Sampling on the flux space of multiple metabolic networks #18

hariszaf · 2021-08-19T17:07:02Z

Two main modules are included on this PR:

about 6,000 bacterial metabolic models have been converted to .mat format using the embl_model_convert.m script. The The script has been used to convert EMBL models that are publicly available here as well as models that were built using publicly available genomes and the carveme software tool for automatic metabolic modelling reconstruction
2 classes called CommunityMetabolicNetwork and CommunityPolytopeSampler that enable sampling on the flux space of multiple metabolic networks.

To enable testing this new module of dingo an input example has been added under the ext_data directory.

The new module has been integrated in the __init__.py and can be used both from terminal and as a function of the dingo package.

This reverts commit 23639fc.

This reverts commit a76b4be.

This reverts commit cb6005e.

This reverts commit 3fc3d12.

This reverts commit ffd7eaf.

vissarion · 2021-08-31T13:25:23Z

ext_data/community_models/e_coli_core.json

@@ -0,0 +1,14786 @@
+{


is this file needed to be included in the repo? It is huge and readily available from http://bigg.ucsd.edu/static/models/e_coli_core.json

similarly for ext_data/community_models/iIT341.json it is that large that github cannot show it

I removed the 2 .json files with a README explaining the reasond for this directory

We could remove the directory completely if you find it of no use.

vissarion · 2021-08-31T13:50:35Z

ext_data/community_models/README.md

+[`iIT341.json`](http://bigg.ucsd.edu/models/iIT341) files from the [BIGG database](http://bigg.ucsd.edu/models)
+and then run `dingo`. 
+
+Remember to remove this `README.md` file if you will decide to use this directory. 


If you leave the README.md file, dingo will give you an
Exception: An unknown input format given to initialize a metabolic network object. message.

We can add a check on the code for the README file if you feel this is necessary.

vissarion · 2021-08-31T13:51:40Z

ext_data/community_models/README.md

+For example, you may have a community of 2 models, *Escherichia coli* and *Helicobacter pylori*, 
+in that case you could get the [`e_coli_core.json`](http://bigg.ucsd.edu/models/e_coli_core) and 
+[`iIT341.json`](http://bigg.ucsd.edu/models/iIT341) files from the [BIGG database](http://bigg.ucsd.edu/models)
+and then run `dingo`. 


could you please add an example of use i.e. a command from terminal that uses dingo to do some computations to e_coli and iIT341 community

Could you have a look now?

TolisChal · 2021-09-15T11:21:30Z

dingo/MetabolicNetwork.py

@@ -223,3 +223,205 @@ def shut_down_reaction(self, index_val):

        self._lb[index_val] = 0
        self._ub[index_val] = 0
+
+
+class CommunityMetabolicNetwork():


Please use a single .py document per class

Done as suggested.

TolisChal · 2021-09-15T11:24:27Z

dingo/MetabolicNetwork.py

+                self._comm_parameters["opt_percentage"],
+            )
+
+    def fba(self):


Which objective function do you use here?
I think FBA has to be separately applied in each model to obtain the maximum value per model.

We need to consider an FBA per organism (single standed network) and something like a community FBA for the total community model a.k.a the μ_c as described in the micom concept..

How about leaving as fba the per organism and build a new function for community growth ?

TolisChal · 2021-09-15T11:25:23Z

dingo/MetabolicNetwork.py

+    def fva(self):
+        """A member function to apply the FVA method on the community metabolic network."""
+
+        if self._comm_parameters["fast_computations"]:


You should set the objective function to the zero vector before FVA() to study the unbiased case.

TolisChal · 2021-09-15T11:28:04Z

dingo/PolytopeSampler.py

+
+
+
+class CommunityPolytopeSampler:


Please use a single .py document per class

Done as suggested.

TolisChal · 2021-09-15T11:30:15Z

dingo/MetabolicNetwork.py

-import sys
-from dingo.loading_models import read_json_file, read_mat_file
+import sys, os
+from dingo.loading_models import read_json_file, read_mat_file, getModelList
 from dingo.fva import slow_fva
 from dingo.fba import slow_fba



Please update the documentation according to your new implementations

…ies; working on the community growth function

Merge branch 'pairs' of https://github.com/hariszaf/dingo into pairs

vissarion · 2023-02-03T12:49:47Z

This is quite old and should be re-implemented from scratch

hariszaf · 2023-06-22T13:58:20Z

Way to go:

implement approach from cobra toolbox to build merged model
sample by asking biomass of species A to be 0 and biomass of species B to be max
sample with the vice versa conditions
sample asking for both biomass functions to be max

vissarion · 2023-06-23T10:14:47Z

Thanks @hariszaf I added issue #67 to keep track on it!

hariszaf added 30 commits July 16, 2021 01:09

unknown

cb6005e

Revert "Create CODE_OF_CONDUCT.md"

3fc3d12

This reverts commit 23639fc.

Revert "Update issue templates"

ffd7eaf

This reverts commit a76b4be.

Revert "unknown"

e251c0a

This reverts commit cb6005e.

Revert "Revert "Create CODE_OF_CONDUCT.md""

3c80cc6

This reverts commit 3fc3d12.

Revert "Revert "Update issue templates""

f82fcce

This reverts commit ffd7eaf.

parse 2 models and build concatenated S

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.mat models for species of a

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.mat models for species of b

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.mat models for species of c

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init classes for community level

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embl models in mat format

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hariszaf added 5 commits August 19, 2021 18:55

modif in comment

f825b4c

add community case

ec73f68

fix args

28484da

modifs

2359c86

modifs to fix main for community

dd39486

vissarion requested review from TolisChal and vissarion August 30, 2021 08:29

vissarion added the enhancement New feature or request label Aug 30, 2021

remove .mat models; they ll be available in a zenodo repo

96f7851

vissarion reviewed Aug 31, 2021

View reviewed changes

replace the 2 model files with a README

95caaa7

vissarion reviewed Aug 31, 2021

View reviewed changes

running from terminal example

2ee3a25

TolisChal reviewed Sep 15, 2021

View reviewed changes

hariszaf added 5 commits September 20, 2021 19:52

one class per file; according modifs to import classes

3518d78

replace the pair-based notion in the get_model_list for multiple spec…

2a7db96

…ies; working on the community growth function

notebook to set the workflow for working with polyround - hops

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merge before adding jupyter notebook for hops and polyround

cb31f4d

Merge branch 'pairs' of https://github.com/hariszaf/dingo into pairs

maybe mapped samples maybe not

747bb13

vissarion marked this pull request as draft December 15, 2022 13:58

vissarion closed this Feb 3, 2023

vissarion mentioned this pull request Jun 23, 2023

Sampling on the flux space of multiple metabolic networks #67

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Sampling on the flux space of multiple metabolic networks #18

Sampling on the flux space of multiple metabolic networks #18

hariszaf commented Aug 19, 2021

vissarion Aug 31, 2021

vissarion Aug 31, 2021

hariszaf Aug 31, 2021

hariszaf Aug 31, 2021

vissarion Aug 31, 2021

hariszaf Aug 31, 2021

vissarion Aug 31, 2021

hariszaf Aug 31, 2021

TolisChal Sep 15, 2021

hariszaf Sep 22, 2021

TolisChal Sep 15, 2021

hariszaf Sep 22, 2021

TolisChal Sep 15, 2021

TolisChal Sep 15, 2021

hariszaf Sep 22, 2021

TolisChal Sep 15, 2021

vissarion commented Feb 3, 2023

hariszaf commented Jun 22, 2023

vissarion commented Jun 23, 2023

Sampling on the flux space of multiple metabolic networks #18

Sampling on the flux space of multiple metabolic networks #18

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hariszaf commented Aug 19, 2021

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vissarion commented Feb 3, 2023

hariszaf commented Jun 22, 2023

vissarion commented Jun 23, 2023