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
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
Future work
- Adding the two color visualization and probe editing to the GUI
- Addting I(t) vs I(t+tau) visualization plot
Project details
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