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Creating a Biolinux AMI at Amazon’s EC2. Joe Steele Amazon E2. Computing cluster – create an account and provide a credit card. Let Amazon take care of the hardware. Cloud BioLinux.

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Creating a Biolinux AMI at Amazon’s EC2

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    1. Creating a BiolinuxAMIat Amazon’s EC2 Joe Steele

    2. Amazon E2 Computing cluster – create an account and provide a credit card. Let Amazon take care of the hardware.

    3. Cloud BioLinux JCVI (J. Craig Venter Institute) created cloud version of NERC BioLinux VM. An Ubuntu machine with over 100 NEBC software packages. Image stored at EC2, is available to be copied at no charge, by EC2 users.


    5. Create a new account

    6. Enter your information

    7. Sign up for an EC2 account

    8. Click on “Sign up for Amazon EC2”

    9. EC2 Account • Signing up for EC2 automatically signs you up for Amazon Simple Storage Service, and Amazon Virtual Private Cloud. • Requires credit card information. • No charges until you start using the services. • Amazon will email with Access Identifiers, and instructions for your first log in.

    10. Click on “AWS Management Console”

    11. Click the EC2 Tab

    12. Launch an Instance

    13. I recommend biolinux

    14. Click “Select”

    15. Pricing • Amazon has a variety of VM sizes available – pricing is at: • You are charged for CPU usage, for data storage, and for data transferred to or from Amazon. Charges continue until a VM is “Terminated”. • You can set up a small test VM for free – select “Micro” for the size.

    16. Kernel defaults are fine

    17. Key files For biolinux, you don’t need to add “User Data”. For some machines,the Amazon key IS needed to connect. When you create a Key Pair (next slide), save the *.pem file to a safe place.

    18. Create a Key Pair

    19. PEM file Save the *.pem file to a safe place. Linux: the *.pem file has to be protected: >chmod 400 <key_file>.pem Windows: Download PuTTYgen, and use it to change the *.pem file to a *.ppk file.

    20. Create security group

    21. Launch

    22. Machine info

    23. “Terminate” to end charges

    24. First connection to Biolinux A window opens, telling you how to connect to your new VM, eg,: “ssh -i key_pair_name.pem” However, for biolinux, or any unbuntu VM, do: ssh –i key_pair_name.pem from a Linux machine, make sure the key_pair_name.pem is set to read only for the user only.

    25. First Connection From Windows: Use PuTTYgen to change key_pair_name.pem to key_pair_name.ppk. Use PuTTY to connect, and put key_pair_name.ppk under “SSH” -> “Auth”. When connected to biolinux, you will be asked to set a password for ubuntu. If not, you need to start NX client: >./

    26. NX Use NX for the graphical display (built in to biolinux already). Open source, can be found at Must ssh into VM FIRST, using the key pair. You can stick with the ubuntu user, or add new users: >adduser <username> >groups >usermod -G <grp1>,<grp2>,ssh <username>

    27. Start NX

    28. “Configure”

    29. Configure NX Note the use of “GNOME” and “LAN”. The Host should be “ec2-72-…”. Also, the “Key…” works with the default key.

    30. BioLinux over NX

    31. BioLinux over NX

    32. BioLinux over NX

    33. BioLinux over NX

    34. Data Stored at Amazon There are large datasets stored at Amazon, available for use – free of charge (mostly). You are charged for any data you copy. to search through them. Datasets that might be of interest in bioinformatics are listed at:


    36. Datasets Human DNA sequences: • 1000 Genomes Project (7,300 GB) • Ensembl Annotated Human Genome - FASTA (115 GB) • Ensembl Annotated Human Genome - MySQL (200 GB) • GenBank (200 GB) • Human Liver Cohort (Sage Bionetworks) (0.6 GB) • Illumina - Jay Flatley's Human Genome Data Set. (350 GB) • YRI Trio Data - complete genome sequence for three individuals (700 GB) Other (might include some human data): • Ensembl - FASTA DB (100 GB) • Influenza Virus (including Swine Flu) - from NCBI (1 GB) • UniGene - from NCBI (10 GB) • PubChem Library - from NCBI (230 GB)

    37. Public Snapshots

    38. Select “Volumes”

    39. Create a Volume

    40. Instance Information

    41. Attach it to your Instance

    42. Mount the Volume From your VM: >sudomkfs –t ext3 /dev/sdf >sudomkdir /mnt/datasets >sudo mount –t ext3 /dev/sdf /mnt/datasets 200GB of genbank data are now in /mnt/datasets

    43. Test Usage for the First Year

    44. CPU charges

    45. Data Transfer charges

    46. Data storage charges