RStudio and Code Ocean – Better Together

Creating an Essential Research Collaboration Environment with R Studio

Today’s high-throughput biomedical research techniques and intensive interdisciplinary collaborations – especially between biologists and computational researchers – require tools and infrastructure that are able to deal with biological big data. 

Computational research faces costly and time-consuming challenges, specifically

  • Reproducibility of analyses – different computing environments and versions of software packages frequently leads to situations where code runs on one machine but not on another making it very difficult to reproduce a colleague’s or partner’s work or reuse an existing analysis pipeline with different data or in the context of a different analysis. Lack of reproducibility leads to the second challenge,
  • Inefficient research collaborations – handing the results of analysis to a collaborator for additional analysis or combining elements different researchers have developed independently often results in failure. Significant troubleshooting and IT support are often required to get the code working which delays the project.
  • Inability to quickly configure resources – common tasks such as adding memory or cores during project scale-up can lead to delays. Even more problematic is adding new software packages or updating versions across several users which can take up significant time and resources. 

At Code Ocean we have developed a solution that addresses these challenges: Compute Capsules™. Compute Capsules allow researchers to put their code, environment, data and results into a secure container which can be shared easily with colleagues and collaborators. Within the Compute Capsules computational researchers can still work using their favorite IDEs like RStudio and make these workspaces seamlessly accessible to others.

The advantages of this approach are two-fold: researchers can work in their preferred environment, such as RStudio and collaborate by sharing the Capsule. New collaborators can access the workspace and start working immediately. 

This creates a way to speed up analysis work without having to change established workflows and preferred environments. The Compute Capsules can be saved to a secure AWS cloud and can be shared with a few clicks. Code Ocean’s Compute Capsules therefore turn RStudio into a ready-to-use research collaboration environment.

Watch a demonstration

 

Summary

  • Lack of reproducibility, inefficient collaborations and the time and cost required to configure resources quickly can significantly slow computational projects.
  • Code Ocean’s platform provides a user-friendly interface that allows users to seamlessly work in their preferred environments and easily share their work with collaborators.

Additional Resources 

Webinar on building effective, collaborative teams (featuring Dr. Benita, Head of Science Operations of CytoReason):

https://info.codeocean.com/webinar-boosting-productivity-code-ocean

https://info.codeocean.com/webinar-multi-omics-analysis 

Product sheet:

https://codeocean.com/resources/collateral/

 

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