How to create 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 <module> from metage2metabo.__main__ import main File "/home/brunobqi/anaconda3/lib/python3.7/site-packages/metage2metabo/__init__.py", line 15, in <module> from metage2metabo import m2m, m2m_analysis File "/home/brunobqi/anaconda3/lib/python3.7/site-packages/metage2metabo/m2m_analysis/__init__.py", line 16, in <module> 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 <module> 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"?> <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> — Reply to this email directly, view it on GitHub <#23 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AQHYORAQFSVGDJPTO2K3JR3UXZBXJANCNFSM5MWGSUUQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[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