Barker:Notebook/FALCON

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Project Description/Abstract

  • Flux Assignment (with) LAD Convex Objectives (and) Normalization. LAD, or Least Absolute Deviations, is the 1-norm version of least squares.
  • Here, we list several data sources and procedures used in analyzing input and output for the FALCON method, which is used to estimate metabolic fluxes from expression data.

Please find the source code repository on github. The revision used at the time of publication is XXXX.

Yeast RNA-Seq analysis

We have tested with RNA-Seq data from Lee et al. 2012. We provide the 75% maximum growth rate and 85% maximum growth rate files here for convenience, also used in our study.

In order to quickly test the minimum disjunction method, we include an example GPR rules file for Yeast.

Human Protein and mRNA expression analysis

The script used for the majority of the analysis and processing of expression is proteomic_file_make.py.

To run this script, the following files will need to be downloaded, possibly uncompressed, and their locations will need to be edited in the INPUT section of proteomic_file_make.py.

  • Media:Rec2.genes -- Gene list from Recon 2 (version 2.XXX used in publication).

Notes

  • This project is currently a work in progress. If you are interested, please contact the author.


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