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!

About these ads

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s

Follow

Get every new post delivered to your Inbox.

%d bloggers like this: