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Calendar of Events

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Jun
7
Tue
Introduction to REDCap | June Class @ Health Sciences Library, lower level, Room T229
Jun 7 @ 10:00 am – 12:00 pm

Learn more about this class.

The Pacific Room (Room T229) is located on the lower level of the Health Sciences Library, near the after-hours entrance.

See an interactive map.

Register >

Jun
14
Tue
Navigating NCBI Molecular Data Using the Integrated Entrez System and BLAST @ UW Medicine South Lake Union, Building C, Room 123
Jun 14 @ 8:30 am – 11:30 am

ITHS, the University of Washington Health Sciences Library, Fred Hutch, and the National Network of Libraries of Medicine, Pacific Northwest Region are pleased to host five free NLM National Center for Biotechnology Information (NCBI) workshops on June 14 and 15, 2016, in Seattle, Washington, and online.

This workshop provides an introduction to the NCBI molecular databases and how to access the data using the Entrez text-based search system and BLAST sequence similarity search tool. You will learn the varied types of available molecular data, and how to find and display sequence, variation, genome information using organism sources (Taxonomy), data sources (Bioproject), and emphasizing the central role of the gene as an organizing concept to navigate across the integrated databases (Gene, Nucleotide, Protein, dbSNP, and other resources)

*It is recommended that attendees bring their own laptops or tablets to this workshop

Speaker Biography

Peter Cooper, PhD, is a Staff Scientist at the National Library of Medicine. Peter has directed the NCBI scientific education and outreach efforts for the past 18 years. He also provides user support for the NCBI molecular databases and the BLAST sequence similarity search services and contributes to feature and interface design for the BLAST standalone and web services. Prior to joining the NCBI, Peter pursued diverse biological research interests including peptide neurochemistry, marine environmental toxicology, and taught biology and chemistry. Peter earned a BS from Virginia Tech, a MA in chemistry from Johns Hopkins University, and a PhD in marine science from the College of William and Mary, School of Marine Science in 1996.

Registration

There is no cost to attend this event, but seating is limited. Please register below if you plan to attend. Not an ITHS member? Signing up to become a member will take less than two minutes.

Please sign in below to access this form.

Access to this form is restricted to ITHS Members. Please sign in.

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Members of ITHS are part of a unique catalyst that accelerates discoveries to practice. If you haven't signed up for an ITHS membership yet, learn more and join us.

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REDCap Advanced Class – Data Dictionary | June Class @ Health Sciences Library, lower level, Room T229
Jun 14 @ 10:00 am – 12:00 pm

Learn more about this class.

The Pacific Room (Room T229) is located on the lower level of the Health Sciences Library, near the after-hours entrance.

See an interactive map.

Register

Gene Expression Resources at the NCBI @ Fred Hutchinson Cancer Research Center, Arnold M1-A303
Jun 14 @ 1:00 pm – 4:00 pm

ITHS, the University of Washington Health Sciences Library, Fred Hutch, and the National Network of Libraries of Medicine, Pacific Northwest Region are pleased to host five free NLM National Center for Biotechnology Information (NCBI) workshops on June 14 and 15, 2016, in Seattle, Washington, and online.

In this NCBI workshop, you will find, display, and analyze microarray and sequence-based expression data that are stored in the Gene Expression Omnibus (GEO), Sequence Read Archive (SRA), UniGene, and Epigenomics databases to investigate the potential for expression of transcript splice variants and examine the levels of expression under varied experimental conditions as well as in different tissues and disease states. You will analyze Microarray data the on-demand GEO2R tool and will explore the precomputed transcript analyses that are displayed on the UniGene and GEO Profiles pages. You will explore genome-aligned RNA-Seq data through the Gene database’s sequence viewer displays and analyze raw RNA-Seq reads in the SRA database using NCBI’s SRA-BLAST service.

Speaker Biography

Peter Cooper, PhD, is a Staff Scientist at the National Library of Medicine. Peter has directed the NCBI scientific education and outreach efforts for the past 18 years. He also provides user support for the NCBI molecular databases and the BLAST sequence similarity search services and contributes to feature and interface design for the BLAST standalone and web services. Prior to joining the NCBI, Peter pursued diverse biological research interests including peptide neurochemistry, marine environmental toxicology, and taught biology and chemistry. Peter earned a BS from Virginia Tech, a MA in chemistry from Johns Hopkins University, and a PhD in marine science from the College of William and Mary, School of Marine Science in 1996.

Registration

There is no cost to attend this event, but seating is limited. Please register below if you plan to attend. Not an ITHS member? Signing up to become a member will take less than two minutes.

Please sign in below to access this form.

Access to this form is restricted to ITHS Members. Please sign in.

Not yet an ITHS member?
Members of ITHS are part of a unique catalyst that accelerates discoveries to practice. If you haven't signed up for an ITHS membership yet, learn more and join us.

Lost your password?

Jun
15
Wed
A Practical Guide to NCBI Web and Standalone BLAST @ UW Health Sciences Library, Learning Commons Classroom
Jun 15 @ 8:30 am – 11:30 am

ITHS, the University of Washington Health Sciences Library, Fred Hutch, and the National Network of Libraries of Medicine, Pacific Northwest Region are pleased to host five free NLM National Center for Biotechnology Information (NCBI) workshops on June 14 and 15, 2016, in Seattle, Washington, and online.

This NCBI workshop 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
  • 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; IgBLAST, a tool for analysis of antibody and T-cell receptor sequences; and MOLE-BLAST, a new tool for clustering and providing taxonomic context for targeted loci sequences (16S, ITS, 28S). These aspects of BLAST provide easier access and results that are more comprehensive and easier to interpret. Finally, you will learn how to use the standalone VDB BLAST programs as clients to search whole genome shotgun contigs (WGS) and transcriptome shotgun assembly (TSA) data – two of the fastest growing categories of sequence data available for BLAST searching.

This session includes hands-on instruction.

Speaker Biography

Peter Cooper, PhD, is a Staff Scientist at the National Library of Medicine. Peter has directed the NCBI scientific education and outreach efforts for the past 18 years. He also provides user support for the NCBI molecular databases and the BLAST sequence similarity search services and contributes to feature and interface design for the BLAST standalone and web services. Prior to joining the NCBI, Peter pursued diverse biological research interests including peptide neurochemistry, marine environmental toxicology and taught biology and chemistry. Peter earned a BS from Virginia Tech, a MA in chemistry from Johns Hopkins University, and a PhD in marine science from the College of William and Mary, School of Marine Science in 1996.

Registration

There is no cost to attend this event, but seating is limited. Please register below if you plan to attend. Not an ITHS member? Signing up to become a member will take less than two minutes.

Please sign in below to access this form.

Access to this form is restricted to ITHS Members. Please sign in.

Not yet an ITHS member?
Members of ITHS are part of a unique catalyst that accelerates discoveries to practice. If you haven't signed up for an ITHS membership yet, learn more and join us.

Lost your password?

NCBI’s Medical Genetics Resources: ClinVar, GTR, and MedGen @ UW Health Sciences Library, Pacific Room
Jun 15 @ 8:30 am – 11:00 am

ITHS, the University of Washington Health Sciences Library, Fred Hutch, and the National Network of Libraries of Medicine, Pacific Northwest Region are pleased to host five free NLM National Center for Biotechnology Information (NCBI) workshops on June 14 and 15, 2016, in Seattle, Washington, and online.

In this NCBI session, you will learn how to navigate several free, online programs. These include MedGen, which provides information on conditions with a genetic component, the NIH Genetic Testing Registry (GTR) for reviewing available genetic tests, and ClinVar, which holds information on medically relevant variation.

Speaker Biography

Brandi Kattman, MS, CGC, is a genetic counselor and staff scientist with the National Center for Biotechnology Information (NCBI) at the National Institutes of Health (NIH). Brandi joined the NIH to assist in developing the NIH Genetic Testing Registry and works on other clinical genetics resources such as ClinVar and MedGen. Brandi previously worked at GeneDx, a genetic testing laboratory, with roles as Genetic Counseling Services Program Manager and Director, Cardiology Genetic Services. While at GeneDx, she led the creation and implementation of the laboratory’s information management system (LIMS) and was the primary contact with GeneTests for the over 400 tests listed by GeneDx.

Registration

There is no cost to attend this event, but seating is limited. Please register below if you plan to attend. Not an ITHS member? Signing up to become a member will take less than two minutes.

Please sign in below to access this form.

Access to this form is restricted to ITHS Members. Please sign in.

Not yet an ITHS member?
Members of ITHS are part of a unique catalyst that accelerates discoveries to practice. If you haven't signed up for an ITHS membership yet, learn more and join us.

Lost your password?

Tips for Getting Your Research Published in Academic Journals @ UW Health Sciences Building, Room T747
Jun 15 @ 12:30 pm – 1:45 pm

Doors open at 12 p.m. for networking and the serving of a light lunch and beverages.

Wondering about the best approach to take to get published in academic journals? Been turned down, and thinking about revising and resubmitting?

Publishing in academic journals contributes to the valuable exchange of ideas and is a critical component of any researcher’s career. However, writing for academic journals is highly competitive and can often be a mysterious process. In this presentation, Dr. John Amory will leverage his experience as an Associate Editor and Editorial Board Member and from the publication of 120 peer-reviewed articles to shine a light on the publication process and provide valuable tips on how to get published. His presentation will cover a range of topics, including how to: select an appropriate journal; navigate the publication process, avoid common mistakes; and respond to reviewer feedback.

Dr. John Amory is a Professor and Section Head of General Medicine at the University of Washington. He is also the Director of the ITHS KL2 Multidisciplinary Clinical Research Career Development Program.

By attending this event, you will learn how to:

  • How to decide where to submit your article
  • Understand what qualities editors are looking for in an article
  • Understand what happens after you submit an article to a journal
  • How to respond to reviewers to increase your chance of acceptance
  • What to do if your article is rejected

Speaker Biography
Dr. Amory obtained his M.D. from the University of California, San Francisco where he also completed his residency in internal medicine. He is currently a professor of medicine and section head of general internal medicine at the University of Washington, where he works as an attending physician in the inpatient medicine wards and in the General Internal Medicine Clinic. Dr. Amory’s research interests are the development of novel forms of male contraception and new approaches to the treatment of men with infertility. Dr. Amory has published 120 peer reviewed papers in the field of male reproduction and holds current funding from the NIH grant for contraceptive research.

Registration

There is no cost to attend this event, but seating is limited. Please register below if you plan to attend. Not an ITHS member? Signing up to become a member will take less than two minutes.

Please sign in below to access this form.

Access to this form is restricted to ITHS Members. Please sign in.

Not yet an ITHS member?
Members of ITHS are part of a unique catalyst that accelerates discoveries to practice. If you haven't signed up for an ITHS membership yet, learn more and join us.

Lost your password?

Using NCBI Genome, Assembly, and Gene to Access Genome Sequences and Annotations @ UW Health Sciences Library, Learning Commons Classroom
Jun 15 @ 1:00 pm – 4:00 pm

ITHS, the University of Washington Health Sciences Library, Fred Hutch, and the National Network of Libraries of Medicine, Pacific Northwest Region are pleased to host five free NLM National Center for Biotechnology Information (NCBI) workshops on June 14 and 15, 2016, in Seattle, Washington, and online.

In this NCBI workshop, you will learn how NCBI processes genome-level data and produces annotation through the prokaryotic and eukaryotic genome annotation pipelines. You will find, browse, and download genome-level data for your organism of interest and for environmental and organismal metagenomes using the Genome, BioProject and Assembly resources. In addition to assembled and annotated data, you will retrieve and download draft whole genome shotgun and read-level next-gen sequencing data from the Nucleotide and Sequence Read Archive (SRA) databases. You will access results of precomputed analyses of genomes, as well as perform your own analyses of assembled and unassembled genomic data using NCBI’s genome BLAST and SRA-BLAST services.

This session includes hands-on instruction.

Speaker Biography

Peter Cooper, PhD, is a Staff Scientist at the National Library of Medicine. Peter has directed the NCBI scientific education and outreach efforts for the past 18 years. He also provides user support for the NCBI molecular databases and the BLAST sequence similarity search services and contributes to feature and interface design for the BLAST standalone and web services. Prior to joining the NCBI, Peter pursued diverse biological research interests including peptide neurochemistry, marine environmental toxicology and taught biology and chemistry. Peter earned a BS from Virginia Tech, a MA in chemistry from Johns Hopkins University, and a PhD in marine science from the College of William and Mary, School of Marine Science in 1996.

Registration

There is no cost to attend this event, but seating is limited. Please register below if you plan to attend. Not an ITHS member? Signing up to become a member will take less than two minutes.

Please sign in below to access this form.

Access to this form is restricted to ITHS Members. Please sign in.

Not yet an ITHS member?
Members of ITHS are part of a unique catalyst that accelerates discoveries to practice. If you haven't signed up for an ITHS membership yet, learn more and join us.

Lost your password?

Jul
5
Tue
Introduction to REDCap | July Class @ Health Sciences Library, lower level, Room T229
Jul 5 @ 10:00 am – 12:00 pm

Learn more about this class.

The Pacific Room (Room T229) is located on the lower level of the Health Sciences Library, near the after-hours entrance.

See an interactive map.

Register

Jul
11
Mon
Summer Institute in Statistics for Big Data (SISBID) @ University of Washington
Jul 11 – Jul 27 all-day

The Summer Institute in Statistics for Big Data (SISBID) consists of a series of two-and-a-half day workshops (modules) designed to introduce biologists, quantitative scientists, and statisticians to modern statistical techniques for the analysis of Biological Big Data. The format will involve formal lectures, computing labs, and hands-on case studies. The instructors are world-class faculty with expertise in all aspects of Biological Big Data. Participants are encouraged to enroll in multiple modules.

To register and learn more, visit the UW Department of Biostatistics website

Cite ItThe Institute is supported by grants UL1TR000423, KL2TR000421, and TL1TR000422 from the NIH National Center for Advancing Translational Sciences through the Clinical and Translational Science Awards Program (CTSA). Please help us continue to support your research by citing our grant number(s) in publications we supported.