TABASCO

Summary

Tabasco is a simulator created to address the problem of simulating gene expression at single-base resolution. By defining the logic of transcription and translation rules a priori such as initiation, elongation, termination, and interactions of polymerases and proteins, Tabasco automatically traverses the state of the system as it develops and thus makes simulation at such high resolution computationally feasible. Tabasco was designed to allow us to better understand bacteriophage gene expression. In general, Tabasco would be useful to those interested in explicitly simulating hypotheses of protein-DNA interactions and their relation to gene expression (e.g., eukaryotic gene expression initiation).

People

Sriram Kosuri, Jason Kelly, Drew Endy

Methods

Tabasco avoids previous ‘combinatorial explosion’ problems by tracking the position and state of proteins and genetic elements on the DNA to dynamically generate appropriate reactions, such as promoters being blocked by traversing polymerases. In order to improve computational efficiency, Tabasco makes use of a Gibson-accelerated Gillespie SSA to compute the reaction event timing and the resultant time-evolution of the genetic system.

Software and Installation

The software for Tabasco is freely available here:

Java Source Files
Javadoc Documentation
Compiled Java Byte Code

The simulator was only tested on J2SE version 1.4.2 and higher. A basic knowledge of running java programs is needed. A general outline of the process.

1. Create or Download Byte Code
   • One can either download the source, and compile it using a java compiler to byte code or download the precompiled byte code above.
2. Edit the input file
3. Run TabascoSimulator
4. Average runs together using Averager

Usage

The useful executable classes are