

The people running openresearchdata.ch are organising research hack days on June 5th & 6th at the ETH in Zurich and at the FORS in Lausanne. Participating in those days is free and genetic data will also play a role, with our own Bastian attending in Zurich. You can find more information on this on their websites.

A SOCIAL CONTRACT FOR A NEW KIND OF RESEARCH

Performing open, participant-lead research is not only exciting for the science that is done, but also for a whole lot of ethical questions it brings up. The workshop “Towards developing best practice for ethical participant-led health research” asked what a new social contract for such kind of research should include. The results of this workshops are now published as an open access article in the Journal of Medical Ethics.

SOME CHANGES IN THE BACKEND

Helge Rausch has kindly updated openSNP’s code base to Ruby on Rails 4.2, so you might experience some problems on the site, as this update was just done. As usual, if you encounter any problems, please send us a mail to info@opensnp.org or just reply to this mail.

 

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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New API methods & Vagrant images

Additions to the API

We can announce some minor additions to our API:

  1. You can now grab annotations for a SNP by using http://opensnp.org/snps/json/annotation/$SNP_NAME.json. For example http://opensnp.org/snps/json/annotation/rs7903146.json returns all Mendeley-, PLOS- and SNPedia-annotations we have for Rs7903146.
  2. You can now get additional information for phenotypes. You can get a list of all phenotypes by visiting http://opensnp.org/phenotypes.json. You can use this call to find out the IDs of the phenotypes you are interested in. 
  3. And you can get all phenotypic variation and the description for a given phenotype by visiting http://opensnp.org/phenotypes/json/variations/$PHENOTYPE_ID.json. For example http://opensnp.org/phenotypes/json/variations/12.json gives you the variation for each user at the phenotype with the ID 12.

We also added some more extensive documentation of the API to our Wiki at GitHub. The wiki also lists the attributes each call will return.

Vagrant Image

We compiled two Vagrant-images which should make running the openSNP source and development much easier. Installing Ruby, Redis, PostgreSQL, Java, and all the right versions of the Ruby gems can be painful and often takes a significant amount of time – so we created the Vagrant-Image, which is the whole server-runtime with all gems pre-installed inside a virtual environment for easy development.  This Railscast gives you a nice idea of how to install and use Vagrant.

Our Vagrant-images (downloadable as 32 bit version and 64 bit version) are based on Lucid64 and Lucid32 and come with the Ruby version manager rbenv, Ruby 1.9.2 including bundler, Sun’s Java and Postgres 8.4 (the development-tables are already migrated) pre-installed. Getting the development-server running should now be really easy:

  1. Install the image using vagrant box add opensnp http://opensnp.org/opensnp32.box
  2. Initialize the image inside your openSNP-folder using vagrant init opensnp
  3. Run vagrant up to start your image and afterwards connect to it using vagrant ssh
  4. Go to the mounted directory using cd /vagrant
  5. Run bundle to see if all gems are working as expected and try bundle exec rails s to start the web-server

You can watch this Railscast to learn more about how you can put Vagrant to use and download our Vagrant-image as 32bit version or 64bit version. One caveat: You need to delete the .rvmrc file if you want to run vagrant from inside the directory which has your copy of the openSNP-source code. The file can be found in the root-folder of the openSNP-source code. If you keep the file your copy of RVM might lead to some problems with vagrant. Let us know if you encounter any problems or need help.

Recent Talks – re:publica & SIGINT

In the last post Philipp already told you that we’ve been giving talks on Personal Genetics and a possible future of Biomedicine over the last months. In May Fabian and I visited the re:publica in Berlin and the SIGINT in Cologne. Now the recordings of those conferences are available. So if you couldn’t make it to Berlin and/or Cologne you can watch it those talks.

Unfortunately the talk on The Future of Genetics which we gave on the re:publica wasn’t recorded, but you can at read and download our slides of the talk. And on the same conference I was also part of a (German, sorry rest of the world!) panel discussion called “Die totale Selbstkontrolle als Wunsch und nicht Bedrohung” (total self-control as wish instead as thread) which mainly focussed on the Quantified Self-movement, but also covered a bit of personal genetics.

On the SIGINT we talked about Power to the Patient and how modern technology along with the web, think of personal health records, could be put to use to change how medicine is done. You can again download the slides or as this talk was also recorded watch the video.

Thanks to all of you who joined the conferences, listened to our talks and – most importantly – took their time to discuss the topics with us.

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

A petition on Open Access

We are strong supporters of the open-science movement and are happy to see that there is a new petition aimed at the Obama administration. The goal of this new petition is to make Open Access mandatory for all publications funded by tax-money.

While one of the aims of openSNP is to provide an Open Data platform it would be impossible to provide this service without the great benefits of Open Access, of which we make extensive use when we link to external information and papers. Would all research still be hidden behind paywalls we could not provide you with information on any SNPs. If Open Access would be mandatory we could provide you with even more information and literature!

This is the full text of the petition:

WE PETITION THE OBAMA ADMINISTRATION TO:

Require free, timely access over the Internet to journal articles arising from taxpayer-funded research.

We believe in the power of the Internet to foster innovation, research, and education. Requiring the published results of taxpayer-funded research to be posted on the Internet in human and machine readable form would provide access to patients and caregivers, students and their teachers, researchers, entrepreneurs, and other taxpayers who paid for the research. Expanding access would speed the research process and increase the return on our investment in scientific research.

The highly successful Public Access Policy of the National Institutes of Health proves that this can be done without disrupting the research process, and we urge President Obama to act now to implement open access policies for all federal agencies that fund scientific research.

The best thing is that you don’t have to be a US citizen to sign the petition. Just register on the petition platform and give your signature. In total 25,000 signatures are required before June 19 2012. If this limit is reached the petition will be placed in the Executive Office of the President for review.

The campaign behind it, access2research, is driven by many open access advocates, including Michael Carroll, Heather Joseph, Mike Rossner, and John Wilbanks.

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Some progress on the API: JSON endpoints

Some weeks ago we stated that we are working on implementing the Distributed Annotation System into openSNP. And I’m sorry that I’ll have to announce that we are not finished with this yet. We just underestimated the amount of time it would take to finish this. But to make up for this we just released some JSON (JavaScript Object Notation) endpoints which you can use to get data out of openSNP. JSON can be easily parsed using software and is already widely used, especially in web applications. For a start we added JSON support for the user-index, for genotypes at single SNPs and for all phenotypes of a given user and I’ll briefly discuss how you can access the different JSON endpoints.

Let’s start with the user-index, which can easily be accessed at http://opensnp.org/users.json. This includes the complete list of all openSNP-users and their names, their unique user-IDs and all the genotyping-files (with the unique genotype-IDs and the download-links). We hope that this makes an ideal entry-point if you are looking for genotyping-files and the user-IDs to further query the openSNP-database.

If you want to get genotypes of single or multiple users for a given SNP you can use the JSON endpoint at http://opensnp.org/snps/json/$snpname/$userid.json. Just replace $snpname by the Rs-ID you are interested in and $userid by the unique ID of the user you are interested in. For example: http://opensnp.org/snps/json/rs9939609/1.json gives you my genotype at Rs9939609. If you are interested in the genotypes of multiple users you can concatenate this into a single query by either using commas to provide multiple User-IDs (for example http://opensnp.org/snps/json/rs9939609/1,6,8.json) or by giving a range of user-IDs (for example http://opensnp.org/snps/json/rs9939609/1-8.json).

Similarly you can access all phenotypic information of a given user by using http://opensnp.org/phenotypes/json/$userid.json. Again: Just replace $userid by the unique ID of the user you are interested in. For example http://opensnp.org/phenotypes/json/1.json gives you all the phenotypic information I have entered about myself so far. Concatenating multiple users into one query works just as for the SNP/User-combinations by using commas (http://opensnp.org/phenotypes/json/1,6,8.json) or ranges (http://opensnp.org/phenotypes/json/1-8.json). In any case: If you request data of users or user/SNP-combinations that don’t exist the JSON-hash you will get back includes the key “error”, just like this.

This are all the options you can supply by using our JSON-endpoints right now. There are no API-keys and no rate limits. We will just see how it turns out and if any limiting of the access will be necessary in the future. We hope that this will allow more easily reusing the openSNP-data and you maybe have already some nice ideas for remixes/browser plugins/younameit. If you have any requests, which kind of JSON-endpoints you need or would like us to add, just let us know. We are currently experimenting with this JSON-stuff and are open for any critique, comments, ideas etc. If you want to help us to implement further features into openSNP: Please do so, we are open for everybody who wants to participate and want to invite you to do so. The source code is freely available and there is a Google Group/mailinglist where we discuss bug-fixing, new features etc. So you might want to join us there.

Happy Holidays

We have some last news before we leave for our holidays. Let’s start with the biggest news: We were able to secure a little funding through the WissensWert-contest of the german Wikimedia Foundation (sorry, the posting is in German as well). This means that we will have up to 5000 Euros that we can spent to get some more people, who are in love with sharing as we are, genotyped. We will release more details on this as soon as possible.

Additionally Philipp and I will be in Berlin between 12/27 and 12/31. As we have mentioned before we will give a talk on openSNP and crowd-sourced genome-wide association studies at the 28th Chaos Communication Congress. The talk will be on 12/28 at 11 pm. This talk will be in english and there should be day passes, so if you are in town you can pay us a visit. If you are If you’re able to speak or understand German you can also pay a visit to the 0th Spackeriade which takes place on 12/29. We will talk about the implications of the post-genomics-era on privacy.

Thanks again for all your support, for voting for openSNP in the different contests we have entered, for sharing your data with us, for finding bugs, for spreading the word. Have some nice holidays and maybe we’ll see some of you for a beer in Berlin.

Results of the Binary Battle

We are happy to announce that we won the Mendeley / PLoS Binary Battle. This comes unexpected, although we worked hard to achieve this. As we see openSNP as a community-driven project: We really want to thank all of you: For voting for openSNP in the final round of the Battle. For sharing your data. For finding bugs. For your critique. For your ideas and feature suggestions. For all of your support. This is a great source of motivation, especially if I think of implementing all the upcoming feature-ideas we have.

We also want to send our congratulations to PaperCritic, which came in second, and rOpenSci which is the second runner up. Both are definitely worth a look (as are all the other entries of the binary battle as well). It is really great to see what creative minds can build with open data and open APIs.

As Philipp is currently writing his master thesis (and I’m also working for the last exam of this year) there hasn’t been much new in terms of features in the last weeks. But this should end in a week or two and we already have some plans. And we are also applying for some small funding via the german Wikimedia Foundation and their WissensWert-contest, which funds projects that support open knowledge. We are trying to get the funding in order to get data of more people who are into sharing their data genotyped (and may lack the financial resources to get it done). This could lead to some more data sets on openSNP.

Thanks a lot ! And if you have any questions: Just contact us, we are really looking forward to get in touch with you.

You can vote for us

The Mendeley/PLoS Binary Battle now also features a public vote where you can vote for the Top 10+1 submissions. The result of the public vote will count as one point to be added to the expert judges votes.

If you want to help us, give us your vote and spread the word. Thanks a lot!

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