This PR introduces a comprehensive tutorial for the COBRArrow MATLAB API. The tutorial is designed to guide users through the key functionalities of COBRArrow, including environment setup, sending models to a remote server, fetching models, persisting models to a database, and optimizing models.
Key Sections Covered:
Introduction:
Provides an overview of COBRArrow and its purpose in handling large-scale biochemical reaction models through remote procedure calls (RPC).
Step 1: Environment Setup:
Detailed instructions for ensuring that MATLAB, Python, and the COBRA Toolbox are properly installed and configured.
Specific guidance on Python compatibility with MATLAB, with links to relevant MathWorks documentation.
Step 2: Setting Up COBRArrow:
Instructions on initializing COBRArrow within MATLAB, including how to establish a connection to a remote server.
Step 3: Sending and Optimizing a Model:
Demonstrates how to load a model, send it to the remote server, and run optimizations using remote resources.
Includes examples of setting solver parameters and handling potential errors, such as overwriting existing models on the server.
Additional Methods:
Explains how to fetch models and specific fields from the server, persist models to a database, and list flight information on the server.
Troubleshooting:
Provides common troubleshooting steps for issues related to sending models, running optimizations, and ensuring compatibility.
Acknowledgments:
Notes on current limitations, such as the lack of support for parameter changes in the remote optimization service, and the importance of persisting models to prevent data loss.
Reviewers:
Please review the tutorial for:
Clarity and completeness of the instructions.
Accuracy of the examples provided.
Usability of the script as a learning tool for new users of COBRArrow.
Feedback on improving the tutorial content or identifying any gaps is welcome.
Description:
This PR introduces a comprehensive tutorial for the COBRArrow MATLAB API. The tutorial is designed to guide users through the key functionalities of COBRArrow, including environment setup, sending models to a remote server, fetching models, persisting models to a database, and optimizing models.
Key Sections Covered:
Introduction:
Step 1: Environment Setup:
Step 2: Setting Up COBRArrow:
Step 3: Sending and Optimizing a Model:
Additional Methods:
Troubleshooting:
Acknowledgments:
Reviewers:
Please review the tutorial for:
Feedback on improving the tutorial content or identifying any gaps is welcome.