SfN 2015 - NIMH Data Archives - Jupyter Notebook Demonstration

Jupyter Notebook presentation of:

• accessing data contained in a miNDAR;
• generating an AWS Temporary Security Token using NDA username/password;
• streaming data from s3 objects using miNDAR for S3 paths.

Additional demonstrations added post-SfN:

• Stream VCF file from s3 and do free-text search;
• Stream VCF file from s3 and parse with pyvcf;
• Stream slice from a BAM file located in s3.

Resources

The SETUP.md markdown file in this repository has detailed instructions for setting up the environment on Amazon Web Services base 64 bit Ubuntu (14.04) Linux AMI.

Additional resources:

• How to build htslib and samtools to support access to remote S3 objects with temporary security token (https://www.biostars.org/p/147772/)
• NIMH Data Archives Query Tools https://ndar.nih.gov/query_data.html
• miNDAR page https://ndar.nih.gov/launch_cloud_db.html (requires login)
• Tutorials https://ndar.nih.gov/training.html
• NIMH Data Archives GitHub account (https://github.com/NDAR)

For Additional Help

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