Updated README and docs index.

README.rst

@@ -17,19 +17,30 @@ EMMA (Emma's Markov Model Algorithms)
 
 What is it?
 -----------
-EMMA is an open source collection of algorithms implemented mostly in
-`NumPy <http://www.numpy.org/>`_ and `SciPy <http://www.scipy.org>`_ to analyze
-trajectories generated from any kind of simulation (e.g. molecular
-trajectories) via Markov state models (MSM).
-
-It provides APIs for estimation and analyzing MSM and various utilities to
-process input data (clustering, coordinate transformations etc). For
-documentation of the API, please have a look at the sphinx docs in doc
-directory or `online <http://www.emma-project.org/>`__.
-
-For some examples on how to apply the software, please have a look in the
-ipython directory, which shows the most common use cases as documentated
-IPython notebooks.
+PyEMMA (EMMA = Emma's Markov Model Algorithms) is an open source
+Python/C package for analysis of extensive molecular dynamics simulations.
+In particular, it includes algorithms for estimation, validation and analysis
+of:
+
+  * Markov state models (MSMs)
+  * Hidden Markov models (HMMs)
+  * multi-ensemble Markov models (MEMMs)
+  * Time-lagged independent component analysis (TICA)
+  * Clustering and Featurization.
+
+PyEMMA can be used from Jupyther (former IPython, recommended), or by
+writing Python scripts. The docs, can be found at
+`http://pyemma.org <http://www.pyemma.org/>`__.
+
+Citation
+--------
+If you use PyEMMA in scientific work, please cite:
+
+    M. K. Scherer, B. Trendelkamp-Schroer, F. Paul, G. Pérez-Hernández,
+    M. Hoffmann, N. Plattner, C. Wehmeyer, J.-H. Prinz and F. Noé:
+    PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models,
+	J. Chem. Theory Comput. 11, 5525-5542 (2015)
+
 
 Installation
 ------------

doc/source/index.rst

@@ -35,23 +35,24 @@ Technical features:
 Citation |DOI for Citing PyEMMA|
 --------------------------------
 
-PyEMMA is scientific software, if you use it in your scientific work, please
-consider citing this paper: ::
+If you use PyEMMA in scientific software, please cite the following paper: ::
 
 	@article{scherer_pyemma_2015,
+		author = {Scherer, Martin K. and Trendelkamp-Schroer, Benjamin
+                          and Paul, Fabian and Pérez-Hernández, Guillermo and Hoffmann, Moritz and
+                          Plattner, Nuria and Wehmeyer, Christoph and Prinz, Jan-Hendrik and Noé, Frank},
 		title = {{PyEMMA} 2: {A} {Software} {Package} for {Estimation},
                          {Validation}, and {Analysis} of {Markov} {Models}},
+		journal = {Journal of Chemical Theory and Computation},
+		volume = {11},
+		pages = {5525-5542},
+		year = {2015},
 		issn = {1549-9618},
 		shorttitle = {{PyEMMA} 2},
 		url = {http://dx.doi.org/10.1021/acs.jctc.5b00743},
 		doi = {10.1021/acs.jctc.5b00743},
 		urldate = {2015-10-19},
-		journal = {Journal of Chemical Theory and Computation},
-		author = {Scherer, Martin K. and Trendelkamp-Schroer, Benjamin
-                          and Paul, Fabian and Pérez-Hernández, Guillermo and Hoffmann, Moritz and
-                          Plattner, Nuria and Wehmeyer, Christoph and Prinz, Jan-Hendrik and Noé, Frank},
 		month = oct,
-		year = {2015},
 	}
 
 .. |DOI for Citing PyEMMA| image:: _static/pyemma_paper_doi.svg