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Access and use of electronic resources made available by the Becker Medical Library are governed by license agreements between the School of Medicine and publishers or third parties. Several of the electronic resources carry some restriction on their use. Access may be restricted by user location, number of concurrent users, and/or password.

In short, most people experience access limitations based on the network to which their computer is connected. Below is a quick breakdown of what can be accessed from various networks.

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AccessMedicine
STAT!Ref
UpToDate Online
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American Academy of Pediatrics Journals
Applied Clinical Informatics
Harriet Lane Handbook
Red Book Online
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Partek Flow workshop on campus, July 29th, 2015

Becker Library will host a full day Partek Flow hands-on workshop, on July 29th, 2015. Previous Partek Flow workshops offered on campus have focused only on RNA-Seq analysis pipelines. This workshop will include hands-on training for the analysis of both RNA-Seq and DNA-Seq data.

 Researchers on campus approached us with an interest in organizing licenses for Partek Flow. As part of our investigation into a Partek Flow licensing model appropriate for our Washington University  community, a university-wide free trial of Partek Flow was made available on the Washington University Center for High Performance Computing (CHPC) cluster. During the free trial period, Partek released a new build for DNA-Seq data analysis within Flow. The university-wide Partek Flow free trial is still up and running on the CHPC cluster. Partek Flow logo

This workshop will run from 9:30am-3:30pm in the computer classroom in Farrell Learning and Teaching Center (FLTC Room 602), with the following agenda:

RNA-Seq Session: Starts from importing raw sequencing data in fastq format, perform QA/QC, alignment, quantification and differential expression detection.

DNA-Seq Session: Starts from importing bam files, perform variant detection and annotation, demo on seqduo analysis.

  • Morning Session (9:30am – 12:00pm):
    • Overview
    • Import data
    • Perform QA/AC (Pre-alignment QA/AC, Post-alignment QA/QC)
    • Trim bases
    • Alignment
    • Gene/transcript abundance estimate  
  • Afternoon Session (1:00pm – 3:30pm): 
    • Differential Expression Detection
    • Filter gene list
    • GO Enrichment Analysis
    • Variant Detection
    • Variant annotation and filter
    • Seqduo analysis
    • Visualization
      • Quality score distribution
      • Base composition
      • PCA scatterplot
      • Dotplot
      • Volcano plot,
      • Hierarchical clustering
      • Chromosome view
  • Q&A portion for researchers to ask questions and receive help with the practice data used during the workshop or their own data. The Partek team would appreciate any comments and feedback from researchers who are currently participating in the free trial.

This training is free and open to the WU community. Registration is required. To register for the workshop, please complete the workshop registration form . If you are interested in participating in the Partek Flow free trial or have questions, contact Maze Ndonwi at ndonwim@wusm.wustl.edu or 314 362 4737.

* Please note: Becker Briefs pages may contain links, email addresses or information about resources which are no longer current.