{ "info": { "author": "Magdalena Musielak, Pawel Piatkowski, Kristian Rother, Tomasz Puton, Janusz M. Bujnicki", "author_email": "rother.magdalena@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 4 - Beta", "Programming Language :: Python" ], "description": "# ModeRNA - A program for comparative RNA modeling\n\nCopyright 2009 by Magdalena Rother, Kristian Rother, Tomasz Puton and Janusz M. Bujnicki\n\nVersion 1.7.1\n\nHomepage: iimcb.genesilico.pl/moderna\n\nTechnical Support: rother.magdalena@gmail.com\n\n## Build Status\n[![Build Status](https://travis-ci.org/lenarother/moderna.svg?branch=master)](https://travis-ci.org/lenarother/moderna)\n\n## Installation Instructions\n\n### 1. Quick guide\n \n python setup.py install\n\n### 2. Requirements\n\nModeRNA runs on any modern Windows or Linux PC. It requires the Biopython library.\n\n### 3. Installation on Linux\n\nTo install ModeRNA on Linux, you need to:\n\n* Download the source distribution [Moderna Version 1.7.1 (source)].\n* Unzip the archive. A catalog with the main program moderna.py is created.\n* Make sure Python 2.6 or a higher version is installed. (on Ubuntu Linux, use sudo apt-get install python.\n* Make sure Numpy is installed (sudo apt-get install python-numpy).\n* Make sure BioPython is installed (sudo apt-get install python-biopython).
(tested with BioPython 1.53-1.58)\n* Make sure the moderna/moderna.py file is executable:
chmod a+x moderna/moderna.py\n* Add the path to the moderna directory to your PYTHONPATH variable,e.g.:
export PYTHONPATH=$PYTHONPATH:/home/lena/moderna/\n* run:
python setup.py install\n* After this, you can from any location write:\n\n python\n >>> from moderna.moderna import *\n\n### 4. Installing ModeRNA on Windows\n\nTo install ModeRNA on Windows, you need to:\n\n* Download the source distribution [Moderna Version 1.7.1 (source)].\n* Unzip the archive. A catalog with the main program moderna.py is created.\n* Make sure that these libraries are installed:
(all available from iimcb.genesilico.pl/moderna)\n * Python 2.6 or a higher\n * Numpy\n * BioPython (tested with BioPython 1.53 - 1.58)\n\n* Run from the terminal:\n\n C:/Python26/python.exe setup.py install\n\n* After this, you can write in the Python shell:\n\n >>> from moderna.moderna import *\n\n\n### 5. Legal Disclaimer\n\nModeRNA is released under the GPL license, a copy of which is included in \nthe distribution (See LICENSE_GPL.TXT for details). For the files in the \nPDB/ directory, the Biopython License applies as well. \nSee PDB/LICENSE_BIOPYTHON.TXT for details).\n\nThis software is provided \"as-is\". There are no expressed or implied \nwarranties of any kind, including, but not limited to, the warranties of \nmerchantability and fitness for a given application. In no event shall \nthe authors be liable for any direct, indirect, incidental, special, \nexemplary or consequential damages (including, but not limited to, loss \nof use, data or profits, or business interruption) however caused and on \nany theory of liability, whether in contract, strict liability or tort \n(including negligence or otherwise) arising in any way out of the use \nof this software, even if advised of the possibility of such damage.\n\nThe authors take no responsibility for damage caused by this program \nor its components. \n\n\n### 6. Contributors\n\n* Magdalena Rother - implementation\n* Pawel Piatkowski - implementation\n* Kristian Rother - architecture and unit tests\n* Tomasz Puton - model validation and testing\n* Janusz Bujnicki - concept and supervision\n\n\n### 7. Acknowledgements\n\nCredit goes to our lab colleagues Pawel Skiba, Piotr Byzia, Irina Tuszynska, \nJoanna Kasprzak, Jurek Orlowski, Pawel Lukasz, Tomasz Osinski, Marcin \nDomagalski, Anna Czerwoniec, Stanislaw Dunin-Horkavic, Marcin Skorupski, \nand Marcin Feder for their comments and constructive criticism during \ndevelopment. \n\nThe PDB parser ued by Moderna uses BioPython with kind support by \nThomas Hamelryck. The unit test framework was brought near to us by \nSandra Smit, Rob Knight, and Gavin Huttley. We also would like to thank \nNeocles Leontis, Fabrice Jossinet, Francois Major, and Eric Westhof who \nprovided helpful advice on various occasions.\n\nSpecial thanks go to the group of Russ Altman, who provided us with \ntheir modeling example to test ModeRNA.\n\n\n### 8. References\n\nComponents of ModeRNA are based upon the following pieces of scientific literature:\n\n[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.\n\n[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.\n\n[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.\n\n[4] Michalsky E, Goede A, Preissner R. Loops In Proteins (LIP)\u2013a comprehensive loop database for homology modelling. Protein Eng. 2003 Dec;16(12):979-85.\n\n[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. 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