Proteomics + Bioinformatics Pipeline

A bioinformatics pipeline for proteomics

A locally deployed command line tool and database for the analysis of protein assays across multiple experimental types and tissues
The challenge

Our client provides laboratory materials and kits for performing protein assays. They also analyze the data from these kits on behalf of their users. A set of customers expressed the need to reproduce these analyses onsite as they were unable to send their data to our client for analysis for legal and intellectual property reasons.The client needed a stand alone tool which could reproduce their analysis pipeline that had been developed over more than a decade. The existing microservices platform was translated to a more compact implementation in Python.

Our Solution

Our team explored the client’s existing code base and developed a command line tool that allowed their users to independently reproduce the client's internal analysis automatically at their facilities, within the user’s private network. Our team collaborated with the client to ensure that all data, previously only available in the cloud, were incorporated into the application. As a part of this development, we created a local database to store analysis data. This new data format reduced duplication, was more compact, and supported legacy functionality; becoming their new standard. This tool has been deployed and is in use at a number of test sites, and is now being prepared for full release.

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