$${\color{green} MSConnect}$$

MSConnect is a Web-based, flexible, open-source platform for automated high-throughput MS-based omics. It streamlines the entire process from data collection, data management, data processing and to data visualization by integrating and supporting various third-party tools, allowing for a fully autonomous. The platform is built with Python, Django, JavaScript, and HTML and works with Raw file uploader and Processor.

Please note: while the platform supports all 3rd party applications, they are not included and licensing requirements should be consulted with their respective owners.

$${\color{green} What \space It \space Does }$$

MSConnect is a comprehensive platform that automates the following tasks:

• Data Management: Streamlines the uploading and organization of raw MS files.
• Data Backup: Provides secure storage throughout the processing pipeline.
• Data Processing: Interfaces with third-party tools to analyze MS raw data.
• Result Interpretation: Generates tables and figures for easy interpretation and presentation of results.

$${\color{green} Key \space features \space of \space platform \space }$$

• Vendor-Independent: Compatible with diverse MS applications, ensuring flexibility across platforms.
• Automation: Offers fully autonomous workflows, minimizing manual intervention.
• User-configurable, automated, redundant data backup and purging.
• Third-Party Integration: Seamlessly connects with external software for advanced analysis.
• Visualization Tools: Provides clear and actionable data representations for streamlined interpretation (depends on user workflow may required 3rd party modules).
• Generalized Framework: Adaptable to various omics studies, expanding its applicability.
• Easy installation with Docker container-based deployment and simple integration of other 3rd party Docker images.
• A SQL database linked data structure that allows users to search data and files through a web interface or programmatically.
• A module distribution system between developers and users similar to an app-store.
• Integration of the Django REST framework for API access and Jupyter Notebook for scripting with Python and R.

$${\color{green} What \space It \space Is \space Not }$$

• MSConnect is not a standalone data analysis tool. It depends on third-party software for data processing/analysis
• MSConnect does not come with any data processor or analysis software/license, it provides a wrapper/interface to interact with them.
• It is not limited to any specific MS application; instead, it provides a generalized framework adaptable to various omics studies.
• MSConnect is not a desktop application; it is web-based and requires a server (can be an old PC) for deployment (using Docker to enable fast deployment in less than 30 min).

$${\color{green} Documentation }$$

Download User Manual or visit MSConnect wiki page wiki page.

$${\color{green} What \space You \space Need }$$

• PC computer less than 10 years old (linux, unix, windows) 8 gigs of Ram, 120 gig storage,
• Third-party software for specific MS data analysis tasks. (sofware requirements)
• Ability to set up processing workflow to enable auto processing by following the tutorial. Processing module/wrapper setup

$${\color{green} Requests \space for \space Collaboration }$$

To propose new collaborations or participate in development, submit a request or contact us directly ryan.kelly@byu.edu.

$${\color{green} How \space to \space cite }$$

If you use MSConnect for your work, we request that you cite MSConnect in relevant papers. A manuscript is currently being prepared and will be available soon.