Literature DB >> 20514356

Free Factories: Unified Infrastructure for Data Intensive Web Services.

Alexander Wait Zaranek, Tom Clegg, Ward Vandewege, George M Church.   

Abstract

We introduce the Free Factory, a platform for deploying data-intensive web services using small clusters of commodity hardware and free software. Independently administered virtual machines called Freegols give application developers the flexibility of a general purpose web server, along with access to distributed batch processing, cache and storage services. Each cluster exploits idle RAM and disk space for cache, and reserves disks in each node for high bandwidth storage. The batch processing service uses a variation of the MapReduce model. Virtualization allows every CPU in the cluster to participate in batch jobs. Each 48-node cluster can achieve 4-8 gigabytes per second of disk I/O. Our intent is to use multiple clusters to process hundreds of simultaneous requests on multi-hundred terabyte data sets. Currently, our applications achieve 1 gigabyte per second of I/O with 123 disks by scheduling batch jobs on two clusters, one of which is located in a remote data center.

Year:  2008        PMID: 20514356      PMCID: PMC2877279     

Source DB:  PubMed          Journal:  Proc USENIX Annu Tech Conf


  8 in total

1.  Accurate multiplex polony sequencing of an evolved bacterial genome.

Authors:  Jay Shendure; Gregory J Porreca; Nikos B Reppas; Xiaoxia Lin; John P McCutcheon; Abraham M Rosenbaum; Michael D Wang; Kun Zhang; Robi D Mitra; George M Church
Journal:  Science       Date:  2005-08-04       Impact factor: 47.728

2.  Sequencing genomes from single cells by polymerase cloning.

Authors:  Kun Zhang; Adam C Martiny; Nikos B Reppas; Kerrie W Barry; Joel Malek; Sallie W Chisholm; George M Church
Journal:  Nat Biotechnol       Date:  2006-05-28       Impact factor: 54.908

3.  2020 computing: science in an exponential world.

Authors:  Alexander Szalay; Jim Gray
Journal:  Nature       Date:  2006-03-23       Impact factor: 49.962

4.  Positively disruptive.

Authors: 
Journal:  Nat Genet       Date:  2008-02       Impact factor: 38.330

Review 5.  From genetic privacy to open consent.

Authors:  Jeantine E Lunshof; Ruth Chadwick; Daniel B Vorhaus; George M Church
Journal:  Nat Rev Genet       Date:  2008-05       Impact factor: 53.242

6.  Long-range polony haplotyping of individual human chromosome molecules.

Authors:  Kun Zhang; Jun Zhu; Jay Shendure; Gregory J Porreca; John D Aach; Robi D Mitra; George M Church
Journal:  Nat Genet       Date:  2006-02-19       Impact factor: 38.330

7.  Polony multiplex analysis of gene expression (PMAGE) in mouse hypertrophic cardiomyopathy.

Authors:  Jae Bum Kim; Gregory J Porreca; Lei Song; Steven C Greenway; Joshua M Gorham; George M Church; Christine E Seidman; J G Seidman
Journal:  Science       Date:  2007-06-08       Impact factor: 47.728

8.  The personal genome project.

Authors:  G M Church
Journal:  Mol Syst Biol       Date:  2005-12-13       Impact factor: 11.429

  8 in total
  3 in total

1.  A survey of genomic traces reveals a common sequencing error, RNA editing, and DNA editing.

Authors:  Alexander Wait Zaranek; Erez Y Levanon; Tomer Zecharia; Tom Clegg; George M Church
Journal:  PLoS Genet       Date:  2010-05-20       Impact factor: 5.917

2.  A public resource facilitating clinical use of genomes.

Authors:  Madeleine P Ball; Joseph V Thakuria; Alexander Wait Zaranek; Tom Clegg; Abraham M Rosenbaum; Xiaodi Wu; Misha Angrist; Jong Bhak; Jason Bobe; Matthew J Callow; Carlos Cano; Michael F Chou; Wendy K Chung; Shawn M Douglas; Preston W Estep; Athurva Gore; Peter Hulick; Alberto Labarga; Je-Hyuk Lee; Jeantine E Lunshof; Byung Chul Kim; Jong-Il Kim; Zhe Li; Michael F Murray; Geoffrey B Nilsen; Brock A Peters; Anugraha M Raman; Hugh Y Rienhoff; Kimberly Robasky; Matthew T Wheeler; Ward Vandewege; Daniel B Vorhaus; Joyce L Yang; Luhan Yang; John Aach; Euan A Ashley; Radoje Drmanac; Seong-Jin Kim; Jin Billy Li; Leonid Peshkin; Christine E Seidman; Jeong-Sun Seo; Kun Zhang; Heidi L Rehm; George M Church
Journal:  Proc Natl Acad Sci U S A       Date:  2012-07-13       Impact factor: 11.205

3.  Swift: primary data analysis for the Illumina Solexa sequencing platform.

Authors:  Nava Whiteford; Tom Skelly; Christina Curtis; Matt E Ritchie; Andrea Löhr; Alexander Wait Zaranek; Irina Abnizova; Clive Brown
Journal:  Bioinformatics       Date:  2009-06-23       Impact factor: 6.937

  3 in total

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