Author Archives: Bastian

Crowdfunding DTC Microbiomics & Proteomics

We hope that you all had nice holidays and made it safely into the new year. You may already be tired of all the donation campaigns which are frequent in this season and don’t worry, we won’t ask you for money for openSNP. We do however have some ideas on what you could spent your Christmas bonus: Crowdfunding startups and products became en vogue in 2012 and the whole Quantified Self and Personal Genomics movement fortunately has jumped on the bandwagon as well. Right now there are some projects looking for funding on Indiegogo. For example uBiome, which wants to provide insights into the bacteria living inside you, and Talking20, which wants to do for your proteins what personal genotyping companies did for your genome.
We feel that those projects are picking up where the genotyping and genome/exome sequencing efforts of other companies are currently ending and thus might be of interest for you as well (I mean: Who wouldn’t like to get his microbiome sequenced and have regular metabolite tests? Right?). And of course, we hope that we can include sharing capabilities for willing participants of those projects in future versions of openSNP. We have reached out both projects to get some more information about their ideas and future plans of possible collaboriations. Before we let the projects speak for themselves just a standard disclaimer: We’re not involved with any of those projects and are not making any money out of this. We just like the idea of people having more biological data on themselves.

uBiome

Hello, openSNP Community! I’m a PhD student at Oxford, and together with my co-founders from the University of California, San Francisco, I am honored to work with uBiome, the world’s first citizen science effort to map the human microbiome.

The project is funded through crowdfunding at www.indiegogo.com/ubiome. Each gut kit is $69; gut and mouth kits are $139 for both (+$12 shipping outside the United States for each). We plan to send out the kits in May 2012 and return the results on our website once we get the kits back from everyone. Our kits are available in 196 countries. Data will be freely available to those who sign up, and available to the global research community on an “opt-in” basis. In the long run, we hope to integrate with 23andme and other types of genetic and metagenetic data.

So far, our project has garnered over $55,000 in crowdfunding from over 480 participants in less than a month. Participants from twenty different countries spanning four continents have pledged their support, including the United States, United Kingdom, Australia, New Zealand, Canada, Finland, France, Germany, as well as India, Singapore, and Uruguay. We’ve been featured so far in Wired, Venture Beat, the Los Angeles Times, Scientific American, BoingBoing, and syndicated in 160 newspapers around the world through the Associate Press.

What is the microbiome, you ask?

The microbiome are the bacteria that live on and within us. It sounds kind of funny, but all of us are actually covered in helpful germs (or co-evolved symbionts if you prefer).

Like the rainforest, the healthy human microbiome is a balanced ecosystem. The correct balance of microbes serves to keep potential pathogens in check and regulate the immune system. Microbes also perform essential functions such as digesting food and synthesizing vitamins. Some research also suggests that microbial activity influences mammalian mood and behavior. Studies have linked microbiome imbalance to autism, depression, and anxiety, as well as many gut disorders, eczema, and chronic sinusitis. Infant health even appears to benefit from a proper seeding of microbes at birth, with health consequences ranging into adolescence. For some future-thinking commentary on the microbiome, check out this interesting editorial in Science by Leroy Hood.

uBiome brings this cutting edge technology directly to consumers for the first time through citizen science.

We provide participants with a catalogue of their own microbes, detailing the microbial composition of the body and explaining what is known about each genera of microbe. In addition, uBiome compares participants’ microbiomes with scientific studies on the role of the microbiome in health, diet and lifestyle. uBiome also provides personal analysis tools and data viewers so that users can anonymously compare their own data with crowd data as well as with the latest scientific research.

From a small sample on a cotton swab, your uBiome test helps you to learn more about your body, including:

  • Diet: Certain gut enterotypes are strongly associated with long-term diets, particularly protein and animal fat (Bacteroides) versus carbohydrates (Prevotella). Maybe you are not sticking to your diet as much as you think.
  • Diabetes: Does your gut microflora correlate with people who have diabetes? If you have other symptoms as well, you might want to talk with your doctor.
  • Sinusitis: Is your nasal microbiome associated with the profile of chronic sinusitis? Some studies have found that multiple, phylogenetically distinct lactic acid bacteria were depleted concomitant with an increase in the relative abundance of a single species, Corynebacterium tuberculostearicum.
  • Alcohol consumption: Do you drink a lot of alcohol? If your gut profile clusters with heavy drinkers, you might want to consider cutting back on the booze.
  • Bowel conditions: Do you have Irritable Bowel Disorder (or any other bowel condition)? You may want to purchase our specially designed kit and survey for bowel disorders.

Please join us and help us spread the word about this project. The more people that contribute, the more we can all learn about our health, and contribute to the advance of SCIENCE!

Talking20

Talking20 is a simple blood test that can be ordered online and received in the mail. It’s quick and easy! Results are delivered online in secure profile, and can even be viewed from a smartphone. We are ready to gather data and design experiments that will help us help you learn more about what’s going on inside your body!

Get involved with the Talking20 project by ordering a basic kit and sending it in. Tracking your biological data will help you view changes taking place inside your body, and it will help us design new tests that are useful to everyone. Want to know what eating a burger does to your cholesterol? Interested in tracking stress reduction over the course of a month-long yoga course? We are and we need your help. Your body is talking to you, let’s find out what it’s saying!

This is how Talking20 is measuring your metabolites:

Talking20 is taking proven technologies: (1) dried blood spot collection (done for every newborn in developed countries) and (2) mass spectrometry (used in labs everywhere), and innovatively bringing them together. We believe that actionable information about our bodies are available by looking at our proteins and metabolites. That’s where we need to be looking. Danny Hillis of Applied Minds does a amazing job of explaining this concept in his talk at TEDMED.

Mass spectrometry is a very sensitive method for counting molecules from blood, and is actually used as the ‘gold standard’ to set up hospital tests. With a bit of extra work, mass spec can also be used to measure every other molecule too. Without visiting a lab or even leaving your home, you can now just put a few drops of your blood on a card and mail it to us at room temperature from anywhere in the world! We can then do the analysis and tell you your results wherever you are!

Talking20’s commitment is to make this testing as economical as possible, so you can do it whenever you want. Heather has personally tracked her hormones and cholesterol every few days to learn more about her own life events and diet. Talking20 is also on the verge of completing a cortisol test so we can start watching stress levels in response to different types of exercise!

At Talking20, we want to make many different tests available, so you can start finding out about what is happening inside you. We are offering five of these ‘biomarkers’, to measure your cholesterol, vitamin D, estradiol (estrogen), progesterone, and testosterone. This would normally require you go into the doctor, then into a lab to get a blood draw, and then back to the doctor, and would likely cost $300-500! We believe we can do better!

If you want to support them you should visit their Indiegogo page.

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.

Support for 23andMe-exome-data

In the last weeks some people contacted us because they wanted to upload their exome-data to openSNP. While we started out with a focus on SNP-data (mainly because it’s much more abundant) providing support for exome-data has been on our ToDo-list for a couple of month now, so we did some work on it. Today we start with support for the data which is generated by 23andMe through their Exome-service.

So if you’ve got your exome sequenced through 23andMe you can now upload it to openSNP as well. Unfortunately there are some drawbacks right now:

  1. We only support upload for the VCF (Variant Call Format) and not for the BAM-file which contains the raw reads as well.
  2. We won’t parse all of your data. We will scan your exome for those SNPs which are already in the openSNP-dataset, but we won’t add any new ones to the web interface and won’t make other variants available for browsing on openSNP in the near future.

There are two main reasons for this limited feature-set:

  1. openSNP is our hobby project and we run with limited financial and computational resources. Basically right now we don’t have the computational power and storage to store and parse complete exome-BAM-files to deliver any benefit.
  2. Mining literature for known SNPs is easy, because a unique identifier exists for each SNP. This identifier is used in most publications and is seldom used for other purposes than referencing the SNPs. For Copy Number Variations etc. this isn’t that easy and we still haven’t had a good idea to get around this.

Nevertheless: If you’ve got your exome sequenced through 23andMe you can now upload your VCF-file. We will search for all known SNPs and make your genotypes available on the web-frontend of openSNP. And of course the complete VCF-file will be downloadable for anyone who is interested in it. Have fun uploading your data. And as always: Let us know if something doesn’t work as expected or if you have any further ideas for us.

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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Update on the free genotypings and new features on openSNP

The free genotypings
This night the deadline for free genotypings passed, and we are overwhelmed by the amount of responses. In less than 24 hours after the first blog post over 200 people sent us their applications, and in total over 450 people applied. For us the real work now begins, and we will do our best to go through all the applications, select the most interesting, and then contact every applicant. 
 
Entering Phenotypes
We also used the past weeks to implement some more features into openSNP. This time we focused on end-users entering their data into openSNP, especially on entering phenotypic variations. Entering a lot of phenotypes was a bit cumbersome and took too much time. Now, registered users will find a subtle change to their dashboard: The tab which shows phenotypes you haven’t yet provided now features a small button that allows you to easily fill in your information.
Bild
 A modal window (like the one in the screenshot above) will appear and you can choose your variation from the list of already known answers, or you can choose to add a new one. This should make entering data a lot faster. 
 
Phenotype Recommendations
We also added a recommendation engine for phenotypes, which can be found on individual phenotype pages. An additional tab will show you which phenotypes have most frequently also been entered by users who have entered variations on the page you are looking at. 
Bild
Additionally, you can use this system to get recommendations about similar phenotypes and even variations. If you enter your variation for a phenotype through the old phenotype view you will get a similar picture to this: 
Bild The top row shows you up to three phenotypes and the variation which is often entered by users who have provided similar variations to you. So lets’s say you’ve just entered that your Body Mass Index is above 30, the system might point out that people with this variation frequently have entered that they have a high blood pressure. 
 
The lower row shows you up to three phenotypes which are often entered by users who have entered any information about similar phenotypes as you, irrespective of the variation provided. For example, if you’re interested in visible traits and have just provided information about your eye colour you will see that people who are interested into this also provide information about their hair and skin colour. 
 
Given the rising numbers of different phenotypes which you can enter in openSNP, this should help you to find those that are of interest of you. You might have noticed that you wont get those recommendations if you are using the new quick-entry-feature on your dashboard. Our reasoning for this: Using the dashboard you can enter a large amount of variation in rapid succession. Here, displaying recommendations after each phenotype entered would slow you down. But if you like to “browse” and don’t want to rapidly enter large amounts of data, you might benefit from having some recommendations what might also be of interest for you. 
 
How do you feel about this? Would you like to see an option to get those recommendations also after entering variation using the dashboard? 

Apply now for a free genotyping

At the end of last year we announced that we’ve got some funding from the German WikiMedia foundation to get more people – who are willing to share their results – genotyped. We have now settled on a process that should allow us to perform the project without too many problems. Starting today, you can apply for one of the free genotypings. The deadline for applications is Sunday, 03/25/12 23:59 o’clock, so you still have some time to think about an application. In the two weeks following the deadline, we will select as many participants as we can afford to get genotyped using the 5000 Euros we received from Wikimedia. We’ll get in contact with everybody who has sent an application to let all applicants know whether their application was successful or not.

The genotyping will be done through 23andMe. We will order you a gift kit which will be delivered to your address. These gift kits include prepaid access to the 23andMe website for 12 months, so you can check up on the latest findings about your genetic variation as well. After this 12 month period, those features will expire automatically, you don’t have to cancel any subscriptions.

Our application form contains some standard questions (Where do you live? Does 23andMe deliver to your country? etc.) but also some details about your motivation, why you want to make your dataset available to the public and why your data might be of great interest (For example: Do you have a rare disease where research is lacking?). Additionally, we will also try to get people genotyped who are currently under-represented in publicly available data sets. Most data up to now is from WEIRDs: Western, Educated, Industrialized, Rich and Democratic people (most are probably male, too).

We would like you to deposit the final raw data, which you will then be able to download from 23andMe, into the openSNP database, ideally along with some phenotypic information about yourself. So please think about the possible consequences which may arise by doing so before you apply for one of the genotypings. The application process has some questions about possible consequences as well (just so we get a feeling of whether you know what you are doing). If you get your results, but then find the results too problematic to publish: That is fine. We are aware of this possibility and while it would suck for us as it means less data, you are the one who has the last word in this matter. Some information that might make you a bit more comfortable with the idea of sharing data: We won’t release the names of any applicants (whether successful or unsuccessful) and you can sign up to openSNP using a pseudonym, plus we don’t log any IPs used to access openSNP.

tl;dr

We offer you the chance to get genotyped through 23andMe for free if you are willing to share the data with the public. Here’s the planned schedule:

  • Until 03/25/12 23:59 o’clock you can apply for a genotyping using this application form
  • We select the lucky winners between 03/26/12 and 04/08/12 and get in contact with every applicant.
  • Mid-April: You should receive the 23andMe-kits in your mail.
  • End of May: You should receive the results of the genotyping, so you can upload the results to openSNP.

If you’ve got any questions regarding the application process, the schedule etc., just let us know using the comments or write us an email to info@opensnp.org. We will try to answer all of your questions as fast as possible.

Good luck,
wishes your openSNP-team!

Videos on openSNP & DAS-support

Another thing we have been procrastinating for far too long: Creating videos on the idea of openSNP and some screencasts that show how you can use openSNP to enter data about yourself and how you can get the data out again for your own research. So here we go. The first video is a small “self-interview” I did to tell you a bit how we started, what you should keep in mind privacy-wise before starting to use openSNP etc.

The next video shows you how you can use the openSNP-frontend to enter your phenotype-data, what kind of information the individual SNP-pages can show you and how you can subscribe to the openSNP-RSS-feeds to be notified about the latest genotyping-files etc. A small new feature which is missing from the video as we implemented it after recording the video: The news-page features a tab that includes the latest publications on the SNPs we have in the database. And for all info-junkies: You can also subscribe to the latest publications using RSS.

The last video shows how you can query the APIs which we have implemented. Bonus-Content: This video includes the first preview on how you can use the Distributed Annotation System to visualize individual genotyping files! In short: You can use http://opensnp.org/das/sources to get a list of all DAS-sources we have with openSNP. Each source represents all SNPs we have of a single user, regardless of how many genotyping files a user has provided.

If you want to use a DAS-source in a genome browser, for example in MyKaryoView you can use the features-commmand of DAS. The link for this is http://opensnp.org/das/$user_id/features, where you have to replace $user_id by the ID of the user you are interested in. If you want to query SNPs between chromosomal positions using DAS you can use http://opensnp.org/das/$user_id/features?segment=$chromosome_name:start,stop. So http://opensnp.org/das/1/features?segment=1:1,1000000 will give you all my SNPs on Chromosome 1 between position 1 and 1000000.

If you want to see an example for a visualization using DAS look at the video below. The DAS features are still experimental. I will attend this DAS workshop to get some help with the final implementation, so if you have suggestions: Please let us know!

Enjoy playing around with this features. As usual: Let us know if you find any bugs we have missed!

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.

Videos and Slides on the recent talks

A happy new year from the openSNP-team! Philipp and I are back from our talks. If you couldn’t make it to Berlin you can now watch the videos that were recorded during our talks. You can watch the recordings from our talk on crowdsourcing genome-wide association studies at the 28th Chaos Communication Congress at YouTube or in better quality here. If you are interested in our slides you can get them at SlideShare or as LaTeX-sources at GitHub.

For those of you who speak german: You might be interested in our talk on the privacy implications of the coming post-genomics era, which we gave at the 0. Spackeriade. You can watch it on YouTube as well or download the video. Again: The slides can be found at SlideShare or as LaTeX-sources on GitHub.

Thanks for all who helped on the slides, gave us their feedback and of course all of you who approached us after the talks – in real life or via email – and had some ideas for new features. We already started to work those. Stay tuned to see some changes on openSNP in the next weeks.

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