File Navigation/App Builder Panel

File Navigation

The Files tab on the toolbar to the left opens the Files panel. Under Core Files, metadata, environment, code, and data folders, as well as a .gitignore file are organized. Under Research Data Drive is the scratch folder, and under Results is the result folder. Any additional files are organized under Other Files.‌

File Tree System Contents

Folder	Purpose	Contents
Metadata	Capsule's metadata	metadata.yml
Environment	Capsule's environment files	Dockerfile, postInstall script, environment.yml
Code	Code and related files	Source files
Data	Input data required by Reproducible Runs. May optionally contain small intermediate data	Small data files and attached datasets
Results	Output files generated by the most recent Reproducible Run	Result files
Scratch (Cloud Workstation)	Large Intermediate data that are NOT required by Reproducible Runs	Large data files
Scratch (Reproducible Run)	Large Intermediate data that are generated during Reproducible Runs	Large data files
Cloud Workstation Root File System	Package installations, IDE preferences, temporary files, etc.	The whole file system except the Capsule workspace, and those mounted folders

Managing Capsule Size

The Capsule Usage Information Box can be accessed at the bottom of the File Navigation Panel and used to view your current Capsule space usage. It displays:

• Total usage - broken down by:

  • Attached Data

  • Scratch

  • Results

  • Workspace

    • Code

    • Data

    • Environment

    • Metadata

    • Other files

The limitation for total Capsule size is 5 GB. This can be broken down by folder:

Folder	Counted in Workspace Limit	Comments
Metadata	✅
Environment	✅
Code	✅
Data	✅	Attached Data Assets are mounted and not counted toward the Capsule's size limit
Results	❌	Results is mounted and not counted toward the Capsule's size limit
Scratch (CW) Scratch (RR)	❌	Scratch is mounted and not counted toward the Capsule's size limit
CW Root FS	❌	5GB limit, including existing Capsule environment installations

To reduce storage costs in your Capsule, is understanding the storage location of your files and how long they will remain there. The breakdown is as follows:

Folder	Storage	Persistence
Metadata	EBS (local storage)	Capsule lifetime
Environment	EBS (local storage)	Capsule lifetime
Code	EBS (local storage)	Capsule lifetime
Data	Local data: EBS Internal data Asset: mounted from EFS External data Asset: mounted from S3	Local data: Capsule lifetime Data Assets: has its own lifetime
Results	During computation: EBS When the computation finished, upload to S3	Capsule lifetime unless explicitly deleted from the timeline
Scratch (RR)	Mounted from EFS	Duration of the Reprodicible Run
Scratch (CW)	Mounted from EFS	Capsule lifetime
CW Root FS	EBS (local storage)	Cloud Workstation session

S3, EBS and EFS refer to the types of Amazon Cloud Storage that are possible:

• Simple Storage Service (S3)

• Elastic Block Store (EBS)

• Elastic File System (EFS)

App Builder

The can be navigated to via the side tab. It enables researchers to interact with Capsules without directly interacting with the code. With key user-input parameters, you can use the App Panel to generate results.

For detailed instructions on how to create and interact with the App Builder, refer to the App Panel Guide.