Slides for an i5k webinar featuring a workflow examining a wolbachia in brugia malayi.

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

5. 5
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

12. Reporting

14. Google for
“BioSample Template”

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

28. Please check out slideshare to grab the details.
https://www.slideshare.net/benbusby
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You can now filter BLAST+
Databases like nr, nt and
refseq_genomic by
taxonomy. Check out
https://ftp.ncbi.nlm.nih.gov/
blast/db/v5/blastdbv5.pdf
for details!

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The aspartate-semialdehyde dehydrogenases are not
dramatically different in Drosophila melanogaster
wolbachia and Brugia malayi wolbachia
(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

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

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

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

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

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

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

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

68. Available to
anyone!

69. First 5 lectures
now available
on

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

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80. Other People’s Hackathons

81. @DCGenomics
Communication

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

83. Creating a Community

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

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