Metadata-Version: 1.0
Name: CMCpy
Version: 0.1
Summary: Genetic Code-Message Coevolution in Python
Home-page: http://pypi.python.org/pypi/CMCpy/
Author: David H. Ardell
Author-email: dardell@ucmerced.edu
License: Apache 2.0
Description: =======================================================
        CMCpy -- Code-Message Coevolution Models in Python
        =======================================================
        
        CMCpy provides an object-oriented python API, together with command-line
        interface executables, that implement "Code-Message Coevolution" models.
        These published evolutionary models pertain to the evolution by natural
        selection of a genetic code in coevolution with a population of
        protein-coding genes.
        
        Formally, CMC models are sets of quasispecies coupled together for their
        fitness through a genetic code. The system alternates between quasispecies
        equilibration and adaptive hill-climbing through codon assignments and
        reassignment by code mutation.
        
        CMCpy can reproduce the statistics and results of [Ardell_and_Sella_2001]_,
        [Sella_and_Ardell_2002]_, [Ardell_and_Sella_2002]_ and
        [Sella_and_Ardell_2006]_. CMCpy additionally implements additional
        extensions that have not yet been studied in published work. It is easliy
        feasible to extend the present code-base to implement the model studied by
        [Vetsigian_et_al_2006]_.
        
        CMC evolutionary trajectories are partly a sequence of eigensystem
        solutions. Qualitative differences in results on different platforms can
        originate from differences in convergence criteria when power method-based
        eigensystem solvers are used, or from differences in floating point
        representations. Python defers to the platform C library for float
        representation. The default eigensystem solver is the eig() function in
        Numpy.
        
        Dependencies 
        ============================================ 
        
        CMCpy relies heavily on, and absolutely requires, numpy as a prerequisite.
        You should install numpy with the easy_install framework to be detected as
        installed when installing this package. 
        
        If you wish to play with an experimental CUDA-based power-method eigensystem
        solver, you must install pycuda. This implementation is not faster than the
        NumPy default solver for many systems.
        
        
        Installation
        ============================================
        			
        This installer requires setuptools, the most recent python packaging
        framework. If you do not already have this installed, this package
        will install it for you, so long as you have network access. Otherwise
        preinstall the correct version of setuptools using the EasyInstall
        installation instructions at
        http://peak.telecommunity.com/DevCenter/EasyInstall#installation-instructions 
        
        If you need to install this package somewhere other than the main
        site-packages directory, install setuptools using the instructions for
        Custom Installation Locations before installing this package. The
        instructions are here:
        http://peak.telecommunity.com/DevCenter/EasyInstall#custom-installation-locations
        
        If you have downloaded the source-code package, the easiest way to
        install the package is to execute (from within the source root directory)::
        
        	easy_install .
        
        Mac users may need to run this command with "sudo" prepended.
        
        Usage
        ============================================
        
        CMCpy comes with an executable inside the bin subdirectory to the
        installation source package, a UNIX-compatible script called "cmc". 
        
        Additionally, a platform-specific executable may be automatically generated
        on installation.
        
        Published results with CMC models may be (at least qualitatively) reproduced
        through the --demo option to the executables.
        
        Also try running the --help option to the executables after installation and
        for a command-line example.
        
        Programmers may use the executable in bin as a guide and template for how to
        program against the cmcpy API.
        		       			  
        Documentation 
        ============================================ 
        
        Some documentation of the cmcpy API is available within the "doc"
        subdirectory of the source distribution. HTML, pdf and texinfo alternative
        formats are provided.
        
        Licensing and Attribution 
        ============================================
        
        The CMCpy project is distributed under the terms of the Apache License 2.0
        as described in the file LICENSE.txt
        
        Please cite Becich et al. (2012) in all scientific works that use this code.
        
        Release Notes
        ============================================
        The most recent version is 0.1 released October 2012.
        
        See CHANGES.txt for version-related changes to the CMCpy code-base.
        
        References
        ============================================
        
        .. [Ardell_and_Sella_2001] D.H. Ardell and G. Sella (2001). On the evolution of redundancy in genetic codes. `Journal of Molecular Evolution 53(4/5):269-281`_.
        
        .. [Ardell_and_Sella_2002] D.H. Ardell and G. Sella (2002). No accident: genetic codes freeze in error-correcting patterns of the standard genetic code. `Philosophical Transactions of the Royal Society of London B 357:1625-1642`_.
        
        .. [Sella_and_Ardell_2002] G. Sella and D.H. Ardell (2002). The impact of message mutation on the fitness of a genetic code. `Journal of Molecular Evolution 54(5):638-651`_.
        
        .. [Sella_and_Ardell_2006] G. Sella and D.H. Ardell (2006). The coevolution of genes and genetic codes: Crick's frozen accident revisited. `J. Mol. Evol. 63(3):297-313`_.
        
        .. [Vetsigian_et_al_2006] Vetsigian K., Woese C. R., Goldenfeld N. (2006). Collective evolution and the genetic code. `Proc. Natl. Acad. Sci. U.S.A. 103, 10696-10701`_.
        
        
        .. _Journal of Molecular Evolution 53(4/5):269-281: http://dx.doi.org/10.1007/s002390010217
        
        .. _Philosophical Transactions of the Royal Society of London B 357:1625-1642: http://dx.doi.org/10.1098/rstb.2002.1071
        
        .. _Journal of Molecular Evolution 54(5):638-651: http://dx.doi.org/10.1007/s00239-001-0060-7
        
        .. _J. Mol. Evol. 63(3):297-313: http://dx.doi.org/10.1007/s00239-004-0176-7
        
        .. _Proc. Natl. Acad. Sci. U.S.A. 103, 10696-10701: http://www.pnas.org/cgi/pmidlookup?view=long&pmid=16818880
        
Platform: UNKNOWN
