Update README.md

[philipwfowler]

No description provided.

[Copilot]

Pull Request Overview

This PR updates the README.md file to provide a clearer description of the sbmlsim project and streamlines the documentation by removing internal development notes and replacing them with a placeholder for future research outputs.

• Updated the project description to be more specific about its purpose for training machine learning models on bacterial gene alleles
• Simplified the design section by removing internal development thoughts and focusing on the high-level API design
• Replaced detailed coding guidelines and workflow notes with a placeholder for research outputs

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