Taylor bosc2010

Ronald Taylor, Ph.D. Computational Biology & Bioinformatics Group Computational Sciences & Mathematics Division Pacific Northwest National Laboratory (PNNL) Richland, Washington Email: [email_address] An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics BOSC 2010 – July 9, 2010

General background - cloud computing ,[object Object],[object Object]

Hadoop (1) ,[object Object],[object Object],[object Object]

Hadoop (2) ,[object Object],[object Object],[object Object]

Hadoop (3) ,[object Object],[object Object],[object Object],[object Object]

Hadoop (4) – MapReduce ,[object Object],[object Object],[object Object],[object Object],[object Object]

Hadoop (5) ,[object Object],[object Object],[object Object],[object Object]

HBase (1) ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

HBase (2) ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

HBase (3) ,[object Object],[object Object],[object Object],[object Object],[object Object]

Pig ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Hive ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Cascading ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

NoSQL, non-Hadoop alternatives for scalability in distributed environments ,[object Object],[object Object],[object Object],[object Object]

Amazon Elastic Compute Cloud (EC2) ,[object Object],[object Object],[object Object],[object Object],[object Object]

NoSQL db testing and benchmarking ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Improving MapReduce - example work ,[object Object],[object Object],[object Object],[object Object]

Hadoop Use in Machine Learning ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Knowledgebase possibilities ,[object Object],[object Object],[object Object],[object Object],[object Object]

Hadoop in Bioinformatics - today’s talks ,[object Object],[object Object],[object Object],[object Object],[object Object]

Bioinformatics - work at University of Maryland (Michael C. Schatz, Ben Langmead, and colleagues) ,[object Object],[object Object],[object Object],[object Object]

Bioinformatics - work at University of Maryland (Michael C. Schatz, Ben Langmead, and colleagues) - continued ,[object Object],[object Object],[object Object],[object Object]

Bioinformatics - work at Indiana University (Judy Qiu and her colleagues) ,[object Object],[object Object],[object Object],[object Object]

Bioinformatics - BLAST and GSEA in Hadoop ,[object Object],[object Object],[object Object],[object Object],[object Object]

Bioinformatics - CloudBLAST (2008) ,[object Object],[object Object],[object Object],[object Object],[object Object]

Bioinformatics work at PNNL Using Hadoop/HBase ,[object Object],[object Object],[object Object],[object Object]

Recent Hadoop / bioinformatics papers ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Taylor bosc2010

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Taylor bosc2010