Update README and rename get_model_info notebook

README.md

@@ -6,21 +6,21 @@ This repository contains a re-implementation of the [EuroMix PBK model](https://
 
 ![Model diagram of the EuroMix PBK model](euromix-pbk-model.png)
 
-## Reimplementation in antimony
+## Reimplementation in Antimony
 
-The model was reimplemented in [Antimony](https://tellurium.readthedocs.io/en/latest/antimony.html), see file [euromix.ant](model/euromix.ant). The results of the R simulation and the SBML simulation (using libroadrunner in Python) match.
+The model was reimplemented in [Antimony](https://tellurium.readthedocs.io/en/latest/antimony.html), see file [euromix.ant](model/euromix.ant).
 
-Notebook [validate_antimony_model.ipynb](notebooks/validate_antimony_model.ipynb) shows the results of the validation comparison with the results obtained by the R/MCSim/desolve implementation. Note that the [libRoadRunner](https://www.libroadrunner.org/) engine that is used for the python simulations returns concentrations, also if a species is declared to be `substanceOnly`. Therefore it is necessary to convert the output to amounts by multiplying the concentration with volume of the compartment the species is placed in in order to obtain amounts.
+Notebook [validate_antimony_model.ipynb](notebooks/validate_antimony_model.ipynb) shows the results of the validation comparison with the results obtained by the R/MCSim/desolve implementation. The results of the R simulation and the SBML simulation (using libroadrunner in Python) match. Note that the [libRoadRunner](https://www.libroadrunner.org/) engine that is used for the python simulations returns concentrations, also if a species is declared to be `substanceOnly`. Therefore it is necessary to convert the output to amounts by multiplying the concentration with volume of the compartment the species is placed in in order to obtain amounts.
 
 ## Model annotation
 
-Annotations of the model and its element are specified in the file [euromix.annotations.csv](model/euromix.annotations.csv). This annotations file links the different model elements (e.g., compartments and parameters) to ontological terms and, where relevant, specifies the units of measure. For the annotations of modelling terms, the [BPBK ontology](http://obofoundry.org/ontology/pbpko) is used. For the annotation of the units of measure,  the [UCUM](https://ucum.org/) notation is adopted.
+Annotations of the model and its element are specified in the file [euromix.annotations.csv](model/euromix.annotations.csv). This annotations file links the different model elements (e.g., compartments and parameters) to ontological terms and specifies the units of measure. For the annotations of modelling terms, the [BPBK ontology](http://obofoundry.org/ontology/pbpko) is used. For the annotation of the units of measure, the [UCUM](https://ucum.org/) notation is adopted.
 
 ## SBML conversion and SBML model annotation
 
 Conversion to an annotated SBML file is done automatically using the [SBML PBK workflow](https://github.com/jwkruisselbrink/sbml-pbk-workflow). This workflow follows several steps. It first converts the Antimony model implementation to SBML. Then, it annotates this SBML file using the annotations specified in the [euromix.annotations.csv](model/euromix.annotations.csv) file. After this, it runs validation scripts on the generated SBML file to check for consistency and completeness (e.g, of the units). Finally, it publishes the generated SBML file (and log files) as build artifacts and adds/updates the generated/updated SBML file ([euromix.sbml](model/euromix.sbml)) in this repository.
 
-Notebook [get_model_info.ipynb](notebooks/get_model_info.ipynb) shows how information can be retrieved from the annotated SBML model file (e.g., units, differential equations, diagrams, semantic annotations). Notebook [run_sbml_model.ipynb](notebooks/run_sbml_model.ipynb) demonstrates how to run the SBML model.
+Notebook [get_sbml_model_info.ipynb](notebooks/get_sbml_model_info.ipynb) shows how information can be retrieved from the annotated SBML model file (e.g., units, differential equations, diagrams, semantic annotations). Notebook [run_sbml_model.ipynb](notebooks/run_sbml_model.ipynb) demonstrates how to run the SBML model.
 
 ## Running the Jupyter notebooks