docs: Add citation, web-service URL, fix parameter typo

Author: tsenoner

README.md

@@ -1,12 +1,32 @@
 # ProtSpace
 
-ProtSpace is a visualization tool for exploring protein embeddings or similarity matrix along their 3D protein structures. It allows users to interactively visualize high-dimensional protein language model data in 2D or 3D space, color-code proteins based on various features, and view protein structures when available.
+ProtSpace is a visualization tool for exploring **protein embeddings** or **similarity matrix** along their 3D protein structures. It allows users to interactively visualize high-dimensional protein language model data in 2D or 3D space, color-code proteins based on various features, and view protein structures when available.
+
+## Web Interface
+Try ProtSpace directly in your browser without installation:
+https://protspace.rostlab.org/
+
+## Quick Start with Google Colab
+
+Try ProtSpace instantly using our Google Colab notebooks:
+
+**Note**: Some Google Colab functionalities may not work properly in Safari browsers. For the best experience, we recommend using Chrome or Firefox.
+
+1. **Explore Pre-computed Visualizations**:
+[![Open Explorer In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/tsenoner/protspace/blob/main/examples/notebook/Explore_ProtSpace.ipynb)
+
+2. **Generate Protein Embeddings**:
+[![Open Embeddings In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/tsenoner/protspace/blob/main/examples/notebook/ClickThrough_GenerateEmbeddings.ipynb)
+
+3. **Full Pipeline Demo**:
+[![Open Pipeline In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/tsenoner/protspace/blob/main/examples/notebook/Run_ProtSpace.ipynb)
 
 ## Table of Contents
 
 - [ProtSpace](#protspace)
-  - [Table of Contents](#table-of-contents)
+  - [Web Interface](#web-interface)
   - [Quick Start with Google Colab](#quick-start-with-google-colab)
+  - [Table of Contents](#table-of-contents)
   - [Example Outputs](#example-outputs)
     - [2D Scatter Plot (SVG)](#2d-scatter-plot-svg)
     - [3D Interactive Plot](#3d-interactive-plot)
@@ -23,21 +43,7 @@ ProtSpace is a visualization tool for exploring protein embeddings or similarity
   - [File Formats](#file-formats)
     - [Input](#input)
     - [Output](#output)
-
-## Quick Start with Google Colab
-
-Try ProtSpace instantly using our Google Colab notebooks:
-
-**Note**: Some Google Colab functionalities may not work properly in Safari browsers. For the best experience, we recommend using Chrome or Firefox.
-
-1. **Explore Pre-computed Visualizations**:
-[![Open Explorer In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/tsenoner/protspace/blob/main/examples/notebook/Explore_ProtSpace.ipynb)
-
-2. **Generate Protein Embeddings**:
-[![Open Embeddings In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/tsenoner/protspace/blob/main/examples/notebook/ClickThrough_GenerateEmbeddings.ipynb)
-
-3. **Full Pipeline Demo**:
-[![Open Pipeline In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/tsenoner/protspace/blob/main/examples/notebook/Run_ProtSpace.ipynb)
+  - [Citation](#citation)
 
 ## Example Outputs
 
@@ -66,7 +72,7 @@ protspace-json -i embeddings.h5 -m features.csv -o output.json --methods pca3 um
 ### Running protspace
 
 ```bash
-protspace output.json [--pdb_zip pdb_files.zip] [--port 8050]
+protspace --json output.json [--pdb_zip pdb_files.zip] [--port 8050]
 ```
 
 Access the interface at `http://localhost:8050`
@@ -82,7 +88,7 @@ Access the interface at `http://localhost:8050`
 - Feature-based coloring and marker styling
 - Protein structure visualization (with PDB files)
 - Search and highlight functionality
-- High-quality plot exports
+- High-quality plot exports (SVG for 2D, interactive HTML for 3D)
 - Responsive web interface
 
 ## Data Preparation
@@ -98,6 +104,7 @@ The `protspace-json` command supports:
 
 ### Optional Arguments
 
+- `--delimiter`: Specify delimiter for metadata file (default: comma)
 - `--custom_names`: Custom projection names (e.g., pca2=PCA_2D)
 - `--verbose`: Increase output verbosity
 
@@ -115,6 +122,7 @@ The `protspace-json` command supports:
 - MDS:
   - `--n_init`: Number of initializations (default: 4)
   - `--max_iter`: Maximum iterations (default: 300)
+  - `--eps`: Convergence tolerance (default: 1e-3)
 
 ## Custom Feature Styling
 
@@ -142,20 +150,37 @@ Available shapes: circle, circle-open, cross, diamond, diamond-open, square, squ
 ### Input
 
 1. **Embeddings/Similarity**
-   - HDF5 (.h5) for embeddings
-   - CSV for similarity matrix
+  - HDF5 (.h5) for embeddings
+  - CSV for similarity matrix
 
 2. **Metadata**
-   - CSV with mandatory 'identifier' column matching IDs in embeddings/similarity data
-   - Additional columns for features
+  - CSV with mandatory 'identifier' column matching IDs in embeddings/similarity data
+  - Additional columns for features
 
 3. **Structures**
-   - ZIP containing PDB/CIF files
-   - Filenames match identifiers (dots replaced with underscores)
+  - ZIP containing PDB/CIF files
+  - Filenames match identifiers (dots replaced with underscores)
 
 ### Output
 
 - JSON containing:
   - Protein features
   - Projection coordinates
-  - Visualization state (colors, shapes)
+  - Visualization state (colors, shapes)
+
+## Citation
+
+If you use ProtSpace in your research, please cite:
+
+```bibtex
+@article{SENONER2025168940,
+title = {ProtSpace: A Tool for Visualizing Protein Space},
+journal = {Journal of Molecular Biology},
+pages = {168940},
+year = {2025},
+issn = {0022-2836},
+doi = {https://doi.org/10.1016/j.jmb.2025.168940},
+url = {https://www.sciencedirect.com/science/article/pii/S0022283625000063},
+author = {Tobias Senoner and Tobias Olenyi and Michael Heinzinger and Anton Spannagl and George Bouras and Burkhard Rost and Ivan Koludarov}
+}
+```