Mercurial > repos > workflow4metabolomics > physiofit

annotate physiofit.xml @ 5:2353eeb1c7ff draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 23cfca443338f5ae8eed54b44a5b0d7b02563334
author workflow4metabolomics
date Tue, 19 Mar 2024 14:49:20 +0000
parents f2ba98635c6c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
1 <tool id='physiofit' name='PhysioFit: extracellular flux calculation' version='@TOOL_VERSION@+galaxy0' python_template_version='3.5' profile='21.05'>
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
2 <description>PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake and production fluxes</description>
0
198d81ccc75e planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 188d100128db10dde9bac0bb6c6c60e6946508a1
workflow4metabolomics
parents:
diff changeset
3 <macros>
4
f2ba98635c6c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 45988938658acc0c03ddb0e51b1d51b3d27051ae
workflow4metabolomics
parents: 3
diff changeset
4 <token name='@TOOL_VERSION@'>3.3.5</token>
0
198d81ccc75e planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 188d100128db10dde9bac0bb6c6c60e6946508a1
workflow4metabolomics
parents:
diff changeset
5 </macros>
3
4e885e541368 planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit bc02f9f707e8d8e935d4d905598f6d6a190fd3d7
workflow4metabolomics
parents: 2
diff changeset
6
0
198d81ccc75e planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 188d100128db10dde9bac0bb6c6c60e6946508a1
workflow4metabolomics
parents:
diff changeset
7 <requirements>
5
2353eeb1c7ff planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 23cfca443338f5ae8eed54b44a5b0d7b02563334
workflow4metabolomics
parents: 4
diff changeset
8 <requirement type='package' version="@TOOL_VERSION@">physiofit</requirement>
0
198d81ccc75e planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 188d100128db10dde9bac0bb6c6c60e6946508a1
workflow4metabolomics
parents:
diff changeset
9 </requirements>
3
4e885e541368 planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit bc02f9f707e8d8e935d4d905598f6d6a190fd3d7
workflow4metabolomics
parents: 2
diff changeset
10
0
198d81ccc75e planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 188d100128db10dde9bac0bb6c6c60e6946508a1
workflow4metabolomics
parents:
diff changeset
11 <command detect_errors='exit_code'><![CDATA[
2
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
12 physiofit
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
13 --galaxy
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
14 --config $configfile
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
15 --data $datafile
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
16 -or '$recap'
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
17 -oz $zip
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
18 2> $log
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
19 ]]>
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
20 </command>
0
198d81ccc75e planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 188d100128db10dde9bac0bb6c6c60e6946508a1
workflow4metabolomics
parents:
diff changeset
21 <inputs>
2
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
22 <param name='datafile' type='data' format='tabular, txt' multiple='true' label='Upload data file containing biomass and concentration values'/>
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
23 <param name='configfile' type='data' format='yaml' multiple='true' label='Upload yaml configuration file containing run parameters'/>
0
198d81ccc75e planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 188d100128db10dde9bac0bb6c6c60e6946508a1
workflow4metabolomics
parents:
diff changeset
24 </inputs>
198d81ccc75e planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 188d100128db10dde9bac0bb6c6c60e6946508a1
workflow4metabolomics
parents:
diff changeset
25 <outputs>
2
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
26 <data name='recap' label='Summary file' format='csv'/>
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
27 <data name='zip' label='Results' format='zip'/>
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
28 <data name='log' label='Log' format='txt'/>
0
198d81ccc75e planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 188d100128db10dde9bac0bb6c6c60e6946508a1
workflow4metabolomics
parents:
diff changeset
29 </outputs>
198d81ccc75e planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 188d100128db10dde9bac0bb6c6c60e6946508a1
workflow4metabolomics
parents:
diff changeset
30 <tests>
198d81ccc75e planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 188d100128db10dde9bac0bb6c6c60e6946508a1
workflow4metabolomics
parents:
diff changeset
31 <test>
2
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
32 <param name='datafile' value='data.txt'/>
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
33 <param name='configfile' value='config_file.yml'/>
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
34 <output name='recap'>
0
198d81ccc75e planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 188d100128db10dde9bac0bb6c6c60e6946508a1
workflow4metabolomics
parents:
diff changeset
35 <assert_contents>
2
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
36 <has_text text='experiments'/>
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
37 <has_text text='growth_rate'/>
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
38 <has_text text='Glc_q'/>
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
39 <has_text text='Glc_M0'/>
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
40 <has_text text='Ace_q'/>
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
41 <has_text text='Ace_M0'/>
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
42 <has_text text='optimal'/>
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
43 <has_text text='mean'/>
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
44 </assert_contents>
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
45 </output>
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
46 <output name='zip'>
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
47 <assert_contents>
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
48 <has_archive_member path='.*\.svg' min='3'/>
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
49 <has_archive_member path='.*\.tsv' min='2'/>
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
50 <has_archive_member path='.*\.pdf' min='1'/>
0
198d81ccc75e planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 188d100128db10dde9bac0bb6c6c60e6946508a1
workflow4metabolomics
parents:
diff changeset
51 </assert_contents>
198d81ccc75e planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 188d100128db10dde9bac0bb6c6c60e6946508a1
workflow4metabolomics
parents:
diff changeset
52 </output>
198d81ccc75e planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 188d100128db10dde9bac0bb6c6c60e6946508a1
workflow4metabolomics
parents:
diff changeset
53 </test>
198d81ccc75e planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 188d100128db10dde9bac0bb6c6c60e6946508a1
workflow4metabolomics
parents:
diff changeset
54 </tests>
198d81ccc75e planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 188d100128db10dde9bac0bb6c6c60e6946508a1
workflow4metabolomics
parents:
diff changeset
55 <help><![CDATA[
2
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
56 **PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake & production fluxes**
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
57
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
58 Fluxes are estimated using mathematical models by fitting time-course measurements of the concentration of
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
59 cells and extracellular substrates and products. PhysioFit is shipped with some common growth models, and
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
60 additional tailor-made models can be implemented by users.
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
61
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
62 **PhysioFit includes the following features:**
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
63
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
64 * **calculation of growth rate and extracellular (uptake and production) fluxes**,
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
65 * **a set of steady-state and dynamic models** are shipped with PhysioFit,
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
66 * **tailor-made models** can be constructed by users,
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
67 * Monte-Carlo sensitivity analysis to **estimate the precision of the calculated fluxes**,
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
68 * **evaluation of the goodness of fit and visual inspection of the fitted curves**,
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
69 * shipped as a **library** with both a **graphical** and a **command line** interface,
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
70 * **open-source, free and easy to install** everywhere where Python 3 and pip run,
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
71 * **biologist-friendly**.
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
72
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
73 It is one of the routine tools that we use at the
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
74 `MetaSys team <https://www.toulouse-biotechnology-institute.fr/en/poles/equipe-metasys/>`_
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
75 and `MetaToul platform <https://mth-metatoul.com/>`_ to calculate fluxes.
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
76
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
77 The code is open-source, and available on `GitHub <https://github.com/MetaSys-LISBP/PhysioFit/>`_ under a GPLv3 license.
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
78
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
79 This documentation is available on Read the Docs (`https://physiofit.readthedocs.io <https://physiofit.readthedocs.io/>`_)
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
80 and can be downloaded as a `PDF file <https://readthedocs.org/projects/physiofit/downloads/pdf/latest/>`_.
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
81
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
82 ]]></help>
0
198d81ccc75e planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 188d100128db10dde9bac0bb6c6c60e6946508a1
workflow4metabolomics
parents:
diff changeset
83 <citations>
2
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
84 <citation type='bibtex'>@article{10.1101/2023.10.12.561695,
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
85 author = {Le Grégam, Loïc and Guitton, Yann and Bellvert, Floriant and Heux, Stéphanie and Jourdan, Fabien and Portais, Jean-Charles and Millard, Pierre},
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
86 title = "{Physiofit: a software to quantify cell growth parameters and extracellular fluxes}",
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
87 year = {2023},
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
88 month = {10},
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
89 abstract = '{Quantification of growth parameters and extracellular uptake and production fluxes is central in systems and synthetic biology.
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
90 Fluxes can be estimated using various mathematical models by fitting time-course measurements of the concentration of cells and
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
91 extracellular substrates and products. A single tool is available to calculate extracellular fluxes, but it is hardly interoperable and
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
92 includes a single hard-coded growth model. We present our open-source flux calculation software, PhysioFit, which can be used with any
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
93 growth model and is interoperable by design. PhysioFit includes by default the most common growth models, and additional models can be
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
94 implemented by users to calculate fluxes and other growth parameters for metabolic systems or experimental setups that follow alternative
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
95 kinetics. PhysioFit can be used as a Python library and includes a graphical user interface for intuitive use by end-users and a
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
96 command-line interface to streamline integration into existing pipelines.}',
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
97 doi = {10.1101/2023.10.12.561695},
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
98 url = {https://doi.org/10.1101/2023.10.12.561695},
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
99 }
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
100 </citation>
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
101 </citations>
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
workflow4metabolomics
parents: 1
diff changeset
102 </tool>