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Bioinformatics Training and Education Program

august, 2022

22aug11:00 am1:00 pmElements of Style in Workflow Creation and Maintenance

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Event Details

The Gabriella Miller Kids First Pediatric Research Program (Kids First) is an NIH Common Fund program focusing on the biology of childhood cancer and structural birth defects. The program created the Gabriella Miller Kids First Data Resource, which includes the Kids First Portal, a cloud platform and other tools to foster analysis and collaboration. During this course, participants will learn some simple rules, dubbed Elements of Style, for analyzing large-scale datasets, such as genomic and phenotypic data accessible through the Kids First Data Resource. Using cloud platforms, participants will learn how to build and share processes in ways that assure reproducibility regardless of the computational environment.

Scheduled over five days, 2 hours each day, users will learn about reasoning with jupyter lab notebooks (python or R kernels), code versioning with git, and GitHub, containerization with conda and Docker, workflow development and execution. All of this with an eye towards platform independence, made possible through proper containerization and configuration files used by workflow languages, enabling the work on their laptop, using on-premise computer environments and in the cloud using a platform as a service. This class will use Seven Bridges’ Cavatica platform to conduct cloud-based analyses. Requirements include a browser (Chrome preferred, registration through the Kids First Data Resource Center) and internet access.

Speakers:
Anne Deslattes Mays, PhD https://www.nichd.nih.gov/about/org/od/odss/deslattes-mays
David Higgins, PhD https://d3b.center/team-members/higgins/

Course Description: https://github.com/NIH-NICHD/Kids-First-Elements-of-Style-Workflow-Creation-Maintenance

 

 

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Time

(Monday) 11:00 am - 1:00 pm

Location

Online

Organizer

CBIITCBIITDaoud Meerzaman, meerzamd@mail.nih.gov

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