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Welcome to piLINCS help and documentation Wiki pages.

The goal of piLINCS is provide access to proteomic profiles generated by the LINCS consortium. At present, piLINCS enables access to reduced representation phosphoproteomic ("P100") and global chromatin ("GCP") profiles generated by using mass spectrometry techniques to characterize proteome level molecular signatures of (responses to) small molecule and genetic perturbations in a number of different cell lines (for details see LINCS/Broad). These different profiles are obtained by merging QC+NORM level processed GCT files from Panorama repository, and subsequently processed further to create various 'views' of such obtained overall data set to facilitate its use by the community.

Quick help for users

• Getting started
• Filtering on (assay, cell type, perturbation, dose) tuples
• Downloading the entire data set
• Exporting subsets of profiles for user defined tuples
• Types of profiles that can be viewed and/or exported
• Analyzing data using iLINCS

More on piLINCS

• piLINCS poster: UC Irvine LINCS Outreach Meeting, March 10th, 2016
• Download piLINCS logo
• piLINCS flowchart

Documentation for developers

ETL workflow

• Load peptide annotations
• Load replicate annotations
• Load data points (peak areas)

For Developers

• Run on your server
• Configuration file
• H2 in-memory database
• Development with IntelliJ Idea

For Developers at the University of Cincinnati

• Restart piLINCS from GitHub
• Use GIMM14
• MySQL database
• Apache Proxy

For Data Scientists

• Quantile normalization

Things in progress

• TODO

Links

• Description of Panorama datasets
• Panorama technical documentation
• LINCS-DCIC