Genomic data science with the Galaxy workbench
Learn to do data-intensive science with Galaxy
](https://depot.galaxyproject.org/hub/attachments/events/2019-sacnas/2019-sacnas-flier.pdf)There will be a full day pre-conference workshop at 2019 SACNAS that will introduce participants to best practices, tools, and platforms for doing data-intensive research. This STEM focused session will familiarize students with the field of Genomic Data Science. Participants will be introduced to the field of genomics, learn about current large scale genome sequencing projects, and perform hands-on genomic data analysis. No prior computational experience is required.
Bring your laptop and your curiosity.
Wednesday, October 30, 9am- 6pm
Room 318AB
Workshop attendees will be introduced to practical examples of how genomic data is used in research and clinical applications, highlighting techniques, technologies, and platforms used in genomic analysis. The current state of genomic science will be discussed, with emphasis on large scale sequencing projects of NHGRI involving hundreds of thousands of individuals (CCDG, CMG, AnVIL).
Workshop participants will work with genomic data using the Galaxy workbench. Through guided hands-on exercises, attendees will learn best practices in data science using the Galaxy data integration and analysis framework, with emphasis on components that enable reproducibility, transparency, and accessibility. Participants will work through sample pipelines analyzing how genes are expressed at different levels in different conditions, individuals and cell types, and data visualization with RStudio.
Participants of this workshop will achieve a basic understanding of Genomic Data Science. The presentations and hands-on exercises will provide practical exposure to the field of Genomics for young scholars.
Workshop goals
The goals of this workshop are to
- provide background of Genomics, highlighting techniques and large scale sequencing efforts,
- demonstrate how genomics is performed using lecture and hands-on exercises.
Schedule
| Time | Topic |
|---|---|
| 9 am | Introduction to Human Genomics (presentation) Human Genome Project ) DNA sequencing technologies Research genomics Clinical genomics |
| 10 am | Practical Human Genomics (presentation) Techniques Analysis Tools |
| 11 am | Human Genomics at scale (presentation) GSP - scaling, logistics CCDG, CMG - discoveries, challenges, caveats AnVIL - opportunities |
| 12 pm | Data Science - Galaxy (hands-on) Data management Data access, sharing Job processing + reproducibility |
| 1 pm | Lunch (on your own) |
| 2 pm | Data Science - Galaxy analysis with RNA-Seq (hands-on) Mapping data to genomes |
| 3 pm | Data Science - Galaxy for Differential Gene Expression (hands-on) Compare how genes are expressed at different time and levels |
| 4 pm | Data Science - RStudio interactive viz (hands-on) ggplot2 (for scripting figures + layouts) Heatmaps |
| 5 pm | Data Science - Galaxy/RStudio - advanced exercises (hands-on) ChIP-seq analysis Metagenomics |
| 6 pm | Fin |
Instructors
- Dave Clements, Galaxy Project and Johns Hopkins University
- Mo Heydarian, Galaxy Project and Johns Hopkins University
Registration
Registration is free but space is limited. You are strongly encouraged to register soon.
Travel Scholarships
The Galaxy Community Fund is
- augmenting SACNAS Travel Scholarships awards, and
- also offering scholarships to workshop participants who are not receiving SACNAS Travel Scholarships.
The scholarships cover the first $110 of housing costs for the evening of Tuesday, October 29 (the night before the workshop). You can apply for a travel scholarship when you register.
Help Get the Word Out!
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