Talking about computational medicine, genomics and other fun biomedical datasciency stuff at Vanderbilt!

1. Ben Busby, Ph.D.
Data Science Education Something…
NCBI et al
Founder, Department of Bioinformatics and Data Science, FAES
ben.busby@nih.gov, @dcgenomics, LinkedIn
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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“Joseph Halstead” is another incredibly common name (+team)

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Robert Butler and Lucy Wang (+team)

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86. MASSIF-BLAST

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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

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Planned Events
RNAseq – UNC, March 11-13 2019;
Palo Alto, June 2019
Smaller events at USF and Pittsburgh
Human PanGenomics – UCSC, 25-27 March 2019;
Haplotype Annotation, Baltimore, June 2019
Variant Synthetic Dataset Generation –
Boston, April 15-16, 2019
AMR and Prokaryotic Genome Annotate-athon
NIH Campus, August 2019

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Virus Discovery!

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RNA-seq Indexing!

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RNA-seq Indexing!

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https://github.com/NCBI-Hackathons/RNA-Seq-in-the-Cloud

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Building a Usable Human Pangenome!

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Building a Usable Human Pangenome!

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Building a Usable Human Pangenome!

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Building a Usable Human Pangenome!

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Building a Usable Human Pangenome!

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Building a Usable Human Pangenome!

119. Creating a Community
https://biohackathons.github.io
MACHINE LEARNING
PROJECT MANAGEMENT
PRODUCT MANAGEMENT

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121. NCBI Visiting Bioinformaticians Group
May 2018
Visiting
Bioinformatician
Program

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AA/Typhi

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