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Creating and Managing Projects

Creating a New Project

Click the New Project button at the bottom of the sidebar to open the project creation wizard. The form includes:

  1. Project Name (required) — A text field for naming your project. This name will appear in the Project dropdown in the sidebar.

  2. Organism — A searchable dropdown with 32,000+ species from NCBI RefSeq. Start typing to filter (e.g., "arabidopsis", "homo", "oryza").

  3. Scientific Hypothesis (optional) — Describe the hypothesis you want to test with this RNA-Seq data.

  4. NCBI Accession(s) — Enter one or more NCBI BioProject accession IDs (e.g., PRJNA288044). Separate multiple accessions with commas.

  5. Fetch — Retrieves SRA (Sequence Read Archive) run metadata for the entered accession IDs.

Project Setup Workflow

After clicking Fetch, the platform retrieves run metadata from NCBI. You will then be guided through additional setup steps:

  1. Select runs and annotate each with a Sample Name, Group Name, and whether it is a Treat (treatment) or Control sample.
  2. Define contrasts — Specify which groups to compare by selecting a Reference (control) and Target (treatment) for differential expression analysis.
  3. AI Copilot (optional) — If enabled, an AI assistant helps refine your hypothesis and suggests contrasts based on your data.
  4. Click Submit to save and submit the project, or 💾 Save Draft to save progress and continue later.

Note

  • Draft — Saved via "Save Draft", can be continued later
  • Pending — Submitted via "Submit", waiting for RNA-Seq pipeline
  • Processing — Pipeline is running
  • Completed — Data files available, all visualization tabs accessible

Editing an Existing Project

Open the Project Summary tab and click the ✏️ Edit Project button. This opens the wizard in edit mode where you can:

  • Add new NCBI accessions — Fetch and add more SRA runs
  • Modify sample annotations — Update Sample Name, Group Name, or Treat/Control
  • Add new contrasts — Define additional comparisons (original contrasts cannot be deleted)
  • Update hypothesis — Refine your scientific hypothesis
  • Change organism — Select a different organism from the dropdown

Runs used by existing contrasts are protected from deletion. Click Submit to save changes, 💾 Save Draft to save progress, or Cancel to discard.

Switching Between Projects

Use the Project dropdown in the sidebar to switch between saved projects at any time. Selecting a different project reloads all visualizations with that project's data.