diff --git a/README.rst b/README.rst index 88c710715..9f566fd97 100644 --- a/README.rst +++ b/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 `_ and `SciPy `_ 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 `__. - -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 `__. + +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 ------------ diff --git a/doc/source/index.rst b/doc/source/index.rst index 6373bbed8..6360bf226 100644 --- a/doc/source/index.rst +++ b/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