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License: GNU Lesser General Public License v3.0
Python package for large-scale community selection in microbiota
License: GNU Lesser General Public License v3.0
Following the issue in AuReMe/metage2metabo#38, a new miscoto could be developed to predict the dead end and the orphan metabolites in a community.
miscoto instance
adds a fact for the host even when it is not given as an argument
https://github.com/cfrioux/miscoto/blob/master/miscoto/miscoto_instance.py#L63
Hello,
Is it possible to specify a culture media directly with its biocyc ID in the seeds.sbml file ? Like this one, for example.
Thanks.
Version 1.4.3 Pyasp (major dependency of the package) binaries were removed, creating a 404 not found error at the install step of the packages. Pyasp 1.4.4 (the latest) cannot be used because it does not support latest OS. Plus: Pyasp is archived.
Fix = use https://github.com/aluriak/clyngor and https://github.com/Aluriak/clyngor-with-clingo instead of Pyasp. The last one has strong assets as it installs automatically the binaries of Clingo.
Requires modifications to query.py and meneco.py
If one provides an LP instance in miscoto scopes
or miscoto mincom
together with seeds and/or targets, they will be added to the end of the instance. We should not modify any of the user's inputs. Instead, we should copy the contents of the instance as a temp file and add the seeds/targets in it. Then remove the temp file at the end of the analysis.
Hi,
Thanks for this pipeline. I am at the same time looking at m2m. I wonder how to generate a "seed" file in .xml especially if I have no idea about the medium that would be used for the community I am working on.
Any suggestions? I am not interested into a specific pathways but more how "my" bacteria community cooperate.
Thanks for your help!
Nico
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