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Getting Biologists off ACID

Getting Biologists off ACID. Ryan Verdon 3/13/12. Outline. Thesis Idea Specific database Effects of losing ACID What is a NoSQL database Types of NoSQL databases with examples. Thesis Idea. Amount of biological data is growing exponentially Hardware cannot keep up with the growth.

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Getting Biologists off ACID

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  1. Getting Biologists off ACID Ryan Verdon 3/13/12

  2. Outline • Thesis Idea • Specific database • Effects of losing ACID • What is a NoSQL database • Types of NoSQL databases with examples

  3. Thesis Idea • Amount of biological data is growing exponentially • Hardware cannot keep up with the growth

  4. Database Survey • In 2003, a survey was conducted of 111 biological databases. • 96 (i.e. 87%) of the 111 considered databases have Hypertext references to other databases, • 40 to 44 (i.e. 36% to 40%) are implemented as flat files, • 41 (or 42) (i.e. 37%) are implemented using a relational database management system, • 7 (i.e. 6%) use an object database management system, • 3 (.i.e. 3%) use an object-relational database management system, • and all databases collect data from different sources.

  5. Specific Database

  6. Flybase • Primary biology database on the insect family Drosophilidae (fruit fly) • Important research from fruit flies includes • Genes • Recombination • Signaling networks (important for major diseases) • Stem cells • Growth control

  7. Info on the Flybase database • Single server relational database • Over 135 tables • Uses Chado schema • Gives data a “type” • Creates a graph that relates the different types

  8. Effects of losing ACID

  9. ACID • Atomicity • Consistency • Isolation • Durability

  10. CAP Theorem • Consistency • Availability • Partition tolerance

  11. BASE consistency model • Basically Available • Soft state • Eventually consistent • Given enough time where no changes are made, all replicas will see the same data

  12. NoSQL

  13. What is a NoSQL database • Any non-relational database • Hierarchical • Graph • Object oriented • Etc.

  14. Why were NoSQL databases created • To overcome limitations of relational databases • Predefined layout • Scaling • SQL • Large feature set

  15. Major types of NoSQL databases • Key-value stores • Column-oriented databases • Document based stores

  16. Key-value stores • Stored values are indexed for retrieval by keys • Can store unstructured or structured data • Similar to DHTs

  17. Example: Dynamo • Created by Amazon, only used internally • Highly available even in the face of continual failures • Amazon realized many services only need primary-key access • Best seller lists • Shopping carts • Session management

  18. Column-oriented databases • Contain extendable columns of closely related data • Can greatly benefit from compression

  19. Example: HBase • Apache open-source project • Based off of Google’s Bigtable database • Ties in closely with Hadoop and map-reduce

  20. Document based stores • Data stored as a collection of documents • Documents can have any number of fields and any length • Documents are accessed via a unique key • Capabilities of the query language heavily depend on the implementation

  21. Example: MongoDB • Started by 10gen • Supports • Replication • Map-reduce • Sharding • Used by lots of large companies including • Disney • Craigslist

  22. Questions ?

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