TABASCO

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== Summary ==
== Summary ==
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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).
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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 ==
== People ==
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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.
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.
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== Code ==
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== Software and Source ==
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Code will be made available soon
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The software for Tabasco is freely available here:
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[http://model.mit.edu/Tabasco/source Java Source Files] <br>
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[http://model.mit.edu/Tabasco/doc/ Javadoc Documentation] <br>
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[http://model.mit.edu/Tabasco/classes Compiled Java Byte Code] <br>
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== Usage ==
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The useful executable classes are
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=== TabascoSimulator ===
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=== TabascoJpegMake ===
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=== Averager ===
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== Examples ==

Revision as of 21:44, 25 July 2005

Contents

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 Source

The software for Tabasco is freely available here:

Java Source Files
Javadoc Documentation
Compiled Java Byte Code


Usage

The useful executable classes are

TabascoSimulator

TabascoJpegMake

Averager

Examples

Personal tools