The next generation of large dataset analysis, with examples from NCBI, plus tools made in hackathons, and community resources for bioinformatics!

1. Ben Busby, Ph.D.
Genomics Outreach Coordinator, Bioinformatics Training Lead
NCBI
Founder, Department of Bioinformatics and Data Science
FAES
ben.busby@nih.gov
Making the Transition from Sharing Data to Sharing Knowledge

4. 4
EUtils (Search API) Command Line
EDirect
Google for
EDirect Cookbook

5. 5
EDirect Local Caching!

6. 6
PubMed and PMC (Open) FTP

7. 7
Instead of PubMed FTP…
An automated tool (alpha)
Pubrunner.org

9. ©MartineZilversmit2013

25. COOL
THING
#1 !
https://trace.ncbi.nlm.nih.gov/Traces/study/
?stat_search= 1561

32. Please check out slideshare to grab the details.
https://www.slideshare.net/benbusby
32

33. 33

34. 34

35. 35

36. 36

37. 37

38. 38
Punch line: lsrr is not different in typically virulent vs
avirulent strains of E coli so now I need to look at
expression -- but how do I do that?
(Fast section over.)

39. 39

40. 40

41. 41

43. 43
tar -xvzf ncbi-magicblast...
makeblastdb -dbtype nucl -in <fasta> -parse_seqids
magicblast -db <fasta> -sra SRR… -splice F -no_unaligned

44. 44
magicblast -db <fasta> -sra SRR… -splice F -no_unaligned
-num_threads X

48. 48

49. 49

51. 51

52. 52

53. Polygenic SNP Search Tool
https://github.com/NCBI-
Hackathons/PSST

54. 54

55. https://github.com/NCBI-
Hackathons/GenomicRobots

56. https://github.com/NCBI-Hackathons/Complex_Phenogeno

57. phenvar.colorado.edu

58. Combined score is
the average of SVs,
mappability, GC..
NCBI region list
Encode blacklist

60. 60
EUtils (Search API) Command Line
EDirect
Google for
EDirect Cookbook

61. 61
EUtils (Search API) Command Line
EDirect
Google for
EDirect Cookbook

63. https://github.com/NCBI-
Hackathons/ViruSpy

64. https://github.com/NCBI-
Hackathons/EndoVir

65. https://github.com/NCBI-
Hackathons/VirusFriends

66. 66

68. https://www.ncbi.nlm.nih.gov/core/assets/sra/files/Factsheet_SRA.pdf

69. Available to
anyone!

70. First 5 lectures
now available
on

72. 72

75. 75

76. https://ncbi-hackathons.github.io/GeneExpressionAging/ideogram

77. 77

78. 78

79. 79

80. 80

81. Other People’s Hackathons

82. @DCGenomics
Communication

83. Creating a Community
https://ncbi-hackathons.github.io

84. Creating a Community

85. Come work at NCBI for 4-6 weeks!
Email bioinformatics-training@ncbi.nlm.nih.gov
for more information!

86. Resources for Bioinformaticians!

87. Resources for Bioinformaticians!

88. Resources for Bioinformaticians!

89. Resources for Bioinformaticians!

90. Resources for Bioinformaticians!