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Training, Community and Finding Help
2020-06-02
k8hertweck, vortexing

There are a variety of resources for training on various aspects of bioinformatics, analytics and data skills available at the Fred Hutch, in the Seattle area and on the web.

Resources At Fred Hutch

Note: Currently resources at the Hutch are in flux due to staffing changes and evolving data science support mechanisms. Stay tuned for new training opportunties beyond the peer-to-peer resources dsecribed here.

In Person Courses

All in person training has been put on hold.

Community Groups

Currently, peer-to-peer training and support for data intensive work at the Fred Hutch is mainly avilable via the Fred Hutch Bioinformatics and Computational Research (FH-BCR) Slack workspace here. This Slack workspace is open to Fred Hutch Cancer Center staff (with fredhutch or scca emails) as well as collaborators at some local institutions. The workspace hosts a question and answer channel as well as evolving chnanels to meet community needs such as supporting groups organizing to develop and distribute new resources to the community, collaborations with external companies/efforts that aim to develop shared Fred Hutch infrastructure, and topic-oriented groups like these:

  • Workflow Manager User Group: Discusses issues related to the use of workflow managers Nextflow and Cromwell at Fred Hutch, including support for shifting from bash or snakemake pipelines, software containerization and configuration for local and shared workflow useage. The group welcomes users of all levels of expertise as well as those just interested in learning about how workflow managers can move their science forward. See the #workflow-managers channel on FH-BCR Slack for more information.

  • R User Group: Discusses programming, data analysis, and troubleshooting in R for users of a wide range of expertise and research topic, as well as tools based in R such as Shiny applications. See the #r-user-comm channel on FH-BCR Slack for more information.

  • Python User Group: Discusses programming, data analysis, and troubleshooting in Python and related topics in general software development. See the #python-user-comm channel on FH-BCR Slack for more information.

Office Hours

  • SciComp Next Gen/HPC Office Hours: Scientific Computing (SciComp) supports researchers interested in emerging technologies like next generation sequencing and cloud computing. Staff are available to answer questions about getting started building analytical pipelines in the cloud, and generally making computation more scalable and reproducible. Email scicomp to find out the current dates, times and (typically remote) meeting location information.

Resources In Seattle

Resources On the Web

Classroom-Style Courses

These resources are organized in a lecture type format as slides, screencasts, and video. Most are work-at-your-own-pace, but some may be linked to a course calander.

Interactive Coding Platforms

These resources offer classes that are work-at-your-own-pace with a major focus on hands-on problem-sets and projects.

  • DataQuest: A subscription service that offers programs and courses focused on data anlysis and engineering in Python and R.

    • Tiered payment system with basic and premium plans
  • CodeAcademy: A subscription service that offers coding programs and courses in many different languages.

    • Tiered payment system with limited content available for free

Free ebooks

Misc