refactor: use cytoscape-biological-flow npm package

Replaces the inline BiologicalFlowLayout engine with the standalone
cytoscape-biological-flow npm package (v1.0.0), registered as a
Cytoscape.js layout extension.

- Adds cytoscape-biological-flow as a dependency
- Registers the extension in CyjsLayout
- Adds 'biological-flow' to CyjsAlgorithms
- Removes the standalone BiologicalFlow engine implementation

The layout algorithm is now maintained at:
https://github.com/jmg421/cytoscape-biological-flow

See: https://www.npmjs.com/package/cytoscape-biological-flow

Author: jmg421

package-lock.json

@@ -146,6 +146,7 @@
     "allotment": "1.18.1",
     "chroma-js": "^2.4.2",
     "cytoscape": "^3.34.0",
+    "cytoscape-biological-flow": "^1.0.0",
     "cytoscape-canvas": "^3.0.1",
     "cytoscape-pdf-export": "^0.0.2",
     "cytoscape-svg": "^0.4.0",
@@ -190,4 +191,4 @@
     "zod": "^3.25.56",
     "zustand": "^4.4.7"
   }
-}
+}

package.json

@@ -1,15 +1,14 @@
 /**
- * Biological Flow Layout — contributed by Nodes Bio
+ * Biological Flow Layout — powered by cytoscape-biological-flow
  *
  * A hierarchical layout optimized for biological pathway visualization:
- * - Topological sort assigns columns (left→right signal flow)
+ * - Left-to-right signal flow direction
  * - Barycenter heuristic minimizes edge crossings
  * - Handles cycles via DFS back-edge removal
  *
- * This is a client-side port of the LayoutOptimizer algorithm
- * originally developed for the MedMap pathway visualization tool.
+ * Contributed by Nodes Bio (https://nodes.bio)
  *
- * @see https://github.com/cytoscape/cytoscape-web/issues/XXX
+ * @see https://github.com/jmg421/cytoscape-biological-flow
  */
 import { LayoutAlgorithm } from '../../..'
 import { LayoutAlgorithmType } from '../../../LayoutAlgorithm'
@@ -24,7 +23,7 @@ export const biologicalFlow: LayoutAlgorithm = {
     'Uses topological sort for layer assignment and barycenter heuristic ' +
     'for crossing minimization. Handles cycles gracefully.',
   parameters: {
-    name: 'preset', // Uses preset because positions are pre-computed
+    name: 'biological-flow',
     fit: true,
     padding: 80,
     animate: false,

src/models/LayoutModel/impl/BiologicalFlow/biologicalFlowLayout.test.ts

@@ -1,10 +1,11 @@
 import { LayoutAlgorithm } from '../../../LayoutAlgorithm'
+import { biologicalFlow } from './biologicalFlow'
 import { circle } from './circle'
 import { concentric } from './concentric'
 import { cose } from './cose'
 import { grid } from './grid'
 
-const CyjsLayouts: LayoutAlgorithm[] = [grid, circle, cose, concentric]
+const CyjsLayouts: LayoutAlgorithm[] = [grid, circle, cose, concentric, biologicalFlow]
 
 export const CyjsAlgorithms: Record<string, LayoutAlgorithm> =
   CyjsLayouts.reduce<Record<string, LayoutAlgorithm>>((acc, layout) => {

src/models/LayoutModel/impl/BiologicalFlow/biologicalFlowLayout.ts

@@ -1,11 +1,15 @@
 import cytoscape, { EdgeDefinition, NodeDefinition } from 'cytoscape'
+import biologicalFlow from 'cytoscape-biological-flow'
 
 import { IdType } from '../../../IdType'
 import { Edge,Node } from '../../../NetworkModel'
 import { LayoutAlgorithm } from '../../LayoutAlgorithm'
 import { LayoutEngine } from '../../LayoutEngine'
 import { CyjsAlgorithms } from './Algorithms/cyjsAlgorithms'
 
+// Register the biological-flow layout extension
+cytoscape.use(biologicalFlow)
+
 export const CyjsLayout: LayoutEngine = {
   // Cytoscape.js Layout
   name: 'Cytoscape.js',