Resources
Software
These tools are the result of in-house methodological developments and were extensively used in our group for teaching and research. They are free for academic purposes, and in some cases a Software License Agreement must be signed. Commercial licenses are subject to a fee. Contact N. Zamboni for more information.
The central public repository is external page https://github.com/zamboni-lab
SLAW: Scalable LC-MS Analysis Workflow
SLAW is an all-inclusive and massively scalable package for processing of untargeted LC-MS in metabolomics and lipidomics. It offers some smart functionalities for DDA data. The simplest way of obtaining SLAW is to pull the Docker container. More information can be found on Github.
Repository: external page https://github.com/zamboni-lab/SLAW
Reference: Delabriere A, Warmer P, Brennsteiner V and Zamboni N, SLAW: A scalable and self-optimizing processing workflow for untargeted LC-MS, Anal. Chem. 2021 (external page doi)
SUMOFLUX
Toolbox for Targeted 13C metabolic flux ratio analysis by surrogate modeling, i.e. by machine learning.
Repository: external page https://github.com/zamboni-lab/sumoflux
Reference: Kogadeeva M, Zamboni N, SUMOFLUX: A Generalized Method for Targeted 13C Metabolic Flux Ratio Analysis, PLOS Computational Biology, 2016, external page doi
MNS (Metabolic Network Segmentation)
Toolbox for Metabolic Network Segmentation based on metabolome profiling data.
Repository: external page https://github.com/zamboni-lab/MNS
Reference: Kuehne et al, Metabolic network segmentation: A probabilistic graphical modeling approach to identify the sites and sequential order of metabolic regulation from non-targeted metabolomics data. PLoS Comput Biol. 2017 Jun 9;13(6):e1005577. external page doi
Download MNS package v1.0 (ZIP, 37.2 MB) (GPL v3 license).
Download Data and scripts used in the paper. (ZIP, 111.1 MB)
anNET
Network-embedded, thermodynamic analysis of metabolomics data.
Free for Academic purposes upon signing a Software License Agreement.
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FiatFlux (obsolete)
13C flux ratio analysis of microbial metabolism.
Free for Academic purposes upon signing a Software License Agreement.
FiatFlux is conceptually deprecated. We recommend using SUMOFLUX instead.
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