This document provides an overview of bioinformatics resources from the National Center for Biotechnology Information (NCBI). It describes NCBI search tools like EUtils and PubMed FTP for accessing literature and sequence data. Variation APIs and other tools for analyzing genomic variants are also mentioned. The document promotes upcoming bioinformatics training opportunities at NCBI and lists example problems related to neurofibromatosis type 2 (NF2) that could be addressed using NCBI resources, such as identifying biological networks affected by NF2 mutations or clustering NF2 patient subpopulations.

1. Ben Busby, Ph.D.
Genomics Outreach Coordinator, Bioinformatics Training Lead
NCBI
Chair, Department of Bioinformatics and Data Science
FAES
ben.busby@nih.gov
A Crash Course in Bioinformatics with Examples from NCBI

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EUtils (Search API) Command Line
EDirect

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PubMed and PMC (Open) FTP

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Instead of PubMed FTP…
An automated tool (alpha)

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Variation APIs

15. Graphic Credit:
Spencer Martin, UBC

16. © Martine Zilversmit 2013

17. http://1.usa.gov/1J1xmYs
NCBI NGS Online Workshop – Available on the
NCBI YouTube Channel!

18. Graphic Credit:
Spencer Martin, UBC

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25. … and many, many more

28. phenvar.colorado.edu

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

31. Matching Expressed Variants in-memory;
Analyzing with Graphs
https://f1000research.com/articles/5-674/v1

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33. • August 14-16, NIH Campus
• September 25-27, Pittsburgh, PA
• January 8-10, NIH Campus
• February 19-21, Baylor College of Medicine
• March 11-14, NIH Campus
• April 2-4, 2018, UCSC
• May 15-17, 2018, Ann Arbor, MI
• June 20-22, Boulder CO
Come work at NCBI for 4-6 weeks!
Email bioinformatics-training@ncbi.nlm.nih.gov
for more information!

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Two additional problem tracks that may be of interest…
Are there biological networks that may be affected by NF2
mutations?
Can we document which networks are affected by NF2 and other gene
mutations that have been identified as relevant to the disease. How
do these networks affect each other, phenotype progression, and
treatment outcomes?
Can we make it simple to cluster subpopulations of NF2 patients?
Can we mine literature and other derived datasets to determine
subpopulations of NF2 patients? Can we point patients to more
appropriate clinical trials? Can we do quick screens of patient data to
classify the subtype of a new patient?

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…and now, logistics!