ePURE_JSBML: A Tool for Constructing a Deterministic Model of a Reconstituted Escherichia coli Protein Translation
Yoshihiro Shimizu1, Naoki Tanimura2, Tomoaki Matsuura3
1Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan.
Abstract:
A protein synthesis system is one of the most important and complex biological networks, which translates DNA-encoded information into specific functions. Here, ePURE_JSBML, a tool for constructing biologically relevant large-scale and detailed computational models based on a reconstituted cell-free protein synthesis system, is presented; the user can specify the mRNA sequence, initial component concentration, and decoding rule. Model construction is based on Systems Biology Markup Language (SBML) using JSBML, a pure Java programming library. The tool generates simulation files, executable with Matlab, that enable a variety of simulation experiments including the synthesis of proteins of a few hundred residues.
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