How to create of seed and targets files in sbml format?

[brunorbqi]

Hello ! How do I create the seeds and target files in sbml format ? On github page has exemples but I was unable to download.

[sthiele]

SBML are XML files that have a section listOfSpecies, there you can list all your seed metabolites (see below). For more info about SBML see https://sbml.org/documents/.

<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1">
<model id="EsiCyc">
  <listOfCompartments>
    <compartment id="CCO__45__EXTRACELLULAR"/>
    <compartment id="CCO__45__CYTOSOL"/>
    <compartment id="CCO__45__OUT"/>
  </listOfCompartments>
  <listOfSpecies>
    <species id="Acceptor" compartment="CCO__45__CYTOSOL"/> 
    <species id="ACP" compartment="CCO__45__CYTOSOL"/> 
    <species id="ADP" compartment="CCO__45__CYTOSOL"/>
    <species id="AMMONIA" compartment="CCO__45__CYTOSOL"/>
    <species id="AMP" compartment="CCO__45__CYTOSOL"/>
    <species id="ATP" compartment="CCO__45__CYTOSOL"/>
    <species id="SULFATE" compartment="CCO__45__CYTOSOL"/>
    <species id="THIAMINE" compartment="CCO__45__CYTOSOL"/>
    <species id="UDP" compartment="CCO__45__CYTOSOL"/>
    <species id="Vitamins__45__B12" compartment="CCO__45__CYTOSOL"/>
    <species id="COB__45__I__45__ALAMIN" compartment="CCO__45__CYTOSOL"/>
    <species id="WATER" compartment="CCO__45__CYTOSOL"/>
    <species id="ZN__43__2" compartment="CCO__45__CYTOSOL"/>
    </listOfSpecies>
  </model>
</sbml>

Github tip: If you navigate to the SBML files in this repository like here, then you can press the Raw button to access the raw files like https://raw.githubusercontent.com/bioasp/meneco/next/Ectodata/seeds.sbml.

Also see the samples section of the README

[cfrioux]

In addition, there exists a solution to automatise the process by providing a simple text file with a list of encoded identifiers that will be turned into a SBML file. e.g. M_glucose_c for glucose extracellular.

As an example, the content below:

M_glucose_c
M_water_c

will generate the following seed file:

<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1">
<model id="seeds">
  <listOfCompartments>
    <compartment id="c"/>
  </listOfCompartments>
  <listOfSpecies>
    <species id="M_glucose_c" name="glucose" compartment="c"/> 
    <species id="M_water_c" name="water" compartment="c"/> 
    </listOfSpecies>
  </model>
</sbml>

[brunorbqi]

Hello !!! I have installed the m2m with the following command line: pip install Metage2Metabo

And executed as follows: m2m seeds -o (my output directory) --metabolites seeds.txt And got the following error: m2m seeds -o Biologia_de_Sistemas/babortus_2.0/Finalizacao_do_Modelo_B_abortus/Acabando --metabolites seeds.txt Traceback (most recent call last): File "/home/brunobqi/anaconda3/bin/m2m", line 5, in from metage2metabo.main import main File "/home/brunobqi/anaconda3/lib/python3.7/site-packages/metage2metabo/init.py", line 15, in from metage2metabo import m2m, m2m_analysis File "/home/brunobqi/anaconda3/lib/python3.7/site-packages/metage2metabo/m2m_analysis/init.py", line 16, in from metage2metabo.m2m_analysis.graph_compression import powergraph_analysis, check_oog_jar_file File "/home/brunobqi/anaconda3/lib/python3.7/site-packages/metage2metabo/m2m_analysis/graph_compression.py", line 25, in from bubbletools import convert ModuleNotFoundError: No module named 'bubbletools'

Em ter., 25 de jan. de 2022 às 03:49, Clémence Frioux < @.***> escreveu:

In addition, there exists a solution https://metage2metabo.readthedocs.io/en/latest/command.html#m2m-seeds to automatise the process by providing a simple text file with a list of encoded identifiers that will be turned into a SBML file. e.g. M_glucose_c for glucose extracellular.

As an example, the content below:

M_glucose_c M_water_c

will generate the following seed file:

<?xml version="1.0" encoding="UTF-8"?>

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[sthiele]

Looks like you're missing dependencies. You should report this issue at the metage2metabo issue tracker. As a quick fix you can try installing the missing bubbletools package.

pip install bubbletools