Score Dev Doc Update

docs/contribution/contribution.md

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+
+**Navigation**
+
+- [Background](../index.md) 
+- [Operation](../operation/operation.md)
+
+---
+
+# Contribution Guidelines
+
+We appreciate your interest in contributing to the Overture! Please take the time to read and follow these guidelines before submitting your contributions. By participating in this project, you are expected to abide by the [Code of Conduct](https://github.com/overture-stack/SCORE/blob/readme-update/code_of_conduct.md). Please take the time to read it carefully before contributing.
+
+## Running score from Source Code
+
+To contribute to score, you'll need to run the application from the source code. Here's how you can do that:
+
+1. **Clone the Repository**: First, clone the score repository to your local machine using `git clone https://github.com/overture-stack/SCORE.git`.
+
+2. **Install Dependencies**: Navigate to the cloned directory and install all required dependencies.
+
+3. **Run the Application Locally**: After installing the dependencies, start the application locally. This usually involves running a command like `npm start` or `python manage.py runserver`, again depending on the language and framework used.
+
+4. **Test Your Changes**: Before submitting a pull request, make sure to test your changes thoroughly. Run the automated tests (if available) and perform manual testing to ensure that your contribution does not introduce regressions.
+
+## Issues and Feature Requests
+
+Before opening a new issue or feature request, please check if a similar one already exists. If so, please add a comment to the existing issue instead of creating a new one. When submitting an issue or feature request, please include a detailed description of the problem or feature you would like to see, along with any relevant code, error messages, or screenshots. This will help us better understand the issue and respond more efficiently.
+
+### Pull Requests
+
+We welcome and encourage pull requests from the community. To submit a pull request, please follow these steps:
+
+1. **Fork the Repository**: Fork the score repository on GitHub.
+2. **Clone Your Fork**: Clone your forked repository to your local machine.
+3. **Create a New Branch**: Create a new branch for your changes.
+4. **Make Your Changes**: Implement your changes and commit them to your branch.
+5. **Push Your Changes**: Push your changes to your forked repository.
+6. **Submit a Pull Request**: Open a pull request against the main repository.
+
+Please ensure your code adheres to the following guidelines before submission:
+
+- The code should be well-documented and readable.
+- The code should be tested.
+- Include a clear description of the changes made and the reason for the changes in the pull request.
+
+For any questions or discussions regarding your pull request, please refer to the GitHub issues system or join our [Slack channel](http://slack.overture.bio/) for further assistance.
+
+We use GitHub issues and pull requests for communication-related to code changes. For general discussion, feel free to join our [Slack channel](http://slack.overture.bio/).
+
+Thank you for contributing to Overture-Stack!
+
+---
+
+**Navigation**
+
+- [Background](../index.md) 
+- [Operation](../operation/operation.md)
+
+---

docs/index.md

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+# Score Developer Documentation
+
+---
+
+**Navigation**
+- [Operation](./operation/operation.md)
+- [Contribution](./contribution/contribution.md) 
+
+---
+
+# Background
+
+Score's primary function is to facilitate the secure upload and download of file data to and from an object storage provider. 
+
+Score specializes in data transfer, leaving metadata complexities to its companion application, <a href="https://github.com/overture-stack/score" target="_blank" rel="noopener noreferrer">Song</a>. Song manages metadata validation and tracking, maintaining a separate repository from object storage. Together, Score and Song provide an efficient solution for distributed data organization.
+
+## High Performance Transfers
+
+Score offers a high-performance multipart transfer system with several advantages:
+
+- Enables segmented file downloads, allowing for pause and resume functionality
+- Automatically resumes file transfers if interrupted, for instance, due to connection issues
+- Utilizes parallelization for efficient and rapid file uploads and downloads
+
+## Data Integrity
+
+- Score guarantees file transfer authenticity by conducting <a href="https://www.ietf.org/rfc/rfc1321.txt" target="_blank" rel="noopener noreferrer">MD5 validations</a> on all file uploads and downloads
+
+## BAM & CRAM Slicing
+
+- Score client incorporates <a href="http://www.htslib.org/" target="_blank" rel="noopener noreferrer">samtools</a> features, enabling viewing of reads from BAM files
+- Provides the capability to slice BAM and CRAM files by genomic regions using command line tools
+
+## The Score Client
+
+The Score Client, a command-line tool, simplifies interactions with Score's REST API endpoints. With score client, users can efficiently upload and download files, and access various Score-related parameters. For detailed information on score client commands, refer to our <a href="www.overture.bio/documentation/score/user-guide/commands/" target="_blank" rel="noopener noreferrer">score client reference documentation</a>.
+
+## The Score Client
+
+The Score Client is a user-friendly CLI tool designed to streamline the process of interacting with Score and Song. Key features of the Score Client include:
+
+- **File Management:** Users can efficiently upload and download files using manifest files retrieved from data portals
+- **File Metadata Handling:** The Score Client facilitates the uploading of file metadata, including object IDs and md5 checksums to Song, ensuring that data is consistently tracked and accessible
+- **Integration with Object Storage:** Compatible with S3-compliant object storage providers including AWS, Azure, and Google Cloud
+
+For comprehensive details on the commands and usage of the Score Client, please refer to the [Score Client Reference Documentation](www.overture.bio/documentation/score/user-guide/commands/).
+
+---
+
+**Navigation**
+
+- [Operation](./operation/operation.md)
+- [Contribution](./contribution/contribution.md) 
+
+---