TabularQual converter

Convert between spreadsheets specified in [SpreadSBML specification](.doc/SpreadSBML specification.docx) and SBML-qual for logical models (Boolean and multi-valued).

Web App

Use TabularQual directly in your browser - no installation required!

🔗 Launch Web App

Note: there are currently resource limits on Streamlit cloud, please run it locally for large networks.

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Install

Option 1: Run Web App Locally

# 1) Install dependencies
pip install -r requirements.txt

# 2) Launch the web app
streamlit run app.py

The app will open in your browser at http://localhost:8501

Option 2: Command-Line Tools

# Install dependencies and console script
pip install -r requirements.txt
pip install -e .

Usage

• Spreadsheet ➜ SBML

to-sbml \
  --input examples/Faure2006/Faure2006.xlsx \
  --output examples/Faure2006/Faure2006_out.sbml

SBML ➜ Spreadsheet

to-table \
  --input examples/Faure2006/Faure2006_out.sbml \
  --output examples/Faure2006/Faure2006_reconstructed.xlsx

Options

to-sbml:

• --inter-anno: use interaction annotations only (unless --trans-anno is also set).
• --trans-anno: use transition annotations only (unless --inter-anno is also set).
• If you pass both --inter-anno and --trans-anno or pass neither, the converter will include both interaction and transition annotations.

to-table:

• --template: optionally specify a template file for README and Appendix sheets
• --colon-format: use colon notation for transition rules (: means >=). Default uses operators (>=, <, etc.)

Examples:

# Interactions only
to-sbml --input in.xlsx --output out.sbml --inter-anno

# Transitions only
to-sbml --input in.xlsx --output out.sbml --trans-anno

# Both (default)
to-sbml --input in.xlsx --output out.sbml

# Use doc/template.xlsx as template for creating tables
to-table --input in.sbml --output out.xlsx --template doc/template.xlsx

# Use colon notation for rules (A:2 instead of A >= 2)
to-table --input in.sbml --output out.xlsx --colon-format

Transition Rules Syntax

The Transition-Rules column supports boolean and comparison expressions using the following operators and syntax (space will be ignored):

• Logical operators: & (AND), | (OR), ! (NOT)
• Parentheses: ( and ) for grouping expressions
• For multi-value model: threshold-based activation:
  • Colon notation: A:2 means "A is at level 2 or higher" (A >= 2)
  • Negated colon: !A:2 means "A is below level 2" (A < 2)
  • Explicit comparisons: A >= 2, B <= 1, C != 0 for precise control
  • Equivalent expressions: !CI:2 & !Cro:3 is the same as CI < 2 & Cro < 3 or CI <= 1 & Cro <= 2
• Simple species references:
  • A - Species A is active (level >= 1 for multi-valued, or level = 1 for binary)
  • !A - Species A is inactive (level = 0)

Examples:

• A & B - Both A and B are active (level ≥ 1 for multi-valued)
• A:2 | B < 1 - A is at level 2+ OR B is inactive
• N & !CI:2 & !Cro:3 - N active AND CI below level 2 AND Cro below level 3
• (A & B) | (!C & D != 1) - Complex grouped expression

Notes

• The reader ignores a first README sheet if present, and reads Model, Species, Transitions, and Interactions.
• The SBML to Spreadsheet converter automatically uses doc/template.xlsx if available for README and Appendix sheets.
• TODO: automatically detect Species:Type, Interactions:Target, Source and Sign；Validation of annotations.