Research Protocols

Standardized protocols are the foundation of reproducible research. AcaTrove's protocol management system provides a structured environment for creating, versioning, and sharing research protocols across your lab and workspace.

Accessing Protocols

Navigate to /protocols from the sidebar. The protocols page lists all protocols you have created or that have been shared with you, organized by category and recency.

Protocol list with categories and version indicators

Creating a New Protocol

1. Click + New Protocol on the protocols page.
2. Fill in the protocol details:
   • Title -- A clear, descriptive name (e.g., "Western Blot Protocol for Membrane Proteins" or "RNA Extraction from Plant Tissue").
   • Category -- Classify the protocol (Molecular Biology, Cell Culture, Imaging, Computational, Animal, Chemical, Other).
   • Description -- A brief summary of what the protocol accomplishes and when to use it.
   • Materials -- List all required reagents, equipment, and consumables with quantities and specifications.
   • Steps -- Enter each step of the protocol in order. Each step supports rich text formatting, including bold, italic, lists, and inline images.
   • Safety Notes -- Document any safety considerations, required PPE, or hazard information.
   • Expected Results -- Describe what a successful execution of the protocol produces.
   • Troubleshooting -- Common problems and their solutions.
   • Tags -- Add keywords for searchability.
3. Click Save.

Protocol editor with step-by-step instructions and materials list

Versioning

Every time you edit a saved protocol and save the changes, AcaTrove creates a new version. The version history is accessible from the protocol detail page:

• View any previous version to see the protocol as it existed at that point.
• Compare two versions side by side to see what changed.
• Revert to a previous version if a recent change introduced errors.

Versioning ensures that experiments run under a specific version of a protocol can always reference that exact version later.

Sharing Protocols

Protocols support the same visibility levels as other AcaTrove resources:

• Private -- Only you can view and edit.
• Lab -- All members of your lab can view. Editing permissions can be restricted to the protocol owner or extended to lab members.
• Workspace -- All workspace members can view.

Share a protocol by clicking Share on its detail page and selecting the visibility level.

Linking Protocols to Projects

When a project uses a specific protocol, link them together:

1. Open the project and navigate to its Protocols tab.
2. Click Link Protocol and select from your available protocols.
3. The linked protocol appears in the project context, and any project publication can reference the specific protocol version used.

Forking Protocols

If you need to modify a shared protocol for your specific use case without changing the original, click Fork on the protocol detail page. This creates a copy in your account that you can edit independently. The fork maintains a reference to the original protocol for traceability.

Searching Protocols

The protocols page includes a search bar that uses semantic search. You can search by protocol name, category, materials, or any text within the steps. This helps you discover existing protocols before creating a new one from scratch.

Tips

• Include photographs or diagrams in protocol steps where visual guidance helps (e.g., gel loading patterns, equipment setup).
• Always specify reagent concentrations, incubation times, and temperature precisely -- ambiguity undermines reproducibility.
• Link your protocol to the Null Hypothesis Reporter entry when an experiment produces null results, so others can see exactly what was tried.
• Review and update protocols at least once per year to incorporate improved methods.