This document appears to be a slide deck presentation given by Ben Busby on making the transition from sharing data to sharing knowledge. Some of the key points covered in the presentation include EUtilities command line and EDirect tools for accessing NCBI resources, PubMed and PMC open FTP, tools like Pubrunner.org as an alternative to PubMed FTP, examples of bioinformatics resources and tools developed through NCBI hackathons posted on GitHub, and an opportunity to work at NCBI for 4-6 weeks through their bioinformatics training program.

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

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

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

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

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

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49. phenvar.colorado.edu

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

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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

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

62. Available to
anyone!

63. First 5 lectures
now available
on

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71. Blog post coming soon!

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

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85. MASSIF-BLAST

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92. 92Crusoe, et al.

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94. Other People’s Hackathons

95. Other People’s Hackathons

96. @DCGenomics
Communication

97. Creating a Community
https://biohackathons.github.io

98. Creating a Community

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

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

101. Creating a Community
https://biohackathons.github.io

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