Modelbrick Assembler, version 1.0, created: August 22, 2008 Developed by the 2008 iGEM team from the University of Groningen Author: Sander Onur (contact: a 'dot' r 'dot' onur 'at' gmail 'dot' com) This script is meant to be self-explanatory, for any questions regarding its workings, please contact: igemgroningen@googlegroups.com or contact the author directly. Before running, make sure that your library file is entitled 'partslibrary.mat' and that it is located in the same directory as this file. Note that partnames are CaSe-CeNsItIvE. This script is meant to be a proof of concept. It has only been tested on the University of Groningen 2008 iGEM project in combination with the 'partslibrary.mat' file as it is available on 2008.igem.org/Teams:Groningen (October 28, 2008). -- Description of files included: mba.m - MATLAB script, requires the Mathworks MATLAB SimBiology package. partslibrary.mat - MATLAB workspace data containing SimBiology models of all .xml files mentioned below. These .xml files can be used as composable parts, by importing them to the MATLAB Workspace (via SimBiology): Chassis: ecoli.xml - relevant characteristics of one E.coli cell. Parts: B0015.xml - terminator B0031.xml - RBS efficiency 0.07 B0034.xml - RBS efficiency 1 C0051.xml - cI C0062.xml - LuxR E0040.xml - GFP R0040.xml - TetR promoter R0065.xml - LuxR/cI hybrid promoter Luxmut.xml - LuxR mutated promoter with weakened binding site (had no partnumber at time of writing) Pools: ci.xml gfp.xml hsl.xml luxr.xml luxrhsl.xml -- Short description: The chassis contains information about the cellular volume and the amount of RNA polymerases and Ribosomes available. Every modelbrick contains all information about the species and reactions of the part it represents. Additionaly promoters models carry a label of their specific inducers/repressors and coding regions carry a label of their product. Species pools should be present in the workspace and are called upon when needed during assembly. The Modelbrick Assembler first opens SimBiology and loads the partslibrary to MATLAB's workspace. Then it allows you to enter the parts in the order you want to connect them (different transcription regions should preferably be separated). Subsequently a new model is created by combing the parts and connecting them (the names used in the modelbricks serve as tags and are crucial for this part, if you have any questions about this please contact the author). Your new model is saved to the workspace and appears immediately in the Simbiology desktop. Now you can study the workings of the new device, what remains is to set the simulation settings (time, precision etc.) and you are ready to go! -- Below is an example of how to create the genetic interval switch using the script: >> mba This is the iGEM Groningen Modelbrick Assembler, version 1.0, created: August 22, 2008 For help on using this product visit 2008.igem.org/Teams:Groningen If you have any questions, remarks or suggestions for improving the product, please contact igemgroningen@googlegroups.com Choose a name for your model: Interval Switch Please type the name of the chassis here: ecoli Would you like to add a(nother) transcription region? (y=yes, n=no) y Please type the name of the part you want to add: R0065 Would you like to add another part to this transcription region? (y=yes, n=no) y Please type the name of the part you want to add: B0034 Would you like to add another part to this transcription region? (y=yes, n=no) y Please type the name of the part you want to add: E0040 Would you like to add another part to this transcription region? (y=yes, n=no) y Please type the name of the part you want to add: B0015 Would you like to add another part to this transcription region? (y=yes, n=no) n Would you like to add a(nother) transcription region? (y=yes, n=no) y Please type the name of the part you want to add: Luxmut Would you like to add another part to this transcription region? (y=yes, n=no) y Please type the name of the part you want to add: B0031 Would you like to add another part to this transcription region? (y=yes, n=no) y Please type the name of the part you want to add: C0051 Would you like to add another part to this transcription region? (y=yes, n=no) y Please type the name of the part you want to add: B0015 Would you like to add another part to this transcription region? (y=yes, n=no) n Would you like to add a(nother) transcription region? (y=yes, n=no) y Please type the name of the part you want to add: R0040 Would you like to add another part to this transcription region? (y=yes, n=no) y Please type the name of the part you want to add: B0034 Would you like to add another part to this transcription region? (y=yes, n=no) y Please type the name of the part you want to add: C0062 Would you like to add another part to this transcription region? (y=yes, n=no) y Please type the name of the part you want to add: B0015 Would you like to add another part to this transcription region? (y=yes, n=no) n Would you like to add a(nother) transcription region? (y=yes, n=no) n Assembling device, please wait... SimBiology Model - Interval Switch Model Components: Compartments: 1 Events: 0 Parameters: 73 Reactions: 57 Rules: 0 Species: 44 Your device has been exported to the workspace as 'newmodel' >>