LIMS triggered processing - BA, Internship, IDP - Kuster Lab

Title: Triggering MaxQuant searches from our laboratory information management system

Type: BA, internship, IDP

Category: Pipelining

Programming language: [ Python, SQL ]

Language: [ English ]

Prior experience: [ experience with SQL and Python is required, no biological knowledge necessary ] 

Complexity/Risk: low

Contact person: Matthew The

Brief background description (couple of sentences + literature): Our laboratory information management system (LIMS) tracks data coming from our mass spectrometers and organizes them in projects. At the same time, almost every project requires identification and quantification of proteins, which is typically done with MaxQuant. Currently, our researchers have to manually run these searches, which can easily lead to mistakes due to using the wrong set of parameters.

Brief description of the project (couple of sentences): In this project, you will investigate and implement a queueing system that links our LIMS to MaxQuant, based on the needs of our researchers. Important things to take into consideration are the heterogeneity of the searches the researchers would like to run and to what degree they would like the automation to go, i.e. triggered as soon as the appropriate files come in or requiring some user interaction before submitting the search to the queue.

The LIMS is implemented as a Flask server (Python+MySQL), whereas the current (offline) queueing system is implemented in Bash. However, for maintainability, the queueing system will most likely have to be rewritten in Python.

Expected result: A prototype of a queueing system for MaxQuant triggered through our LIMS, which would save a lot of time for our researchers and prevent trivial errors.