Add new method for FBA analysis

README.md

@@ -159,4 +159,4 @@ and contains more information about the model architecture, output,
 and workflow configuration.
 
 If you encounter an issue not addressed by the docs, feel free to create a GitHub issue, and we will
-get back to you as soon as we can.
+get back to you as soon as we can.

ecoli/analysis/multigeneration/catalyst_count.py

@@ -0,0 +1,27 @@
+"""
+Visualize catalyst counts over time for specified BioCyc reactions across generations.
+For each specific BioCyc ID reaction, this scripts will add all the catalysts which catalyse it:
+```number of catalysts = sum(number of catalysts[i])```
+
+Supports two visualization modes:
+1. 'grid' mode: Each row represents a variant, each column represents a reaction's catalysts
+2. 'stacked' mode: Each reaction's catalysts get their own chart, variants shown as different colored lines
+
+You can specify the reactions and layout using parameters:
+    "catalyst_count": {
+        # Required: specify BioCyc reaction IDs to visualize
+        "BioCyc_ID": ["Name1", "Name2", ...],
+        # Optional: specify generations to visualize
+        # If not specified, all generations will be used
+        "generation": [1, 2, ...],
+        # Optional: specify layout mode ('grid' or 'stacked')
+        # Default: 'stacked'
+        "layout": "stacked"  # or "grid"
+        }
+
+This script is the dummy version of ecoli.analysis.multivariant.catalyst_count, you can turn to origin file for more detail
+"""
+
+from ecoli.analysis.multivariant.catalyst_count import plot
+
+__all__ = ["plot"]

ecoli/analysis/multigeneration/fba_flux.py

@@ -0,0 +1,22 @@
+"""
+Visualize FBA reaction fluxes over time for specified reactions with net flux calculation across multiple variants.
+
+Supports two visualization modes:
+1. 'grid' mode: Each row represents a variant, each column represents a reaction
+2. 'stacked' mode: Each reaction gets its own chart, variants shown as different colored lines
+
+You can specify the reactions and layout using parameters:
+    "fba_flux": {
+        # Required: specify BioCyc reaction IDs to visualize
+        "BioCyc_ID": ["Name1", "Name2", ...],
+        # Optional: specify layout mode ('grid' or 'stacked')
+        # Default: 'stacked'
+        "layout": "stacked"  # or "grid"
+        }
+
+This script is the dummy version of ecoli.analysis.multivariant.fba_flux, you can turn to origin file for more detail
+"""
+
+from ecoli.analysis.multivariant.fba_flux import plot
+
+__all__ = ["plot"]