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analysis
organism
population
run_management
scripts
utility
.gitignore
Makefile
README.rst
__init__.py
parameters.cfg
run_config.py

README.rst

Structure and Landscapes

Description

This Python project investigates the effect population structure has on organisms with smooth or rugged adaptive landscapes. Various sequence to fitness mappings will be explored including:

  • RNA secondary structure
  • Simple Integer Model
  • Bitstrings
  • Kauffman's N-K Model

Authors

Github Repositories

  • git://github.com/jaredc-s/structure_and_landscapes.git
  • git://github.com/jhmarcus/structure_and_landscapes.git
  • git://github.com/nahumj/structure_and_landscapes.git

Requirements

Mandatory

  • Python 2.7

Optional

  • Ned Batchelder's coverage.py
  • Nose
  • Pep8
  • Numpy
  • Matplotlib

Install

1)github: https://github.com/jhmarcus/structure-and-landscapes 2)downloads https://github.com/jhmarcus/structure-and-landscapes/downloads 3)download as zip using the defult archive manager 4)sudo apt-get install python2.7-dev

  • version python2.7-dev (2.7.3-0ubuntu3)
5)sudo apt-get install build-essential
  • version build-essential (11.5ubuntu2)

6)sudo apt-get install pep8 7) pep8 's version (0.6.1-2ubuntu2) 8) sudo apt-get install python-pip 9) pip version (1.0-1build1)

Runsnakerun

http://www.vrplumber.com/programming/runsnakerun/

depedencies for runsnakerun apt-get install python-profiler python-wxgtk2.8 python-setuptools

ViennaRNA

http://www.tbi.univie.ac.at/~ivo/RNA/ http://www.tbi.univie.ac.at/~ronny/RNA/vrna2_source.html

follow instructions on install ./configure make sudo make install

version 2.0.7 download source code and use the default archive manager!

Add this package to PYTHONPATH

Add this line to ~/.bashrc:

export PYTHONPATH=$PYTHONPATH:$PATH_TO_DIRECTORY_CONTAINING_structure_and_landscape

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