GenomeHubs–Life Science Informatics & HPC

By Chris Dagdigian

BioTeam

Category

Seminars

Published on

Abstract

Bioinformaticist-gone-bad Chris Dagdigian has spent the last 15 years as a high performance research IT specialist focusing on building, fixing, growing and optimizing IT systems designed to support & accelerate life science research. As a consultant, Chris gets to see how different organizations (Pharma, Biotech, Government, Academic and Non-profit) approach similar problems and he can relay war stories, trends, trips and tricks as seen directly from the trenches.

This session is intended as a general introduction to the life science informatics domain and will cover the application mix, common workflows and an overview of the most critical requirements and technology challenges facing life science researchers today. Hubs and Portals will be discussed along with a frank discussion of where the life science "sweet spots" are for leveraging platforms like HUBzero across public, private, government and nonprofit research organizations. A specific project involving the use of HUBzero within a US public health agency will also be covered.

Bio

Chris is an infrastructure geek & co-founder of the BioTeam – a specialist consulting firm occupying the niche between high performance computing, IT and discovery-oriented life science research. Chris has spent much of the last 15 years designing, building, fixing and improving research-focused HPC and IT systems for use in demanding production computing environments. He occasionally is known to blog, tweet and speak about industry trends and best practices.

Cite this work

Researchers should cite this work as follows:

  • Chris Dagdigian (2013), "GenomeHubs–Life Science Informatics & HPC," https://help.hubzero.org/resources/987.

    BibTex | EndNote

Submitter

Nikki Huang

Purdue University

Tags

GenomeHubs–Life Science Informatics & HPC
  • GenomeHubs: Life Science Informatics & HPC 1. GenomeHubs: Life Science Infor… 0
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  • Who I am 2. Who I am 30.53053053053053
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  • BioTeam 3. BioTeam 84.38438438438439
    00:00/00:00
  • Disclaimer 4. Disclaimer 176.40974307640974
    00:00/00:00
  • Why I am here 5. Why I am here 211.41141141141142
    00:00/00:00
  • Goal: 6. Goal: "Talk Fast & Get Out Of … 291.02435769102436
    00:00/00:00
  • QUICK SPRINT: LIFE SCIENCE INFORMATICS 7. QUICK SPRINT: LIFE SCIENCE INF… 321.82182182182186
    00:00/00:00
  • Life Science Informatics 8. Life Science Informatics 344.77811144477812
    00:00/00:00
  • The Cliche Example 9. The Cliche Example 436.20286953620291
    00:00/00:00
  • Meta Issue: It is a scary time to be doing Bio-IT 10. Meta Issue: It is a scary time… 494.02736069402738
    00:00/00:00
  • Big Picture / Meta Issue 11. Big Picture / Meta Issue 497.09709709709711
    00:00/00:00
  • The Central Problem Is ... 12. The Central Problem Is ... 562.7961294627961
    00:00/00:00
  • The Central Problem Is ... 13. The Central Problem Is ... 566.73340006673345
    00:00/00:00
  • This is our new normal 14. This is our new normal 582.48248248248251
    00:00/00:00
  • And a related problem ... 15. And a related problem ... 603.97063730397065
    00:00/00:00
  • If we get it wrong ... 16. If we get it wrong ... 707.640974307641
    00:00/00:00
  • A few infrastructure pictures ... 17. A few infrastructure pictures … 792.92625959292627
    00:00/00:00
  • The cliche image 18. The cliche image 801.901901901902
    00:00/00:00
  • Lab local HPC & storage 19. Lab local HPC & storage 841.675008341675
    00:00/00:00
  • Small core w/ multiple NGS instrument 20. Small core w/ multiple NGS ins… 851.685018351685
    00:00/00:00
  • Large Core Facility 21. Large Core Facility 864.46446446446453
    00:00/00:00
  • Large Core Facility: Just Storage 22. Large Core Facility: Just Stor… 875.10844177510853
    00:00/00:00
  • Regional Scientific Computing 23. Regional Scientific Computing… 881.21454788121457
    00:00/00:00
  • Physical data movement station; Unit= 24. Physical data movement station… 905.60560560560566
    00:00/00:00
  • Physical Ingest Repo & 25. Physical Ingest Repo & "Naked"… 915.648982315649
    00:00/00:00
  • 30 of Amazon's largest nodes plus 22 GPU nodes 26. 30 of Amazon's largest nodes p… 941.04104104104113
    00:00/00:00
  • Basic Bio/IT Landscape 27. Basic Bio/IT Landscape 1006.7400734067401
    00:00/00:00
  • Core Compute 28. Core Compute 1014.2475809142476
    00:00/00:00
  • File & Data Types 29. File & Data Types 1050.950950950951
    00:00/00:00
  • Application characteristics 30. Application characteristics 1086.9202535869204
    00:00/00:00
  • Storage & Data Management 31. Storage & Data Management 1117.1171171171172
    00:00/00:00
  • Storage & Data Management 32. Storage & Data Management 1168.0680680680682
    00:00/00:00
  • Data Movement & Data Sharing 33. Data Movement & Data Sharing 1251.4848181514849
    00:00/00:00
  • We Have Both Ingest Problems Physical & Network 34. We Have Both Ingest Problems P… 1264.7647647647648
    00:00/00:00
  • Physical Ingest Just Plain Nasty 35. Physical Ingest Just Plain Nas… 1267.3006339673007
    00:00/00:00
  • Huge Need For Network Ingest 36. Huge Need For Network Ingest 1303.2032032032032
    00:00/00:00
  • Cloud(s) 37. Cloud(s) 1349.94994994995
    00:00/00:00
  • Cloud Hubs & Portals 38. Cloud Hubs & Portals 1433.933933933934
    00:00/00:00
  • Cloud Data Repositories 39. Cloud Data Repositories 1444.8448448448448
    00:00/00:00
  • It all boils down to this ... 40. It all boils down to this ... 1459.0924257590925
    00:00/00:00
  • Life Science In One Slide 41. Life Science In One Slide 1460.8942275608943
    00:00/00:00
  • HUBs for Life Science Informatics 42. HUBs for Life Science Informat… 1506.9736403069737
    00:00/00:00
  • hubzero and one .gov 43. hubzero and one .gov 1511.544878211545
    00:00/00:00
  • hubzero and one .gov 44. hubzero and one .gov 1530.2969636302971
    00:00/00:00
  • hubzero and one .gov 45. hubzero and one .gov 1567.5675675675677
    00:00/00:00
  • Current Status 46. Current Status 1611.8118118118118
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  • Future Status 47. Future Status 1636.4364364364365
    00:00/00:00
  • Time permitting ... 48. Time permitting ... 1696.3630296963631
    00:00/00:00
  • Time? 49. Time? 1698.3650316983651
    00:00/00:00
  • My $.02: Internal Hubzero assessment 50. My $.02: Internal Hubzero asse… 1700.7007007007007
    00:00/00:00
  • My $.02: Internal Hubzero assessment 51. My $.02: Internal Hubzero asse… 1725.9592926259593
    00:00/00:00
  • My $.02: Internal Hubzero assessment 52. My $.02: Internal Hubzero asse… 1748.0146813480149
    00:00/00:00
  • War Stories 53. War Stories 1826.6933600266934
    00:00/00:00
  • One last thing ... 54. One last thing ... 1832.6993660326993
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  • One last thing ... 55. One last thing ... 1834.5679012345679
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  • One last thing ... 56. One last thing ... 1856.7233900567235
    00:00/00:00
  • end; Thanks! 57. end; Thanks! 1913.446780113447
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