Introduction

In this work, we present the Genome Modeling System (GMS), an analysis information management system capable of executing automated genome analysis pipelines at a massive scale. The GMS framework provides detailed tracking of samples and data coupled with reliable and repeatable analysis pipelines. The GMS also serves as a platform for bioinformatics development, allowing a large team to collaborate on data analysis, or an individual researcher to leverage the work of others effectively within its data management system. Rather than separating ad-hoc analysis from rigorous, reproducible pipelines, the GMS promotes systematic integration between the two. As a demonstration of the GMS, we performed an integrated analysis of whole genome, exome and transcriptome sequencing data from a breast cancer cell line (HCC1395) and matched lymphoblastoid line (HCC1395BL). These data are available for users to test the software, complete tutorials and develop novel GMS pipeline configurations. The GMS is available at https://github.com/genome/gms.

Publications

  1. Genome Modeling System: A Knowledge Management Platform for Genomics.
    Cite this
    Griffith M, Griffith OL, Smith SM, Ramu A, Callaway MB, Brummett AM, Kiwala MJ, Coffman AC, Regier AA, Oberkfell BJ, Sanderson GE, Mooney TP, Nutter NG, Belter EA, Du F, Long RL, Abbott TE, Ferguson IT, Morton DL, Burnett MM, Weible JV, Peck JB, Dukes A, McMichael JF, Lolofie JT, Derickson BR, Hundal J, Skidmore ZL, Ainscough BJ, Dees ND, Schierding WS, Kandoth C, Kim KH, Lu C, Harris CC, Maher N, Maher CA, Magrini VJ, Abbott BS, Chen K, Clark E, Das I, Fan X, Hawkins AE, Hepler TG, Wylie TN, Leonard SM, Schroeder WE, Shi X, Carmichael LK, Weil MR, Wohlstadter RW, Stiehr G, McLellan MD, Pohl CS, Miller CA, Koboldt DC, Walker JR, Eldred JM, Larson DE, Dooling DJ, Ding L, Mardis ER, Wilson RK, 2015-07-01 - PLoS Computational Biology

Credits

  1. Malachi Griffith
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  2. Obi L Griffith
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  3. Scott M Smith
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  4. Avinash Ramu
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  5. Matthew B Callaway
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  6. Anthony M Brummett
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  7. Michael J Kiwala
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  8. Adam C Coffman
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  9. Allison A Regier
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  10. Ben J Oberkfell
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  11. Gabriel E Sanderson
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  12. Thomas P Mooney
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  13. Nathaniel G Nutter
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  14. Edward A Belter
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  15. Feiyu Du
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  16. Robert L Long
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  17. Travis E Abbott
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  18. Ian T Ferguson
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  19. David L Morton
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  20. Mark M Burnett
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  21. James V Weible
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  22. Joshua B Peck
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  23. Adam Dukes
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  24. Joshua F McMichael
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  25. Justin T Lolofie
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  26. Brian R Derickson
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  27. Jasreet Hundal
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  28. Zachary L Skidmore
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  29. Benjamin J Ainscough
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  30. Nathan D Dees
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  31. William S Schierding
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  32. Cyriac Kandoth
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  33. Kyung H Kim
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  34. Charles Lu
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  35. Christopher C Harris
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  36. Nicole Maher
    Developer

    Department of Medicine, Washington University School of Medicine, United States of America

  37. Christopher A Maher
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  38. Vincent J Magrini
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  39. Benjamin S Abbott
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  40. Ken Chen
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  41. Eric Clark
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  42. Indraniel Das
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  43. Xian Fan
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  44. Amy E Hawkins
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  45. Todd G Hepler
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  46. Todd N Wylie
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  47. Shawn M Leonard
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  48. William E Schroeder
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  49. Xiaoqi Shi
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  50. Lynn K Carmichael
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  51. Matthew R Weil
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  52. Richard W Wohlstadter
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  53. Gary Stiehr
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  54. Michael D McLellan
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  55. Craig S Pohl
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  56. Christopher A Miller
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  57. Daniel C Koboldt
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  58. Jason R Walker
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  59. James M Eldred
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  60. David E Larson
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  61. David J Dooling
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  62. Li Ding
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  63. Elaine R Mardis
    Developer

    The Genome Institute, Washington University in St. Louis, United States of America

  64. Richard K Wilson
    Investigator

    The Genome Institute, Washington University in St. Louis, United States of America

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Summary
AccessionBT000134
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByRichard K Wilson