Project Structure

Learn about the 5 sections of every Panomics project.

All Panomics projects share a common structure that makes collaborative analysis straightforward.

Project Metadata

The project metadata can be split into 2 categories, each serving a specific purpose.

Direct Metadata

This helps team members understand what the project is all about. It includes:

• title

• external ID (e.g.: GEO identifier)

• description

• overall design

• tags

Inherited Metadata

This is the metadata inherited from the samples associated with the project. It can include information about the tissue, disease, treatment compounds, etc. Projects can be filtered using any of the metadata fields configured at the organization level.

Analyses

This is where all project analyses reside. From this section, users can:

• list and filter all project analyses

• mark analyses as done

• publish or unpublish analyses

• view audit trail

• export analyses as cell atlases (applicable only to single cell analyses)

• delete analyses

Analysis list

For more details, visit the dedicated pages.

Samples

This is where all project samples reside.

Samples can be associated with more than one project.

From this section, users can:

• list and filter all project samples

• import new samples

• remove samples from the project

• upload/edit metadata

• change the samples' status (see sample lifecycle)

• create new analyses

Sample list

For more details, visit the dedicated pages.

Assets

The Assets page functions as a versatile file explorer within Panomics. It allows users to manage project files by creating folders, uploading, downloading, and moving files.

For compute results, it offers a read-only view, with the option to copy analysis results to the JupyterLab or RStudio mounts.

The JupyterLab and RStudio mounts connect directly to the runtime’s shared drive, providing a secure way to transfer files to or from the project.

Readme

The readme is a collaborative document used to describe the analytical decisions made, write down hypothesis, or ask for feedback.