Amazon Elastic Block Store for facile sharing and archiving of biological data

Amazon’s Web Services offers enormous potential for people who need to process, store, and share large amounts of data.

And it’s a huge boon for bioinformatics. It’s cost effective and it’s fasta. Hah. Get it? It’s “>fasta”. Archiving and sharing data has never been easier.

Here’s a quick tutorial on creating an Elastic Block Store volume that you can share with your colleagues.

1. Create a volume

  • From the AWS Management Console, click on the EC2 tab, then on “Elastic Block Store > Volumes”
  • Click on “Create Volume”.
  • Pick an appropriate size for your volume. For EBS volumes that I am going to use to store and archive data, I create a volume 1.5 times the size of the data. This lets me store an unpacked version and a packed version simultaneously, making it easy to update data at a later date.
  • Add some informative tags.

2. Attach the volume to an EC2 instance.

From the Volumes window in the Management Console, select the new volume, then right click and Select “Attach”. I attach devices starting at

3. Format the volume.

Once you’ve created and mounted a volume, you’ll need to attach it to an EC2 instance. Fire one up and SSH in.

ssh -i @yourdns.amazonaws.com
> sudo mkfs.ext3 /dev/sdf

Mount points are available at /dev/sdf through /dev/sdp.

4. Mount the volume

> sudo mkdir /mnt/data
> sudo mount -t ext3 /dev/sdf /mnt/data

If you are potentially going to be dealing with many versions of data overtime, you might want to version your mount points. This will allow you to attach multiple EBS volumes at different sensible directories:

> sudo mkdir /mnt/data-v0.2
> sudo mount -t ext3 /dev/sdf /mnt/data-v0.2

Alternatively, you might consider handle versioning when creating snapshots of your volume.

5. Set the EBS volume to mount automatically (optional)

> sudo emacs /etc/fstab
/dev/sdh /mnt/data ext3 defaults 0 0

And you’re done! Now what?

Throw some data on there. Do some computes. Go nuts.

Share your data

Sharing your data is as easy as creating a snapshot.

1. Create a snapshot

Power down your instance. From the Management interface, select the volume and choose “Create Snapshot”.

Tips for effective data archiving and sharing

1. Add informative tags.

Be sure to add informative tags such as the release date and version of the data.

Release Date = 02 Jan 2011
Source = Todd’s Data Emporium
Contact = data@tharris.org

2. Include informative READMEs on the volume itself.

3. Be sure to make the snapshot public!

Updating your data

Updating your data to the next release of your resource is simple. Mount the original volume to an instance, copy in new data, then create a new snapshot.

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