About the Database:

• Contains 322 curated protocols from published studies
• Categorises features into: Protocol Variables, Analysis Methods, Cell Profiles, Study Characteristics, and Measured Endpoints
• Enables discovery of protocol optimization strategies across different applications

Using the Search Box:

• Quick Filter: Type any term to instantly filter across all displayed columns
• Smart Search: DataTables automatically matches words out of order and performs partial word matching
• Multiple Terms: Enter space-separated words to find records containing ALL terms (e.g., "maturation day30")
• Exact Phrase Search: Use double quotes for exact phrase matching (e.g., "cardiac maturation")
• Column-Specific Filters: Use the category buttons to show/hide relevant groups of columns
• Export Results: Use the "Install" button to download your filtered data

Advanced Search Examples:

• Find specific protocols: Enter a protocol ID number (e.g., "152")
• Multiple criteria: "dmem isoproterenol B27" finds protocols mentioning all three terms
• Authors/references: "Strober" Search by author surname or publication year
• Combined approaches: First use category toggles to focus on relevant columns, then refine with search terms

Tip: Start with a broad search, then refine using the category buttons to focus on specific protocol aspects.

How to Use Variable Search

Find protocols across the database based on specific features, target outcomes, or a combination of both.

• Step 1: Select a Search Mode
  • Normal Mode: Find protocols that contain ALL selected features
  • Enrichment Mode: Find protocols based on a target topic's key characteristics
  • Combined Mode: Find protocols by target topic and filter by specific features
• Step 2: Select Search Parameters
  • For Normal Mode: Select specific protocol features from the right panel
  • For Enrichment Mode: Select a target topic/outcome from the left panel
  • For Combined Mode: Select both a target topic AND specific features
• Step 3 (Optional): Apply Enrichment Category Filters
  • When using Enrichment or Combined modes, you can filter by feature categories
  • The toggle buttons help focus on specific aspects like Protocol Variables, Analysis Methods, etc.

Search Results

Results are displayed in a table showing:

• Protocol ID: Unique identifier for each protocol
• Title: Title or description of the protocol
• DOI: Digital Object Identifier (clickable link to the publication)
• Similarity Rank: In Normal mode, shows how closely the protocol matches your criteria
• Feature Found: In Enrichment mode, shows which categories contain matching features

Tips:

• • Use the "Filter records" box to further narrow down results
• • Export your results to CSV using the Export button
• • For broader results, select fewer features in Normal mode
• • For more specific results, use Combined mode with multiple constraints

Search Results

How To Use The Enrichment Browser

• Step 1: Select a target parameter/outcome from the dropdown menu (e.g., "Best Contractile Force" or "Disease Modeling").
• Step 2: Review the enrichment results table showing protocol features significantly associated with your selected outcome.
• Step 3: Use the "Filter records" search box to narrow down results by specific terms or values.
• Important Note: The enrichment analysis may include protocols that don't directly report your selected metric. This is intentional and part of the data mining approach—we analyze which features are statistically overrepresented across the entire dataset, even in studies that measure related but different outcomes.
• Results Explanation:
  • Target Label: The outcome you selected
  • Feature: Specific protocol component or characteristic
  • Importance: Statistical measure of association strength
  • P-value: Statistical significance (lower values = stronger evidence)
  • Category: Which experimental domain the feature belongs to
• Data Source: Results are derived from our comprehensive database of 322 hiPSC-CM protocols using advanced statistical techniques.
• Export: Use the "Export CSV" button to download results for your own analysis.

How to Use Protocol Benchmarking

Compare your cardiac myocyte (CM) protocol against established standards from our database to evaluate its maturity and effectiveness.

• Step 1: Choose Your Protocol Method
  • Either upload your protocol PDF (Install Here) OR
  • Select an existing protocol directly from our database by ID (experimental data will be auto-loaded)
• Step 2: Upload Experimental Measurements
  • If you uploaded your own protocol, upload your experimental data PDF (Install Here)
  • If you selected a protocol from the database, experimental data will be auto-loaded
• Step 3: Select Protocol Purpose
  • Choose the purpose/application of your protocol (required)
  • This helps contextualize your results within similar applications
• Step 4 (Optional): Add Reference Protocols
  • You can benchmark against existing protocols in the database by selecting their IDs
  • Or upload your own reference protocol + data pairs (up to 2 pairs)

Understanding Results

Results are displayed as a radar chart with 18 maturity indicators across multiple categories. Moving outward on the chart indicates more adult-like (mature) characteristics.

• Data Point Types:
  • Hollow points: Predicted data (no experimental value provided)
  • Solid points: Experimental data within normal range
  • Dark points: Experimental data exceeding best bounds
  • Light points: Experimental data below worst bounds
• Navigation:
  • Use the "Next Reference" button to cycle through different reference protocols
  • Hover over data points for detailed information