Slides for CMU open science symposium. Outlining tools that can be used to index and extract open data easily and quickly!

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

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

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

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

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

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45. phenvar.colorado.edu

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

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