This document summarizes Ben Busby's presentation on making the transition from sharing data to sharing knowledge at NCBI. The presentation discusses NCBI tools and resources like EUtils, EDirect, PubMed FTP, and SRA. It also highlights several genomic analysis tools developed through NCBI hackathons and available on GitHub. The document lists Busby's contact information and encourages attendees to check his SlideShare profile and NCBI's bioinformatics training program for more details.

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

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

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EDirect Local Caching!

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PubMed and PMC (Open) FTP

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

9. ©MartineZilversmit2013

11. Reporting

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

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

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

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

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

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

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

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

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

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

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

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

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

63. Available to
anyone!

64. First 5 lectures
now available
on

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

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74. phenvar.colorado.edu

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

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78. Other People’s Hackathons

79. @DCGenomics
Communication

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

81. Creating a Community

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

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