Platforms for scientific data analysis

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There is no magic, only awesome  Building a platform for scientiﬁc data analysis D e e p a k S i n g h ( @ m n d o c i ) P r i n c i p a l P r o d u c t M a n a g e r - A m a z o n E C 2

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Good morning!

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bioinformatics

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Collection

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Curation

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Analysis

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so what?

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Image: Yael Fitzpatrick (AAAS)

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lots of data

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lots of people

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lots of places

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constant change

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we want to make our data more effective

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versioning

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provenance

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ﬁlter Via asklar under a CC-BY license

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Image: Chris Heiler aggregate

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extend Image: Bethan

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human interfaces Image: Sebastian Anthony

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image: Leo Reynolds communicate

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hard problem

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^ Really hard problem

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How can we be more effective with data?

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Wrong question

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How can we be more effective with our people?

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text Image: Pieter Musterd Remove constraints

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Move data to the users?

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Move tools to the data

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Give tools access to data

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Give data access to tools

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APIs

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so how do   get there?

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information platforms

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the unreasonable effectiveness of data Halevy, et al. IEEE Intelligent Systems, 24, 8-12 (2009)

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accept all data formats

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evolve APIs

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data is a programmable resource

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compute is a   fungible commodity

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Amazon EC2

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ec2-run-instances

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programmable

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Building Blocks

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Genomic data is assembled and analyzed in Complete Genomics’ data center and then is securely transferred over a dedicated network to Amazon Web Services (AWS) for delivery to customers either by shipping hard disk drives or electronically. Automatic transfer of raw data to the cloud in real time during the course of the sequencing run http://blog.basespace.illumina.com/2012/08/10/basespace-‐growth-‐the-‐ numbers/ • 70% of all installed MiSeqs have connected to BaseSpace • BaseSpace on HiSeq in Q4 2012 Sequencing data going straight to the cloud

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Analyze data in the cloud

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Computational compound analysis  Solar panel material   Estimated computation time 264 years    156,314 core cluster across 8 regions 1.21 petaFLOPS (Rpeak) Simulated 205,000 materials 18 hours for $33,000 16¢ per molecule 1 c|net news ! http://news.cnet.com/8301-1001_3-57611919-92/supercomputing-simulation-employs-156000-amazon-processor-cores/

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Migrated clinical trials simulations platform Simulations in 1.2hrs vs. 60hrs! 64% reduction in costs Clinical Pharmacology & Pharmacometrics Molecular Dynamics Computational Genomics Research Application Portfolio 98% time saved for clinical trial simulations Internal System Cloud Individual Clinical Trial Simulation Run Time (Min) 56 56 Total Number of Clinical Trial Simulations 2000 2000 No. Servers 2 256 No. CPU’s 32 2048 Total Analysis Run Time (hr) 60 1.2 Cost ?? $336

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CHARGE Consortium  Aimed at better understanding how human genetics contributes   to heart disease and aging

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Collaborating around data: National Database for Autism Research

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• An online environment to drive collaboration among researchers • Synapse hosts clinical- genomic datasets • Provides a shared compute space and suite of analysis tools for researchers

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Global Collaboration for Global Manufacturing Cloud provides a global, distributed, secure, and scalable environment for collaborative design and manufacturing

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Reproduce. Reuse. Remix

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https://github.com/awslabs/cfncluster

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[plugin ipcluster] setup_class = ipcluster.IPCluster enable_notebook = true notebook_passwd = YOUR-PASS ! [cluster qiime]  node_image_id = ami-2faa7346  keyname = YOUR-KEY  cluster_size = 4  node_instance_type = m2.4xlarge  plugins = ipcluster ! $ starcluster start -c qiime myqiime Source: Justin Riley