docs: Add overview with provisional PSAMM paper reference

docs/index.rst

@@ -7,6 +7,7 @@ Contents:
 .. toctree::
    :maxdepth: 2
 
+   overview
    install
    file_format
    commands

docs/overview.rst

@@ -0,0 +1,30 @@
+
+Overview
+========
+
+PSAMM is a collection of tools related to metabolic modeling, model
+reconstruction, data parsing and formatting, consistency checking,
+automatic gap filling, and model simulations.
+
+PSAMM is developed as an open source project, coordinated through `Github`_.
+The PSAMM software is being developed at the `University of Rhode Island`_ and
+is the subject of a research article that has been submitted for
+review. [Steffensen15]_
+
+.. _Github: https://github.com/zhanglab/psamm
+.. _University of Rhode Island: http://zhanglab.uri.edu/
+
+Software license
+----------------
+
+PSAMM is free software: you can redistribute it and/or modify it under the
+terms of the GNU General Public License as published by the Free Software
+Foundation, either version 3 of the License, or (at your option) any later
+version.
+
+This program is distributed in the hope that it will be useful, but WITHOUT ANY
+WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+PARTICULAR PURPOSE. See the GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along with
+this program. If not, see http://www.gnu.org/licenses/.

docs/references.rst

@@ -2,6 +2,9 @@
 References
 ==========
 
+.. [Steffensen15] Steffensen JL, Dufault-Thompson K, Zhang Y. PSAMM: A Portable
+    System for the Analysis of Metabolic Models. Submitted.
+
 .. [Gevorgyan08] Gevorgyan A, Poolman MG, Fell DA. Detection of stoichiometric
     inconsistencies in biomolecular models. Bioinformatics. 2008;24: 2245–2251.
     :doi:`10.1093/bioinformatics/btn425`.