Skip to content

Commit

Permalink
update readme, author list
Browse files Browse the repository at this point in the history
  • Loading branch information
marinkaz committed Jun 21, 2016
1 parent 3e8d222 commit 3b52875
Show file tree
Hide file tree
Showing 2 changed files with 57 additions and 12 deletions.
22 changes: 22 additions & 0 deletions AUTHORS.rst
Original file line number Diff line number Diff line change
@@ -0,0 +1,22 @@
.. -*- mode: rst -*-
This is a community effort, and as such many people have contributed
to it over the years.

History
-------

This project was started in 2011 as a Google Summer of Code project by
Marinka Zitnik.

People
------

The following people have been core contributors to Nimfa's development and maintenance::

* Yaroslav Halchenko
* Vamsi Krishna
* Mariano Tepper
* Marko Toplak
* Marinka Zitnik <http://cs.stanford.edu/~marinka>
47 changes: 35 additions & 12 deletions README.rst
Original file line number Diff line number Diff line change
Expand Up @@ -12,20 +12,43 @@ Nimfa

Nimfa is a Python module that implements many algorithms for nonnegative matrix factorization.

Documentation and examples are at `Nimfa website`_.
The project was started in 2011 by Marinka Zitnik as a Google Summer of Code project, and since
then many volunteers have contributed. See the AUTHORS.rst file for a complete list of contributors.

.. _Nimfa website: http://nimfa.biolab.si
It is currently maintained by a team of volunteers.

****
Important links
---------------

`Hidden patients and hidden genes - Understanding cancer data with matrix factorization`_ is
a tutorial-like IPython notebook on how one can use Nimfa to analyze breast cancer transcriptome data sets from The
International Cancer Genome Consortium (`ICGC`_). A column about the analysis of cancer data using Nimfa recently
appearead in the `ACM XRDS magazine`_.
- Official source code repo: https://github.com/marinkaz/nimfa
- HTML documentation (stable release): http://nimfa.biolab.si
- Download releases: http://github.com/marinkaz/nimfa/releases
- Issue tracker: http://github.com/marinkaz/nimfa/issues

.. _Hidden patients and hidden genes - Understanding cancer data with matrix factorization: http://nbviewer.ipython.org/github/marinkaz/nimfa-ipynb/blob/master/ICGC%20and%20Nimfa.ipynb
.. _ICGC: https://dcc.icgc.org
.. _ACM XRDS magazine: http://dl.acm.org/citation.cfm?id=2809623.2788526&coll=portal&dl=ACM
Dependencies
------------

Nimfa is tested to work under Python 2.6, Python 2.7, and Python 3.4.

The required dependencies to build the software are NumPy >= 1.7.0,
SciPy >= 0.12.0.

For running the examples Matplotlib >= 1.1.1 is required.

Install
-------

This package uses setuptools, which is a common way of installing
python modules. To install in your home directory, use::

python setup.py install --user

To install for all users on Unix/Linux::

sudo python setup.py install

For more detailed installation instructions,
see the web page http://nimfa.biolab.si

Usage
-----
Expand Down Expand Up @@ -53,7 +76,7 @@ Citing

@article{Zitnik2012,
title = {Nimfa: A Python Library for Nonnegative Matrix Factorization},
author = {{\v{Z}}itnik, Marinka and Zupan, Bla{\v{z}}},
author = {Zitnik, Marinka and Zupan, Blaz},
journal = {Journal of Machine Learning Research},
volume = {13},
pages = {849-853},
Expand All @@ -65,7 +88,7 @@ License
-------

nimfa - A Python Library for Nonnegative Matrix Factorization Techniques
Copyright (C) 2011-2015 Marinka Zitnik and Blaz Zupan
Copyright (C) 2011-2016

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
Expand Down

0 comments on commit 3b52875

Please sign in to comment.