Tutorials

Step-by-step tutorials for learning Surfacia's capabilities.

Tutorial Topics

• Basic Workflow Tutorial
  • Goal
  • Before You Start
  • Minimal Input Example
  • Recommended Path
  • Run the Workflow
  • What to Inspect First
  • Practical Reading Order
  • What a Good First Result Looks Like
  • Common Beginner Mistakes
  • What to Do Next
  • See Also
• Advanced Analysis Tutorial
  • Topics
  • When You Need This Tutorial
  • Step 1: Choose the Right Mode
  • Step 2: Compare Representations, Not Just Scores
  • Step 3: Read SHAP More Carefully
  • Practical Comparison Strategy
  • Best For
  • Warning Signs
• Custom Descriptor Tutorial
  • Design Principles
  • What Makes a Good Surfacia Descriptor
  • Good Candidates
  • Less Helpful Additions
  • Naming Suggestions
  • Validation Checklist
• Machine Learning Tutorial
  • Topics
  • Recommended Workflow
  • How to Judge a Model
  • Small-Data Reality
  • What to Look for in SHAP
  • What to Watch For
  • Practical Outcome

Overview

These tutorials are arranged as a practical learning path rather than a purely technical reference. They are meant to help you go from "I can run Surfacia" to "I can choose the right analysis strategy and trust what I am reading."

Tutorial Structure

Each tutorial follows a consistent structure:

1. Objective: What you'll learn and accomplish

2. Prerequisites: Required knowledge and setup

3. Step-by-step Instructions: Detailed walkthrough

4. Expected Results: What outputs to expect

5. Troubleshooting: Common issues and solutions

6. Next Steps: Related tutorials and advanced topics

Recommended Learning Path

If you are new to Surfacia, this order usually works best:

1. start with Basic Workflow Tutorial

2. move to Machine Learning Tutorial once you have a descriptor table

3. read Advanced Analysis Tutorial when you want to compare analysis modes

4. use Custom Descriptor Tutorial only when you are ready to extend the system itself

Available Tutorials

Basic Workflow Tutorial

Learn the fundamental Surfacia workflow from molecular input to final analysis results.

• Setting up input files

• Running the complete 8-step workflow

• Interpreting results

• Basic visualization

Advanced Analysis Tutorial

Explore advanced features for specialized molecular surface analysis.

• Custom parameter optimization

• Multi-scale descriptor analysis

• Advanced visualization techniques

• Performance optimization

Custom Descriptors Tutorial

Create and integrate custom molecular descriptors.

• Understanding the descriptor framework

• Implementing custom descriptors

• Integration with existing workflows

• Validation and testing

Machine Learning Tutorial

Apply machine learning techniques to molecular surface data.

• Feature selection and engineering

• Model training and validation

• SHAP-based interpretability

• Results interpretation

Getting Started

To begin with the tutorials:

1. Ensure Surfacia is properly installed (see Installation)

2. Begin with a small input table before using large research datasets

3. Follow the tutorials in order for the smoothest onboarding

4. Refer to the Command Reference pages when you want option-level details

Pick a Tutorial by Goal

• If you want a first successful run, start with Basic Workflow Tutorial

• If you want better interpretation, go to Machine Learning Tutorial

• If you want to choose among Mode 1, 2, and 3, read Advanced Analysis Tutorial

• If you want to extend Surfacia itself, read Custom Descriptor Tutorial