Updated documentation.

README.md

@@ -1,22 +1,21 @@
 mergem
 ======
-mergem is a python package for merging genome-scale metabolic models.
-The package can be used as a command-line tool or can be imported within a python script.
+mergem is a python package and command-line tool for merging, comparing, and translating genome-scale metabolic models.
 
 ------
 
 
 Installation
 ------
-To install the latest release  
+Use pip to install the latest release:
 
     pip install mergem
 
 ------
 
 Usage
 ------
-For detailed usage instructions, please refer to the help [documentation](https://mergem.readthedocs.io/en/latest/).
+For detailed usage instructions, please refer to the [documentation](https://mergem.readthedocs.io/en/latest/).
 
 #### Command-line usage
 Command-line options can be viewed using "--help" flag, as shown below:

docs/source/index.rst

@@ -2,21 +2,23 @@
 mergem
 **********
 
-**mergem** is a Python library for merging two or more genome-scale metabolic
-models.
+**mergem** is a Python library for merging, comparing, and translating genome-scale metabolic models.
 The library is publicly available via PyPI at `<https://pypi.org/project/mergem/>`_ and can be pip
 installed.
 mergem can be used on the command-line and can also be imported within python scripts.
 The package can take models in various COBRApy compatible formats such as SBML, JSON, etc. and even
 COBRApy model objects, when the package is imported. The results of a single merge include the merged model,
-jaccard distances between all pairs of models, number of metabolites and reactions merged, and lists of
-models that contain each metabolite and reaction.
+jaccard distances between all pairs of models, number of metabolites and reactions merged, and the mapping 
+of each metabolite and reaction ID in the merged model to the corresponding metabolite or reaction IDs from 
+each of the input models. Users can optionally select the objective, provide an output 
+filename for the merged model, and translate the models to a different namespace.
 
 For each input model, mergem converts the metabolite IDs into a common namespace using a database ID mapping dictionary.
-Reactions are compared using the participating metabolites (after conversion to common namespace). The metabolite ID mapping dictionary contains metabolite identifiers from various databases
-such as ModelSEED, KEGG, ChEBI, and MetaNetX that have been unified per metabolite. The dictionary thus allows for model
-metabolites to be compared more efficiently. The mapping dictionaries can be updated, during which the latest identifier
-information is downloaded from each database and identifiers representing the same metabolite are mapped to one another.
+Reactions are compared using the participating metabolites (after conversion to common namespace). The metabolite ID mapping 
+dictionary contains metabolite identifiers from various databases such as ModelSEED, KEGG, ChEBI, and MetaNetX that have been 
+unified per metabolite. The dictionary thus allows for model metabolites to be compared more efficiently. The mapping dictionaries 
+can be updated, during which the latest identifier information is downloaded from each database and identifiers representing the same 
+metabolite are mapped to one another.
 
 mergem is also available in the user-friendly application `Fluxer <https://fluxer.umbc.edu>`_, which produces tidy flux
 graphs that can visually compare the complete metabolic network from multiple models.
@@ -37,20 +39,4 @@ Documentation for Fluxer based merging can be found on its `tutorial page <https
    acknowledgements
    license
    contact
-
-
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-
-
-.. note::
-
-   This project is under active development.
-
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+

docs/source/usage.rst

@@ -1,20 +1,21 @@
 *********************************
-Using mergem to merge models
+Using mergem to merge, compare, and translate models
 *********************************
-mergem can merge two or more genome-scale metabolic models. The command-line execution can take input models in
+mergem can merge, compare, and translate genome-scale metabolic models. The command-line execution can take input models in
 various COBRApy compatible formats (SBML, JSON, YAML, and MAT).
 mergem can be imported into a python script and the merge function can take cobra objects in addition to filenames.
 A single objective function from any of the input models can be set as the objective for merged model. Alternatively,
 objective functions from all input models can be merged into a single function and set as the objective in the merged
-model.
+model. The metabolite and reaction IDS of the merged or standalone models can be translated to any of the database
+systems supported in mergem.
 
 
 .. _cli:
 
 Command-line
 ==========================
 Once mergem has been installed using pip, the following commands can be run on the command-line.
-Printing help text displays all the options.
+The help argument displays all the options.
 
 ::