Welcome to ReDU (Reanalysis of Data User Interface)


ReDU is a community-minded approach to find and reuse public data containing tandem MS data at the repository scale. ReDU is a launchpad for co- or re-analysis of public data via the Global Natural Product Social Molecular Networking Platform (GNPS). Our aim is to empower researchers to put their data in the context of public data as well as explore questions using public data at the repository scale.

This is a community effort and everyone is encouraged to participate by submitting their own data and sample information instructions. The sharing of new applications (and code) which use ReDU is highly encouraged.


ReDU Tool Schematic

clicking on the image below launches an interactive version - or edited via this link here

Mermaid Live


We are developing two main branches of functionality:

Analyze Your Data

  • Compare Your Data to Public Data via Multivariate Analysis - Projection of your data onto a precalculated principal components analysis score plot of public data.
  • Co-analyze Your Data with Public Data at GNPS - Select files using sample information and assemble public data in groups as desired using the file selector. Launching an analysis loads the files from MassIVE at which point users can add their own data. The following co-analyses can be launched:
  • Molecular Networking at GNPS - link
  • Library Search at GNPS - link
  • PCA of Selected Files - link

Analyze Public Data

  • Explore Multivariate Analysis of Public Data - Explore precalculated principal components analysis score plot of public data.
  • Chemical Explorer - Explore precalculated annotations using public data and default GNPS parameters
  • Re-analyze Public Data at GNPS - Select files using sample information and assemble public data in groups as desired using the file selector. The following co-analyses can be launched:
  • Molecular Networking at GNPS - link
  • Library Search at GNPS - link
  • Chemical Explorer - link
  • Group Comparator - link
  • PCA of Selected Files - link

Data Availability

All sample information can be downloaded from the ReDU-MS2 homepage by clicking "Download Database". The ReDU identification database is publicly available and accessible via (GNPS), MSV000084206.


Code Availability

Code for ReDU can be found on GitHub - link here


Citation


Read our recent submitted preprint: Repository-scale Co- and Re-analysis of Tandem Mass Spectrometry Data.


Issues and Suggestions

Please submit any issues or suggestions via GitHub. The use of the GNPS forum is encouraged.


Page Contributions

Alan K. Jarmusch (UCSD), Mingxun Wang (UCSD), Christine M. Aceves (UCSD)