A package for mRNA sequence translation stochastic simulations
Project description
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
rSNAPsim - RNA Sequence to NAscent Protein Simulation
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
Documentation
Tutorials, Module Documentation, Installiation and more [LINK TO MUNSKY GROUP WEBSITE]
Dependencies:
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]
- 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.
-
gcc not found
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
Project details
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