umcp cs talk_11_3_16_v1

Ben Busby, Ph.D.Genomics Outreach Coordinator

NCBIben.busby@nih.gov

Making the Transition from Sharing Data to Sharing

KnowledgeGenomic Variation in the Rising Era of Individual Genome Sequence

but first...Better PubMed Searches!

For more information go to:ncbi.nlm.nih.gov/learn

Review of terminology and conceptsNext Generation Sequencing

Graphic Credit: Spencer Martin, UBC

Review of terminology and conceptsHow Genomes are Mapped and Assembled

© Martine Zilversmit 2013

http://1.usa.gov/1J1xmYs

NCBI NGS Online Workshop – Available on the NCBI YouTube Channel!

Review of terminology and conceptsHow Genomes are Mapped and Assembled

BioProject

BioProject

dbGaP

dbGaP

2007 2008 2009 2010 2011 2012 2013 2014 2015

14,20153,216

139,311

374,464

485,727

566,181

660,665

876,849

1,002,935

Subjects

dbGaP – GWAS and PheGenI

dbGaP – GWAS and PheGenI

dbGaP – ClinVar

ClinVar

ClinVar

ClinVar – Why Should we Care?

ClinVar – Why Should we Care?

ClinVar – Why Should we Care?

ClinVar – Why Should we Care?

ClinVar – Why Should we Care?

ClinVar – Why Should we Care?

SRA Data Structures

Investigation of NGS:SRA BLAST!

sra-search

sra-search

sra-search

Investigation of NGS:SRA BLAST!

Investigation of NGS:MagicBLAST!

Why SRA Data Structures?

sam-dump.2.6.3 --aligned-region 17:41243452-41277500 SRR925743 > BRCA1.sam

GATK (use screen or &)

.vcf from GATK

hisat2

Read Count generator (spark_genes)

GitHub Repositories

Visualizing Data on Assemblies

Visualizing SRA in the Context of RefSeq

http://www.ncbi.nlm.nih.gov/projects/sviewer/?id=NC_000009.11&app_context=Variation_Viewer_1-1&srz=SRR1556217&v=21967751:21994490

https://goo.gl/8GPv8S

Helping Investigators make reads into [good] genomes!

The NCBI Eukaryotic Annotation Pipeline

The NCBI Prokaryotic Annotation Pipeline

Transcriptome Shotgun Assembly Database

Type Strain Databases

Targeted Locus Studies!

Making OTUs from Metagenomic DataMOLE-BLAST!

“Superbankit!”

Superbankit!

Viral Genomes

Virus Variation

Virus Variation

Virus Variation

Subscribe!

Food Borne Pathogens

Food Borne Pathogens

Food Borne Pathogens

Where to Get More Information!

Where to Get More Information!

E-Utilities (Eutils)

Video available at:http://www.ncbi.nlm.nih.gov/education/webinars/

61

E-Utilities (Eutils)

62

Introducing… Entrez DirectThe E-utilities on the UNIX

command line

esearch –db gene –query “foxp2[gene] AND human[orgn]” | \

elink –target protein –name gene_protein_refseq | \

efetch –format fasta

ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/

63

Edirect Cookbook

64

Moving from FTP-scraping cron jobs to on-demand APIs

65

Edirect Cookbook (DRAFT)

66

New APIs!

67

Generating apps that work with our APIs and Data Structures,

and Improve Metadata:

NCBI Hackathons!

January 2015 4 functional software products 3 days

Hackathons

August 2015 6 Functional Software Products 3 Days

August 2015 6 Functional Software Products 3 Days

August 2015 6 Functional Software Products 3 Days

Hackathons

www.iMetric.io

An Educational Resource for RNAseq

Available to

anyone on AWS

Part of an Online Workshop

First 5 lectures

now available

on

Community Tools

www.iMetric.io

Community Tools

Community Tools

January 2016 6 Functional Software Products 3 Days

January 2016 6 Functional Software Products 3 Days

January 2016 6 Functional Software Products 3 Days

Hackathons

www.iMetric.io

January 2016

6 Functional Software Products 3 Days

Hackathons

January 2016 6 Functional Software Products 3 Days

Hackathons

Hackathons

Hackathons

January 2016 6 Functional Software Products 3 Days

HackathonsJanuary 2016 6 functional software products 3 days

Hackathons

Hackathons

In April, July, August and

October 2016

we built on

those projects .

Hackathons

Finding immunogenic peptides from single RNA-seq samples

DangerTrackDifficult to assess regions

Combined score is the average of SVs, mappability, GC..

NCBI region list

Encode blacklist

Get More Info!

In Twitter @NCBI@DCGenomics

In 2017 we will Build on Those Projects!

Biomedical Informatics Hackathon January 9th – 11th NIH Campus, Bethesda!

NCBI Genomics Hackathon March 20-22nd NIH Campus, Bethesda