twintrans

Python implementation of the twin transcriptional-loop model

https://github.com/ijunier/twintrans

Science Score: 44.0%

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Repository

Python implementation of the twin transcriptional-loop model

Basic Info

Host: GitHub
Owner: ijunier
License: mit
Language: Python
Default Branch: main
Homepage:
Size: 24.3 MB

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Stars: 0
Watchers: 2
Forks: 0
Open Issues: 0
Releases: 2

Created over 3 years ago · Last pushed 6 months ago

Metadata Files

Readme License Citation

README.md

twinTrans

Python implementation of the twin transcriptional-loop model using a Gillespie algorithm

Usage

The code has been tested using Python 3.7.

Basic

The most basic usage consists in running:

bin/twin.py {results_directory}

This will run a simulation with default parameters (lasting $\sim$ 2 min on a 3.1 GHz Intel Core i7). The outcome is composed of two files written out in {results_directory}:

param_var.txt: parameters and variables (and their value) of the simulation
mean_properties.txt: values of various quantities of interest (written out every a fixed number of transcripts as specified by -Net optional argument):
- transcripts_nb: number of transcripts
- time: real time ($s$)
- prod_rate: production rate (= transcripts_nb/time) ($s^{-1}$)
- meanprodtime: average time separating two successive productions of a transcript (should be equal to 1/prod_rate) ($s$)
- meanbindtime: average time separating two successive binding events ($s$)
- meanocftime: average time to form the open complex once the RNAP is bound at the promoter ($s$)
- meanesctime: average time to escape the promoter once the open complex is formed ($s$)
- meaninittime: average time between two successive initiations of elongation ($s$)
- meanelongtime: average elongation time ($s$)

To specificy parameters such as those associated with the promoter ($kb$, $ko$, $\sigmao$ and $ke$), run:

bin/twin.py -h

Promoter-following mode

To follow the topological properties at the promoter, use the option -promfollow

Owner

Name: Ivan Junier
Login: ijunier
Kind: user
Location: Grenoble, France
Company: CNRS (France)

Repositories: 1
Profile: https://github.com/ijunier

Biophysics - bioinformatics (comparative genomics)

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Junier"
  given-names: "Ivan"
  orcid: "https://orcid.org/0000-0002-3522-9599"
title: "twinTrans: Python implementation of the twin transcriptional-loop model"
version: v1.0.0
doi: 10.5281/zenodo.8167497
date-released: 2023-07-20
url: "https://github.com/ijunier/twinTrans"

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