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Open Access Methodology article

TABASCO: A single molecule, base-pair resolved gene expression simulator

Sriram Kosuri, Jason R Kelly and Drew Endy*

Author Affiliations

Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139 USA

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BMC Bioinformatics 2007, 8:480  doi:10.1186/1471-2105-8-480

Published: 19 December 2007

Additional files

Additional File 1:

Visualization of T7 genome simulation using Tabasco. We developed a general visualization tool for depicting graphically and dynamically depicting output from Tabasco. Here, we show output from a Tabasco simulation of three T7 phage simultaneously infecting a single cell over the course of 25 minutes. Each of the three white lines at the top represents a distinct copy of the 39,937 bp T7 genome. The T7 and E. coli RNA polymerases are shown as blue and yellow lines moving directly along and above the genomes; directly below the genomes are promoters (dark blue) and terminators (dark red). In addition, the extent of each genomes entry is shown as a solid white line that extends above and below the genome representation (while genome entry is occurring). Protein levels (solid bars) and mRNA levels (white lines) of T7 genes and other host RNA polymerase and ribosome levels are plotted as numbers of molecules per cell on a log-scale below the genome depictions. Each frame is a snapshot of the simulation taken at 5-second intervals; time is displayed in seconds directly below the genome representations.

Format: MOV Size: 4.5MB Download file

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Open Data

Additional File 2:

Input files for simulations described in the text of the paper.

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Open Data

Additional File 3:

TABASCO website.

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Additional File 4:

Parameter definitions within the input file. The table describes the parameter definitions that are used in the input files that are contained in the supplementary materials.

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