Course Details

  • Date: June 6th, 2016 - June 8th, 2016
  • Time: 9:30 am - 4:30 pm
  • Location:
  • Presenter(s): Peter Cooper (NCBI), Wayne Matten (Division of NLM)

The ‘NCBI Resources for CCR Scientists’ workshop, on June 6 and June 8, 2016, will focus on teaching a wide range of resources developed within NCBI that are relevant for CCR scientists. It will include both hands-on and lecture components. Attending the workshop will enable one to understand the tools and databases available at NCBI and how to best use them for your research. A team of experts from NCBI will be presenting these sessions over two separate days.

NOTE: No sessions on June 7. This is a BYOC (Bring your own laptop Computer) class. Government issued or personal computers are permitted. We will be able to supply a very limited set of computers, so if you want to take the class but cannot bring your own computer please indicate such in the Comment section on the registration form. Please register only if you intend to attend the workshop.


Live Workshop – NIH Bethesda – Bldg 10

  • FAES Room 4 (June 6th) and

  • FAES Room 3 (June 8th)

Remote Simulcast – NCI-Frederick – Scientific Library Training Room, Bldg 549

For more information on the Frederick simulcast, please contact:
Tracie Frederick, Technology Informationist, Scientific Library
NCI at Frederick


Day 1 – Monday, June 6, 2016

9:30 am – 12:30 pm: Using NCBI’s Gene Expression Omnibus (GEO) to Explore Gene Expression

Instructor: Majda Valjavec-Gratian, Ph.D.

This 3-hour mainly hands-on workshop will show you how find and analyze relevant microarray and RNA-Seq datasets in NCBI’s Gene Expression Omnibus resources. After learning about data concepts in GEO, you will use both precomputed analyses in GEO Profiles and the GEO 2 R tool with non-curated experiments to investigate expression of genes of interest.

12:30 – 1:30 pm Lunch Break

1:30 – 4:30 pm: A Practical Guide to NCBI BLAST

Instructor: Peter Cooper, Ph.D.

This session highlights important features and demonstrates the practical aspects of using the NCBI BLAST service, the most popular sequence similarity service in the world. You will learn about useful but under-used features of the service. These include access from the Entrez sequence databases; the new genome BLAST service quick finder; the integration and expansion of Align-2-Sequences; organism limits and other filters; re-organized databases; formatting options and downloading options; and TreeView displays. You will also learn how to use other important sequence analysis services associated with BLAST including Primer BLAST, an oligonucleotide primer designer and specificity checker; the multiple protein sequence alignment tool, COBALT; and SmartBLAST, a new tool for rapid protein identification. These aspects of BLAST provide easier access and results that are more comprehensive and easier to interpret.

Day 2 – Wednesday, June 8, 2016

9:30 am – 12:30 pm: Accessing NCBI Human Variation and Medical Genetics Resources

Instructor: Peter Cooper, Ph.D

In this session, you will learn to use and access resources associated with human sequence variations and phenotypes associated with specific human genes and phenotypes. The webinar will emphasize the Gene, MedGen and ClinVar resources to search by gene, phenotype and variant. You will learn how to map variation from dbSNP and dbVAR onto genes, transcripts, proteins, and genomic regions and how to find genetic tests in GTR. You will also gain experience using additional tools and viewers including PheGenI, a browser for genotype associations, the Variation Viewer and the 1000 Genomes Browser. These provide useful ways to search for, map and browse variants as well as upload and download data in genomic context.

12:30 – 1:30 pm Lunch Break

1:30 – 2:30 pm: Introduction to NCBI command line tools on Cloud Services: EDirect and Standalone BLAST

Instructors: Wayne Matten, Ph.D. and Peter Cooper, Ph.D.

This session provides a quick introduction to NCBI command line tools in a cloud service. You will access an NCBI Amazon Machine Image and use the EDirect commandline interface to the Entrez system and standalone BLAST (including VDB BLAST) to perform basic text and sequence similarity searches. This workshop is essential preparation for the advanced workshop on the next-generation sequence analysis, which BTEP hopes to offer later this year.


2:30 – 4:30 pm: Sequence Read Archive (SRA), including hands-on with SRA-Blast in the AWS-Cloud

Instructor: Ben Busby, Ph.D.

This final session will describe how NCBI has enhanced several of its genomics resources in the last several months and how some of its public databases can be queried for computational biology and clinical questions, particularly those involving cancer biology.  The improved access to the underlying genomic data in several ways will be showcased, including making it possible to BLAST into our large genomic databases, and how to use popular genomics tools such as GATK and HISAT2 directly with SRA.  There will be a demo and hands-on exercise on how to use SRA-search and SRA-BLAST.