rsnapsim 0.0.7

A package for mRNA sequence translation stochastic simulations

Python 2.7 or 3.5+ Version of the Single Molecule Translation Simulator (MatLab) by Dr. Luis Aguilera

Computational Design and Interpretation of Single-RNA Translation Experiments

Translated by Will Raymond - 2018/2019

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rSNAPsim - RNA Sequence to NAscent Protein Simulation

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Project Goal

Provide a Python module that takes nucleotide sequence as an input and does the following:

• Choose a file or pull a file from GeneBank
• Analyzes the sequence and identifies proteins
• Detects or adds fluorescent tags
• Simulates translation trajectories and converts to intensity vectors of A.U. under various conditions
  • Constructs with Rare codons only or Common codons, FRAP or Harringtonite assays
• Provides analyses of the trajectories
• Allows the user to save or export the data
• Commandline / GUI implementations

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Documentation

Tutorials, Module Documentation, Installiation and more [LINK TO MUNSKY GROUP WEBSITE]

Dependencies:

• NumPy
• SciPy
• BioPython
• matplotlib
• pandas
• SnapGene Reader

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Instillation

Pip install

upon release the current release will be added to PyPI for pip installation

General

open up a Terminal or Command Prompt and run pip install rSNAPsim

Anaconda

Open up the Anaconda Prompt (anaconda console) and run conda pip install rSNAPsim

Compilation of the C++

• Download the latest stable Eigen release
• Place the eigen-version into the ssa_cpp folder and rename it to "eigen"
• open a command prompt/terminal or anaconda prompt and cd to this directory
• run "python setup.py build_ext --inplace"

if it says Cannot open include file: 'eigen/Eigen/Dense': and exit status 2 you have eigen in the wrong directory

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Future work

• Adding the two color visualization and probe editing to the GUI
• Addting I(t) vs I(t+tau) visualization plot