Merge pull request #11 from BioSystemsUM/develop

Nitrate Ratio

README.md

@@ -31,15 +31,15 @@ With this in mind, this package aims to accelerate this process by being able to
 ## Installation
 ### Pip
 
-``` pip install diel_models==1.1.2 ```
+``` pip install diel_models==1.2.2 ```
 
 ## Getting Started
 Using this package, you can handle generic or multi-tissue models by:
 
 * Assigning day and night;
 * Inserting specified metabolites into the storage pool allowing their transition between day and night, and vice versa; 
 * Supressing the photon reaction flux at night; 
-* Setting the flux of the nitrate reactions to 3:2 according to the literature; 
+* Setting the flux of the nitrate reactions to 3:2 by default (according to the literature) or other desired ratio; 
 * (optional) Taking the day and night biomass reactions and creating a total biomass reaction resulting from the junctions of both. Supressing at the same time the flow of the individual reactions to zero and setting the total biomass reaction as the objective function.
 
 If each method is to be applied individually it is essential that the first 3 steps are applied in that order specifically.
@@ -59,6 +59,21 @@ storage_pool_metabolites = ['Metabolite_ID_1', 'Metabolite_ID_2', 'Metabolite_ID
 diel_models_creator(model, storage_pool_metabolites, ['Photon_Reaction_ID'], ['Nitrate_Reaction_ID'], 'Biomass_Reaction_ID')
 ```
 
+where the nitrate uptake ratio is 3:2, since _day_ratio_value_ is 3 and _night_ratio_value_ is 2.
+
+Alternatively, the ratio value can be set to a value other than 3:2.
+
+```python
+import cobra
+from diel_models.diel_models_creator import diel_models_creator
+
+model = cobra.io.read_sbml_model('.../.../desired_single_tissue_model.xml')
+
+storage_pool_metabolites = ['Metabolite_ID_1', 'Metabolite_ID_2', 'Metabolite_ID_3']
+
+diel_models_creator(model, storage_pool_metabolites, ['Photon_Reaction_ID'], ['Nitrate_Reaction_ID'], 'Biomass_Reaction_ID', day_ratio_value=desired_value_1, night_ratio_value=desired_value_2)
+```
+
 - Multi-tissue model:
 
 ```python
@@ -74,7 +89,9 @@ tissues = ['Tissue_ID_1', 'Tissue_ID_2']
 diel_models_creator(model, storage_pool_metabolites, ['Photon_Reaction_ID'], ['Nitrate_Reaction_ID'], 'Biomass_Reaction_ID', tissues)
 ```
 
-This is possible due to the created *Pipeline* class that derives from a *Step* class with abstract methods - both present in this package, in the [pipeline.py](src/diel_models/pipeline.py) file.
+where the nitrate uptake ratio is 3:2, but it's also possible to adjust this ratio to different values.
+
+Running the entire pipeline is possible due to the created *Pipeline* class that derives from a *Step* class with abstract methods - both present in this package, in the [pipeline.py](src/diel_models/pipeline.py) file.
 
 ## Expanding the pipeline
 
@@ -120,7 +137,8 @@ from diel_models.new_class import NewClass
 from diel_models.pipeline import Pipeline
 
 def diel_models_creator(model: Model, storage_pool_metabolites: List[str], photon_reaction_id: List[str],
-                        nitrate_exchange_reaction: List[str], param1, biomass_reaction_id: str = None, tissues: List[str] = None) -> Model:  
+                        nitrate_exchange_reaction: List[str], param1, biomass_reaction_id: str = None, tissues: List[str] = None,
+                        day_ratio_value: int = 3, night_ratio_value: int = 2) -> Model:  
 
     storage_pool_metabolites_with_day = [metabolite + "_Day" for metabolite in storage_pool_metabolites]
     photon_reaction_id_night = [photon_night_reaction + "_Night" for photon_night_reaction in photon_reaction_id]

docs/conf.py

@@ -12,7 +12,7 @@
 project = 'diel_models'
 copyright = '2023, Luciana Martins and João Capela'
 author = 'Luciana Martins and João Capela'
-release = 'v1.1.0'
+release = 'v1.2.2'
 
 sys.path.insert(0, os.path.abspath('../src/'))
 

docs/diel_models_docs.md

@@ -13,23 +13,24 @@ Python 3.12
 ```
 
 ### Description
+*diel_models* is a python package generated from this project and has its own [ReadtheDocs](https://dielmodels.readthedocs.io/) file.
 
 Despite numerous successful studies, modeling plant metabolism remains challenging for several reasons, such as limited information, incomplete annotations, and dynamic changes in plant metabolism that occur under different conditions, including night and day.
 In particular, the integration of these day-night cycles (diel cycles) is complex, laborious, and time-consuming.
 
 With this in mind, this package aims to accelerate this process by being able to transform a non-diel model into a diel model.
 
-### Installation
+## Installation
 
-``` pip install diel_models==1.1.2 ```
+``` pip install diel_models==1.2.2 ```
 
-### Getting Started
+## Getting Started
 Using this package, you can handle generic or multi-tissue models by:
 
 * Assigning day and night;
 * Inserting specified metabolites into the storage pool allowing their transition between day and night, and vice versa; 
 * Supressing the photon reaction flux at night; 
-* Setting the flux of the nitrate reactions to 3:2 according to the literature; 
+* Setting the flux of the nitrate reactions to 3:2 by default (according to the literature) or other desired ratio; 
 * (optional) Taking the day and night biomass reactions and creating a total biomass reaction resulting from the junctions of both. Supressing at the same time the flow of the individual reactions to zero and setting the total biomass reaction as the objective function.
 
 If each method is to be applied individually it is essential that the first 3 steps are applied in that order specifically.
@@ -49,6 +50,21 @@ storage_pool_metabolites = ['Metabolite_ID_1', 'Metabolite_ID_2', 'Metabolite_ID
 diel_models_creator(model, storage_pool_metabolites, ['Photon_Reaction_ID'], ['Nitrate_Reaction_ID'], 'Biomass_Reaction_ID')
 ```
 
+where the nitrate uptake ratio is 3:2, since _day_ratio_value_ is 3 and _night_ratio_value_ is 2.
+
+Alternatively, the ratio value can be set to a value other than 3:2.
+
+```python
+import cobra
+from diel_models.diel_models_creator import diel_models_creator
+
+model = cobra.io.read_sbml_model('.../.../desired_single_tissue_model.xml')
+
+storage_pool_metabolites = ['Metabolite_ID_1', 'Metabolite_ID_2', 'Metabolite_ID_3']
+
+diel_models_creator(model, storage_pool_metabolites, ['Photon_Reaction_ID'], ['Nitrate_Reaction_ID'], 'Biomass_Reaction_ID', day_ratio_value=desired_value_1, night_ratio_value=desired_value_2)
+```
+
 - Multi-tissue model:
 
 ```python
@@ -64,9 +80,11 @@ tissues = ['Tissue_ID_1', 'Tissue_ID_2']
 diel_models_creator(model, storage_pool_metabolites, ['Photon_Reaction_ID'], ['Nitrate_Reaction_ID'], 'Biomass_Reaction_ID', tissues)
 ```
 
-This is possible due to the created *Pipeline* class that derives from a *Step* class with abstract methods - both present in this package, in the pipeline.py file.
+where the nitrate uptake ratio is 3:2, but it's also possible to adjust this ratio to different values.
+
+Running the entire pipeline is possible due to the created *Pipeline* class that derives from a *Step* class with abstract methods - both present in this package, in the [pipeline.py](src/diel_models/pipeline.py) file.
 
-### Expanding the pipeline
+## Expanding the pipeline
 
 It is possible to add other classes to the *diel_models_creator* function, if desired, for example to create a different adjustment that needs to be taken into account in the diel models.
 To expand the pipeline, it is necessary to create a new class that inherits from the *Step* class and implement the abstract methods.
@@ -98,7 +116,7 @@ class NewClass(Step):
     pass
 ```
 
-Then you need to adjust the *diel_models_creator* function to integrate the new class. This function is in the diel_models_creator.py file.
+Then you need to adjust the *diel_models_creator* function to integrate the new class. This function is in the [diel_models_creator.py](src/diel_models/diel_models_creator.py) file.
 
 ```python
 from typing import List
@@ -110,7 +128,8 @@ from diel_models.new_class import NewClass
 from diel_models.pipeline import Pipeline
 
 def diel_models_creator(model: Model, storage_pool_metabolites: List[str], photon_reaction_id: List[str],
-                        nitrate_exchange_reaction: List[str], param1, biomass_reaction_id: str = None, tissues: List[str] = None) -> Model:  
+                        nitrate_exchange_reaction: List[str], param1, biomass_reaction_id: str = None, tissues: List[str] = None,
+                        day_ratio_value: int = 3, night_ratio_value: int = 2) -> Model:  
 
     storage_pool_metabolites_with_day = [metabolite + "_Day" for metabolite in storage_pool_metabolites]
     photon_reaction_id_night = [photon_night_reaction + "_Night" for photon_night_reaction in photon_reaction_id]
@@ -128,4 +147,25 @@ def diel_models_creator(model: Model, storage_pool_metabolites: List[str], photo
 
 Finally, you can run the *diel_models_creator* function with the new class.
 
-Just as you can expand methods in the pipeline, you can modify or remove others.
+Just as you can expand methods in the pipeline, you can modify or remove others.
+
+## Where to find the publication results
+
+### AraGEM:
+
+* Details about the fluxes in the AraGEM diel model reactions in the day and night phases, as well as in the original model where calculated in [aragem_reactions_fluxes.py](validation/arabidopsis/aragem_reactions_fluxes.py) file.
+* Validation of the metabolites exchange reactions through simulation using pFBA where performed in [simulation_sp.py](validation/arabidopsis/simulation_sp/simulation_sp.py) file.
+* [DFA file](DFA/differential_flux_analysis.py) and respective [Test file](tests/integration_tests/test_dfa.py).
+* [Plot](tests/reconstruction_results/MODEL1507180028/results_troppo/DielModel/dfa/diel_model_DFA_pathway_result.png) from the pathway enrichment method representing the amount of differentially expressed reactions between day and night in each pathway.
+* [PCA](PCA/gráfico_pca_df_filtrado.png) plot with the sampling values filtered by the differentially expressed reactions.
+
+### _Quercus suber_:
+
+* Details about the fluxes in the _Quercus suber_ diel model reactions in the day and night phases, as well as in the original model where calculated in [quercus_reactions_fluxes.py](validation/quercus/quercus_reactions_fluxes.py) file.
+* Slight adjustments to the biomass reaction in the generated diel model can be found [here](validation/quercus/comparison/auxiliar_model_change.py).
+* Validation of the metabolites exchange reactions through simulation using pFBA where performed in [simulation_sp_multi_quercus.py](validation/quercus/simulation_sp/simulation_sp_multi_quercus.py) file.
+* The comparison between the flux of the biomass reaction for both diel multi-tissue models are in the [quercus_diel_models_comparison.py](validation/quercus/comparison/quercus_multi_tissue_diel_models_comparison.py) file.
+
+### QY for the several models:
+
+* The scripts for quantum yield and assimilation quotient calculation for the _Zea mays L._ (2011), _Arabidopsis thaliana_ (2010), _Populus trichocarpa_ (2020), _Solanum lycopersicum_ (2015), _Solanum lycopersicum_ (2022) and _Solanum tuberosum_ (2018) models can be found in the [QY](validation/QY) folder.

docs/requirements_rtd.txt

@@ -3,11 +3,4 @@ rst-to-myst
 sphinx-rtd-theme
 sphinx-autobuild
 myst-parser
-cobra~=0.26.2
-pandas~=1.5.3
-statsmodels~=0.13.5
-matplotlib~=3.7.1
-numpy>=1.22
-scipy~=1.10.1
-setuptools~=65.6.3
-scikit-learn~=1.2.2
+cobra

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = diel_models
-version = 1.1.2
+version = 1.2.2
 description = diel_models:
 long_description = file: README.md
 long_description_content_type = text/markdown

src/diel_models/diel_models_creator.py

@@ -11,7 +11,8 @@
 
 
 def diel_models_creator(model: Model, storage_pool_metabolites: List[str], photon_reaction_id: List[str],
-                        nitrate_exchange_reaction: List[str], biomass_reaction_id: str = None, tissues: List[str] = None) -> Model:
+                        nitrate_exchange_reaction: List[str], biomass_reaction_id: str = None, tissues: List[str] = None,
+                        day_ratio_value: int = 3, night_ratio_value: int = 2) -> Model:
     """
     Function that allows you to run the pipeline in one go,
     returning the resulting model, where the arguments are all relative to the original model.
@@ -30,6 +31,10 @@ def diel_models_creator(model: Model, storage_pool_metabolites: List[str], photo
         id for biomass_reaction, defaults to None in case no biomass reaction defined.
     tissues: List[str], optional
             List of tissues in the multi-tissue model, defaults to None for generic models.
+    day_ratio_value: int, optional
+        The ratio of nitrate uptake during the day, default is 3.
+    night_ratio_value: int, optional
+        The ratio of nitrate uptake during the night, default is 2.
 
     Returns
     -------
@@ -49,15 +54,17 @@ def diel_models_creator(model: Model, storage_pool_metabolites: List[str], photo
             StoragePoolGenerator(model, storage_pool_metabolites_with_day, tissues),
             PhotonReactionInhibitor(model, photon_reaction_id_night),
             BiomassAdjuster(model, biomass_day_id, biomass_night_id),
-            NitrateUptakeRatioCalibrator(model, nitrate_exchange_reaction_day, nitrate_exchange_reaction_night)
+            NitrateUptakeRatioCalibrator(model, nitrate_exchange_reaction_day, nitrate_exchange_reaction_night,
+                                         day_ratio_value=day_ratio_value, night_ratio_value=night_ratio_value)
         ]
 
     else:
         steps = [
             DayNightCreator(model),
             StoragePoolGenerator(model, storage_pool_metabolites_with_day, tissues),
             PhotonReactionInhibitor(model, photon_reaction_id_night),
-            NitrateUptakeRatioCalibrator(model, nitrate_exchange_reaction_day, nitrate_exchange_reaction_night)
+            NitrateUptakeRatioCalibrator(model, nitrate_exchange_reaction_day, nitrate_exchange_reaction_night,
+                                         day_ratio_value=day_ratio_value, night_ratio_value=night_ratio_value)
         ]
 
     pipeline = Pipeline(model, steps)

src/diel_models/nitrate_uptake_ratio.py

@@ -7,7 +7,7 @@
 class NitrateUptakeRatioCalibrator(Step):
 
     def __init__(self, model: Model, id_nitrate_uptake_reaction_day: List[str],
-                 id_nitrate_uptake_reaction_night: List[str]) -> None:
+                 id_nitrate_uptake_reaction_night: List[str], day_ratio_value: int = 3, night_ratio_value: int = 2) -> None:
         """
         Constructor
 
@@ -19,14 +19,21 @@ def __init__(self, model: Model, id_nitrate_uptake_reaction_day: List[str],
             Identification of day nitrate uptake reaction(s) - in case of for example, multi tissue models.
         id_nitrate_uptake_reaction_night: List[str]
             Identification of night nitrate uptake reaction(s) - in case of for example, multi tissue models.
+        day_ratio_value: int, optional
+            The ratio of nitrate uptake during the day, default is 3.
+        night_ratio_value: int, optional
+            The ratio of nitrate uptake during the night, default is 2.
         """
         self.model: Model = model
         self.id_nitrate_uptake_reaction_day: List[str] = id_nitrate_uptake_reaction_day
         self.id_nitrate_uptake_reaction_night: List[str] = id_nitrate_uptake_reaction_night
+        self.day_ratio_value: int = day_ratio_value
+        self.night_ratio_value: int = night_ratio_value
 
     def ratio_set(self) -> None:
         """
-        This function establishes a 3:2 ratio of nitrate uptake between day and night, respectively.
+        This function establishes a 3:2 ratio (by default) of nitrate uptake between day and night, respectively.
+        The ratio can be changed.
 
         Raises:
             ValueError: If the nitrate uptake reaction ID is not present in the given model.
@@ -39,8 +46,8 @@ def ratio_set(self) -> None:
                 nitrate_uptake_reaction_night = self.model.reactions.get_by_id(nitrate_uptake_night_reaction)
 
                 same_flux = self.model.problem.Constraint(
-                    nitrate_uptake_reaction_day.flux_expression * 2 -
-                    nitrate_uptake_reaction_night.flux_expression * 3, lb=0, ub=0)
+                    nitrate_uptake_reaction_day.flux_expression * self.night_ratio_value -
+                    nitrate_uptake_reaction_night.flux_expression * self.day_ratio_value, lb=0, ub=0)
                 self.model.add_cons_vars(same_flux)
 
             else: