rsnapsim

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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ssa c++ library

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
• DnaFeaturesViewer

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Instillation

Within a conda enviroment:

conda install eigen 
pip install rsnapsim-ssa-cpp 
pip install rsnapsim

Within a Google Colab:

!apt install libeigen3-dev
!ln -sf /usr/include/eigen3/Eigen /usr/include/Eigen
!pip install rsnapsim-ssa-cpp
!pip install rsnapsim
!pip install --upgrade rsnapsim 

Compilation of the C++

The c++ model should attempt to compile when you pip install the ssa-cpp module, however in the event that it cannot here are some common errors:

• cannot include eigen3/Eigen/Dense
  • This means eigen was not installed correctly from the conda installiation, you may have to manually download eigen and pass the argument to the setup.py command. python setup.py build_ext --inplace -I[PATH TO EIGEN FOLDER]
• gcc not found

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Example Colab Notebooks

• Simulating Translation
• Simulating Constructs with Different codon usages
• Intensity Analyses
• Harringtonine / FRAP simulations
• Model Maker/ Designer
• MW/Diffusion Calculations

Future work

• Example notebooks of all functions