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influx_si v7.0.1_1 #255

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17 changes: 10 additions & 7 deletions tools/influx_si/README.rst
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Metabolic flux estimation
-------------------------

`influx_si` can be used for metabolic flux estimation based on labeling data from MS and/or NMR measurements. `influx_s` is used for stationary labeling and `influx_i` for instationary one (hence the '_s' and '_i' in the names). Tha name `influx_si` is used as common for both tools.
`influx_si` can be used for estimation of metabolic fluxes and concentrations based on labeling data from MS and/or NMR measurements. `influx_s` is used for stationary labeling and `influx_i` for instationary one (hence the '_s' and '_i' in the names). The name `influx_si` is used as common for both tools.

The input for `influx_si` in one or several FTBL files, each describing a given labeling experiment and options to use during estimation. In addition, for `influx_i` a file with time course data has to be provided for each FTBL file.
The input for `influx_si` is an MTF (Multiple TSV Files) collection describing metabolic network, label transition, labeling data and options to use during estimation.

The output is a zip archive with files generated by `influx_si`. Among the most important is file ending with `_res.kvh` which contains the main information about estimated parameters, their statistics and so on.
If, in your FTBL file, you have requested ploting information, it can be found in respective .pdf file.
The output is a zip archive with files generated by `influx_si`. File ending with `.tvar.sim` which contains the estimated fluxes and concentrations. Other files ending with `.sim` contain simulated measurements. File ending with `.stat` has results of chi2 test assessing quality of fit.

For detailed documentation about `influx_si` and accompanying tools see https://metasys.insa-toulouse.fr/software/influx/doc/
If, in your `.opt` file, you have requested plotting information (`plot_smeas.R` or `plot_ilab.R`), it can be found in the respective `.pdf` file.

For getting a standalone version of `influx_si` see https://metasys.insa-toulouse.fr/software/influx/
For detailed documentation about `influx_si` and accompanying tools see https://influx-si.readthedocs.io

For getting a standalone version of `influx_si <https://anaconda.org/bioconda/influx_si>`_, you can install it e.g. with `conda <https://docs.conda.io/en/latest/miniconda.html>`_ package manager: ::

conda install -c conda-forge -c bioconda influx_si

Author: Serguei Sokol
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License: GPL2

© INRAE 2020
© INRAE/INSA/CNRS 2023
378 changes: 175 additions & 203 deletions tools/influx_si/influx_si.xml

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4 changes: 4 additions & 0 deletions tools/influx_si/macros.xml
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<?xml version="1.0"?>
<macros>
<token name="@TOOL_VERSION@">7.0.1</token>
</macros>
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