Interactive analysis apps: Galaxy, Jupyter notebooks and RStudio

Allie Hajian
  • Updated

Applications running on a Cloud Environment - Galaxy, Jupyter notebooks and RStudio - are an interactive analysis mode in Terra that allow you to visualize your data and run statistical analyses in real time. You can adjust the configuration of your Cloud Environment virtual machine or cluster to fit your computational needs, or use a custom Docker or startup script to enable collaborators and others to reproduce your work. 

Galaxy

Galaxy is an open web-based platform for highly accessible bioinformatic research, similar to Terra. You can learn more about how to use Galaxy from the Galaxy documentation or by visiting the Galaxy community hub

Galaxy is (from the Galaxy community hub)

  • Accessible: programming experience is not required to easily upload data, run complex tools and workflows, and visualize results.
  • Reproducible: Galaxy captures information so that you don't have to; any user can repeat and understand a complete computational analysis, from tool parameters to the dependency tree.
  • Transparent: Users share and publish their histories, workflows, and visualisations via the web.
  • Community centered: Our inclusive and diverse users (developers, educators, researchers, clinicians, etc.) are empowered to share their findings.

See the blog post A Galaxy of tools at your fingertips.

Learn more about Galaxy on Terra here

Jupyter notebooks

Jupyter notebooks are an open-source analysis environment that include both rich text documentation and code. In a notebook, you can investigate study data in real time with interactive analysis and visuals.

  • Import data of any size - including processed genomics, phenotype and transcriptomics data stored in the cloud
  • Analyze with custom or pre-built libraries using R or Python. 

Notebooks combine analysis methods, findings and documentation in a single place, in a form that's straightforward to distribute. A logical evolution of the traditional scientific paper, Jupyter notebooks dramatically shorten the path between reading how an analysis was done and actually being able to reproduce it. 

Learn more about Jupyter notebooks on Terra here

RStudio

Integrated RStudio capabilities and Bioconductor support include a variable explorer, an R Markdown editor, a debugger and a terminal function that enable

  • Richer IDE experience for R development
  • Support for launching RShiny apps
  • Git integration 

You can spin up a cloud environment pre-configured to run the server version of RStudio right in your Terra workspace. The integration is a result of our collaboration with the Bioconductor team as part of the AnVIL project.

For some additional context, check out our Terra Blog post on the subject, or watch this seven minute video tutorial on using RStudio on Terra for analysis.

Learn more about RStudio in Terra Support

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