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Read .xml models #26

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hariszaf opened this issue Oct 1, 2021 · 4 comments · Fixed by #50
Closed

Read .xml models #26

hariszaf opened this issue Oct 1, 2021 · 4 comments · Fixed by #50
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enhancement New feature or request good first issue Good for newcomers Hacktoberfest
Milestone
1.0.0

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@hariszaf
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hariszaf commented Oct 1, 2021

To address the challenges that come along with the metabolic network reconstruction process,
the metabolic modeling community has adopted the Systems Biology Markup Language (SBML)
to a great extent.

Therefore, most metabolic models are in a .xml format and this is the reason that supporting
this format would benefit dingo the most.

To this end, dingo could make use of the libsbml library via its Python interface.
@vissarion vissarion added enhancement New feature or request good first issue Good for newcomers Hacktoberfest labels Oct 4, 2021
@vissarion vissarion added this to the 1.0.0 milestone Nov 11, 2021
@Ghostfreak-077
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Sir, I am a pythonist and I would like to solve this issue. but, I am not much into networks, so can you guide me to solve the issue.

@himanshuParashar0101
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kindly assign this issue to me

@vissarion
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Please go ahead and submit a PR.

@hariszaf
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Hello there.
Was there any progress reg. this issue?
Thanks a lot!

hariszaf added a commit to hariszaf/dingo that referenced this issue Dec 13, 2022
@hariszaf
build model from sbml file, issue GeomScale#26
047f262
hariszaf added a commit to hariszaf/dingo that referenced this issue Dec 14, 2022
@hariszaf
build model from sbml file, issue GeomScale#26
5478032
@vissarion vissarion linked a pull request Dec 16, 2022 that will close this issue
Load models #50
Merged
vissarion pushed a commit that referenced this issue Dec 23, 2022
@hariszaf
Load models (#50)
7e86be3 
* minor edits

* minor edits

* fix fba - fva

* fixed refs

* build model from sbml file, issue #26

* sbml models supported; mat moved to cobra; tests for all formats

* fix conflicts

* add cobra in poetry

* rename cobra

* fix poetry.lock
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enhancement New feature or request good first issue Good for newcomers Hacktoberfest
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Load models hariszaf/dingo
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@vissarion @hariszaf @himanshuParashar0101 @Ghostfreak-077