Cell_simulator

Purpose

Integrated development environment for the design of synthetic biological systems, from DNA sequence to systems level

Introduction

Mathematical modeling module includes a software tool for host aware design of synthetic gene circuits. Host context is implemented based on the coarse-grained mechanistic whole cell model from Weisse, 2015.

Documentation

function diluted_species = degradation(species)

• variable species denotes the diluted molecular species (M) diluted

function p = translation(ribocomplex,codons)

• variable ribocomplex denotes the ribosome/mRNA complex species (M)
• variable codons denotes size of mRNA in bases triplets

function mRNA = transcription(tx_rate)

• variable tx_rate denotes the promoter transcription rate (M/sec)

function r_or_mRNA = ribosome_unbind(complex)

• variable complex denotes the dissociating ribocomplex (M)

function ribocomplex = ribosome_bind(species)

• variable species denotes the molecular species (M) bound

function dil_species = dilution(species)

• variable species denotes the diluted molecular species (M/sec) diluted