Updating main README and introductory README for scripts

Author: samseaver

README.md

@@ -1,44 +1,57 @@
-[![Build Status](https://travis-ci.org/ModelSEED/ModelSEEDDatabase.svg?branch=master)](https://travis-ci.org/ModelSEED/ModelSEEDDatabase)
-
-# ModelSEEDDatabase
-This repository contains the definitive copy of the biochemistry and metadata used to construct models using the ModelSEED/ProbAnno approach
-
-You can contribute by submitting revisions to the biochemistry though pull requests
-
-# Python Environment
-
-1) Install Conda:
-https://conda.io/projects/conda/en/latest/user-guide/install/index.html
-
-2) Set up a python 3 conda environment:
-```
- conda create -n msd-env python=3
-```
- 3) Activate:
-```
- conda activate rdkit-env
-```
-
-4) Install rdkit and openbabel for handling biochemical structures:
-```
- conda install -c rdkit rdkit
- conda install -c openbabel openbabel
-```
-
-5) Install eQuilibrator for retrieving thermodynamics data:
-```
-conda install wxPython
-pip install quilt
-```
-
-6) Export path to local python libraries
-```
-export PYTHONPATH=$PYTHONPATH:<path-to-repository>/ModelSEEDDatabase/Libs/Python/
-```
-
-7) Test it by running:
-```
-./Scripts/Structures/Print_Structure_Formula_Charge.py
-git status -s
-```
-(there should be no change in the formula and charge in the compounds.tsv file, if there is, our recommendation is that you panic and throw your laptop out of the window.)
+<!--[![Build
+Status](https://travis-ci.org/ModelSEED/ModelSEEDDatabase.svg?branch=master)](https://travis-ci.org/ModelSEED/ModelSEEDDatabase)-->
+# ModelSEED Biochemistry Database
+
+<a href="https://www.biorxiv.org/content/10.1101/2020.03.31.018663v2">The
+ModelSEED Database for the integration of metabolic annotations and
+the reconstruction, comparison, and analysis of metabolic models for
+plants, fungi, and microbes.</a>
+
+## Abstract
+
+For over ten years, ModelSEED has been a primary resource for the
+construction of draft genome-scale metabolic models based on annotated
+microbial or plant genomes. Now being released, the biochemistry
+database serves as the foundation of biochemical data underlying
+ModelSEED and KBase. The biochemistry database embodies several
+properties that, taken together, distinguish it from other published
+biochemistry resources by: (i) including compartmentalization,
+transport reactions, charged molecules and proton balancing on
+reactions;; (ii) being extensible by the user community, with all data
+stored in GitHub; and (iii) design as a biochemical “Rosetta Stone” to
+facilitate comparison and integration of annotations from many
+different tools and databases. The database was constructed by
+combining chemical data from many resources, applying standard
+transformations, identifying redundancies, and computing thermodynamic
+properties. The ModelSEED biochemistry is continually tested using
+flux balance analysis to ensure the biochemical network is
+modeling-ready and capable of simulating diverse
+phenotypes. Ontologies can be designed to aid in comparing and
+reconciling metabolic reconstructions that differ in how they
+represent various metabolic pathways. ModelSEED now includes 33,978
+compounds and 36,645 reactions, available as a set of extensible files
+on GitHub, and available to search at https://modelseed.org and KBase.
+
+## Related Links
+
+* <a href="https://modelseed.org">ModelSEED</a>
+* <a href="https://github.com/ModelSEED/ModelSEEDDatabase">(this) Git repository</a>
+* <a href="https://kbase.us">KBase</a>
+
+## Documentation
+
+We provide some documentation for the database and everything required
+in this repository to build and maintain it in these directories:
+
+### [Biochemistry](Biochemistry/README.md)
+
+This holds the main database files.
+
+### [Scripts](Scripts/README.md)
+
+This holds the scripts that we use to build and maintain the database.
+
+### [Solr](Solr/README.md)
+
+This holds the Solr schema and examples on how to access the
+biochemistry at various endpoints.

Scripts/README.md

@@ -0,0 +1,62 @@
+# ModelSEED Biochemistry Database Script Environment
+
+We've developed a small python library for loading and manipulating
+the biochemistry database according to our needs and we written a set
+of scripts that uses the library for our needs.
+
+The main set of scripts that we used for the most recent publication of the ModelSEED Biochemistry Database are:
+
+* [Biochemistry](Biochemistry/README.md)
+
+* [Structures](Structures/README.md)
+
+* [Thermodynamics](Thermodynamics/README.md)
+
+* [Curation](Curation/README.md)
+
+* [Statistics](Statistics/README.md)
+
+In the last case, the scripts were used to generate some of the figures and tables in our latest publication.
+
+### Python Environment
+
+All these scripts run in a Python 3 environment, and some require additional packages which we explain here:
+
+1) Install Conda
+https://conda.io/projects/conda/en/latest/user-guide/install/index.html
+
+2) Set up a python 3 conda environment
+```
+ conda create -n msd-env python=3
+```
+ 3) Activate
+```
+ conda activate msd-env
+```
+
+4) Install rdkit and openbabel for handling biochemical structures
+```
+ conda install -c rdkit rdkit
+ conda install -c openbabel openbabel
+```
+
+5) Install eQuilibrator for retrieving thermodynamics data
+```
+conda install wxPython
+pip install quilt
+pip install equilibrator_api
+```
+_(you might not need to install `wxPython`, I had trouble with dependencies on a mac)_
+
+6) Export path to local python libraries
+```
+export PYTHONPATH=$PYTHONPATH:<path-to-repository>/ModelSEEDDatabase/Libs/Python/
+```
+
+7) Test
+```
+./Biochemistry/Reprint_Biochemistry.py
+git status -s
+```
+(The script should run without throwing any errors and there should be
+no change in the biochemistry data)