Metadata-Version: 1.1
Name: moderna
Version: 1.7.4
Summary: ModeRNA - A program for comparative RNA modeling
Home-page: http://iimcb.genesilico.pl/moderna
Author: Magdalena Musielak, Pawel Piatkowski, Kristian Rother, Tomasz Puton, Janusz M. Bujnicki
Author-email: rother.magdalena@gmail.com
License: new BSD
Description: 
        # ModeRNA - A program for comparative RNA modeling
        
        Copyright 2009 by Magdalena Rother, Kristian Rother, Tomasz Puton and Janusz M. Bujnicki
        
        Version 1.7.1
        
        Homepage: iimcb.genesilico.pl/moderna
        
        Technical Support: rother.magdalena@gmail.com
        
        ## Build Status
        [![Build Status](https://travis-ci.org/lenarother/moderna.svg?branch=master)](https://travis-ci.org/lenarother/moderna)
        
        ## Installation Instructions
        
        ### 1. Quick guide
         
           python setup.py install
        
        ### 2. Requirements
        
        ModeRNA runs on any modern Windows or Linux PC. It requires the Biopython library.
        
        ### 3. Installation on Linux
        
        To install ModeRNA on Linux, you need to:
        
        * Download the source distribution [Moderna Version 1.7.1 (source)].
        * Unzip the archive. A catalog with the main program moderna.py is created.
        * Make sure Python 2.6 or a higher version is installed. (on Ubuntu Linux, use sudo apt-get install python.
        * Make sure Numpy is installed (sudo apt-get install python-numpy).
        * Make sure BioPython is installed (sudo apt-get install python-biopython).<br> (tested with BioPython 1.53-1.58)
        * Make sure the moderna/moderna.py file is executable: <br> chmod a+x moderna/moderna.py
        * Add the path to the moderna directory to your PYTHONPATH variable,e.g.: <br> export PYTHONPATH=$PYTHONPATH:/home/lena/moderna/
        * run:<br> python setup.py install
        * After this, you can from any location write:
        
            python
            >>> from moderna.moderna import *
        
        ### 4. Installing ModeRNA on Windows
        
        To install ModeRNA on Windows, you need to:
        
        * Download the source distribution [Moderna Version 1.7.1 (source)].
        * Unzip the archive. A catalog with the main program moderna.py is created.
        * Make sure that these libraries are installed:<br> (all available from iimcb.genesilico.pl/moderna)
          * Python 2.6 or a higher
          * Numpy
          * BioPython (tested with BioPython 1.53 - 1.58)
        
        * Run from the terminal:
        
            C:/Python26/python.exe setup.py install
        
        * After this, you can write in the Python shell:
        
            >>> from moderna.moderna import *
        
        
        ### 5. Legal Disclaimer
        
        ModeRNA is released under the GPL license, a copy of which is included in 
        the distribution (See LICENSE_GPL.TXT for details). For the files in the 
        PDB/ directory, the Biopython License applies as well. 
        See PDB/LICENSE_BIOPYTHON.TXT for details).
        
        This software is provided "as-is". There are no expressed or implied 
        warranties of any kind, including, but not limited to, the warranties of 
        merchantability and fitness for a given application. In no event shall 
        the authors be liable for any direct, indirect, incidental, special, 
        exemplary or consequential damages (including, but not limited to, loss 
        of use, data or profits, or business interruption) however caused and on 
        any theory of liability, whether in contract, strict liability or tort 
        (including negligence or otherwise) arising in any way out of the use 
        of this software, even if advised of the possibility of such damage.
        
        The authors take no responsibility for damage caused by this program 
        or its components. 
        
        
        ### 6. Contributors
        
        * Magdalena Rother   - implementation
        * Pawel Piatkowski   - implementation
        * Kristian Rother    - architecture and unit tests
        * Tomasz Puton       - model validation and testing
        * Janusz Bujnicki    - concept and supervision
        
        
        ### 7. Acknowledgements
        
        Credit goes to our lab colleagues Pawel Skiba, Piotr Byzia, Irina Tuszynska, 
        Joanna Kasprzak, Jurek Orlowski, Pawel Lukasz, Tomasz Osinski, Marcin 
        Domagalski, Anna Czerwoniec, Stanislaw Dunin-Horkavic, Marcin Skorupski, 
        and Marcin Feder for their comments and constructive criticism during 
        development. 
        
        The PDB parser ued by Moderna uses BioPython with kind support by 
        Thomas Hamelryck. The unit test framework was brought near to us by 
        Sandra Smit, Rob Knight, and Gavin Huttley. We also would like to thank 
        Neocles Leontis, Fabrice Jossinet, Francois Major, and Eric Westhof who 
        provided helpful advice on various occasions.
        
        Special thanks go to the group of Russ Altman, who provided us with 
        their modeling example to test ModeRNA.
        
        
        ### 8. References
        
        Components of ModeRNA are based upon the following pieces of scientific literature:
        
        [1] Czerwoniec A, Dunin-Horkawicz S, Purta E, Kaminska KH, Kasprzak JM, Bujnicki JM, Grosjean H, Rother K. MODOMICS: a database of RNA modification pathways. 2008 update. Nucleic Acids Res. 2008 Oct 14.
        
        [2] Yang H, Jossinet F, Leontis N, Chen L, Westbrook J, Berman H, Westhof E. Tools for the automatic identification and classification of RNA base pairs. Nucleic Acids Res. 2003 Jul 1;31(13):3450-60.
        
        [3] Gendron P, Lemieux S, Major F. Quantitative analysis of nucleic acid three-dimensional structures. J Mol Biol. 2001 May 18;308(5):919-36.
        
        [4] Michalsky E, Goede A, Preissner R. Loops In Proteins (LIP)–a comprehensive loop database for homology modelling. Protein Eng. 2003 Dec;16(12):979-85.
        
        [5] Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B, de Hoon MJ. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics. 2009 Jun 1;25(11):1422-3. Epub 2009 Mar 20.
        
        
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Programming Language :: Python
