Code Ocean

Code + (optional) data + computational environment = the minimum required for computational reproducibility.

What is a compute capsule?

Covering: 1) what is a compute capsule 2) uploading code and data 3) configuring your environment, 4) publishing on Code Ocean.

Getting Started

How do I upload my code to Code Ocean?

/code, /data, /results, and symbolic links.

Paths

Files must be saved to the /results folder.

Saving files

Take advantage of  preloaded public datasets, or upload your own.

Using public datasets

Pipelines, analyses, visualizations, and statistical checks are all great fits for publishing on Code Ocean.

What is, and is not, a good fit for publishing and sharing on Code Ocean?

Uploading code and data

Configuring your computational environment: an overview

Choose from among a curated collection of runtime environments covering common languages and frameworks.

Selecting a base environment

Install any libraries, packages, or dependencies your code needs in order to run.

The package management system

Download, extract, compile – use the full set of tools available on Linux to set up your runtime environment.

Using the postInstall script for further customization

The "buildLog" result file contains the console output from package installation commands and postInstall execution.

Monitoring and inspecting the result of the environment setup phase

How to use the package management system and postInstall script to install languages, interpreters, and compilers.

Setting up new or additional languages on Code Ocean via the package managers

The computational environment

Questions? Email support@codeocean.com

Find answers and get help from Intercom Support and Community Experts

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