readme

README.md

@@ -1,8 +1,11 @@
-# zeolite-map
-Zeolite map in JavaScript to visualize the data from the 2023 Digital Discovery paper
-# IZA Distance Matrix Visualization
+<div align="center">
+  <img src="https://raw.githubusercontent.com/dskoda/Zeolites-AMD/main/figs/toc.jpg" width="500"><br>
+</div>
 
-This repository contains an interactive visualization of the IZA (International Zeolite Association) Distance Matrix, showing relationships between zeolite frameworks.
+# Interactive Map for: Inorganic synthesis-structure maps in zeolites with ML and crystallographic distances
+
+
+This repository contains an interactive visualization of the IZA (International Zeolite Association) Distance Matrix computed for the manuscript: [Inorganic synthesis-structure maps in zeolites with machine learning and crystallographic distances](https://doi.org/10.1039/D3DD00134B)
 
 ## Description
 
@@ -11,11 +14,11 @@ The visualization represents zeolite frameworks as nodes, with links connecting
 ## How to Use
 
 1. Visit the [GitHub Pages site](https://yourusername.github.io/your-repo-name) to view the visualization.
-2. Adjust the number of nearest neighbors using the slider on the left sidebar.
-3. Search for specific frameworks by entering labels in the search box.
+2. Adjust the number of nearest neighbors using the slider on the left sidebar. The recommended setting is something between 2-6 nearest neighbors to aid the visualization.
+3. Search for specific frameworks by entering labels in the search box (space- or comma-separated)
 4. Find the shortest path between two frameworks by entering their labels in the path search box.
-5. Use the "Replot Graph" button to rearrange the layout.
-6. Zoom and pan the visualization using your mouse or touchpad.
+5. Use the "Replot Graph" button to rearrange the layout as needed. Sometimes nodes and edges can get on the way, so just refresh the graph if they are inconveniently placed.
+6. Zoom and pan the visualization to explore the map.
 
 ## Features
 
@@ -24,32 +27,18 @@ The visualization represents zeolite frameworks as nodes, with links connecting
 - Search functionality for specific frameworks
 - Shortest path finding between two frameworks
 - Color-coded nodes and links for easy interpretation
-- Zoom and pan capabilities
-
-## Colors
-
-- Default nodes: Green
-- Searched nodes: Red
-- Neighbor nodes: Light red
-- Path nodes: Blue fill with blue outline
-- Path links: Blue, dashed
-
-## Reference
-
-This visualization is based on the work described in the following paper:
-
-[Insert paper title here]
-DOI: https://doi.org/10.1039/D3DD00134B
-
-## Author
-
-Daniel Schwalbe-Koda
-
-## License
 
-[Include license information here]
+## Citing
 
-## Acknowledgments
+This data has been produced for the following paper:
 
-- International Zeolite Association (IZA) for providing the structural data
-- [Any other acknowledgments]
+```bibtex
+@article{SchwalbeKoda2023Inorganic,
+    title = {Inorganic synthesis-structure maps in zeolites with machine learning and crystallographic distances},
+    author = {Schwalbe-Koda, Daniel, Widdowson, Daniel E., Pham, Tuan Anh, Kurlin, Vitaliy E.},
+    year = {2023},
+    journal = {arXiv:2307.10935},
+    doi = {10.48550/arXiv.2307.10935},
+    url = {https://doi.org/10.48550/arXiv.2307.10935},
+    arxiv = {2307.10935},
+}