AFL Software Overview

Introduction

This document provides an overview of the software ecosystem that powers the Autonomous Formulation Lab (AFL). The AFL software stack is designed to control hardware components, manage experiments, analyze data, and enable autonomous operation through an agent-based architecture.

System Architecture

1. Software Layers

• Hardware control layer
• Experiment management layer
• Data analysis layer
• Autonomous agent layer

2. Communication Protocols

• Internal communication between modules
• External communication with instruments
• API specifications

Core Components

1. AFL-Agent

• Purpose and capabilities
• Agent architecture
• Decision-making framework
• Experimental planning algorithms

2. Hardware Control Software

• OT-2 robot control integration
• Pneumatic system control
• Electronics module interface
• Video and UI system management

3. Experiment Management

• Experiment definition format
• Workflow orchestration
• Error handling and recovery
• Logging and monitoring

4. Data Management

• Data storage architecture
• File formats and organization
• Metadata standards
• Data backup strategies

Installation and Setup

1. System Requirements

• Hardware requirements
• Operating system compatibility
• Network requirements
• Storage recommendations

2. Installation Procedures

• Software dependencies
• Installation steps
• Configuration options
• Validation tests

3. User Account Management

• Access control
• Permission levels
• Authentication methods

User Interfaces

1. Command Line Interface

• Available commands
• Scripting capabilities
• Remote access

2. Web Interface

• Dashboard features
• Experiment monitoring
• Data visualization
• Configuration management

3. API Access

• RESTful API documentation
• Client libraries
• Authentication

Development and Extension

1. Development Environment Setup

• Recommended tools
• Development workflow
• Testing framework

2. Plugin Architecture

• Creating new instrument interfaces
• Developing custom analysis modules
• Extending agent capabilities

3. Contributing Guidelines

• Code standards
• Documentation requirements
• Pull request process

Troubleshooting and Maintenance

1. Logging and Diagnostics

• Log file locations
• Diagnostic tools
• Common error messages

2. Software Updates

• Update procedure
• Version compatibility
• Rollback procedures

3. Backup and Recovery

• Backup strategies
• Recovery procedures
• Data integrity verification