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This is the github software repository of the BU_Wellesley_Software team for the 2011 iGEM competition. Our repository is divided into four directories housing three applications and one executable. The Trumpet and OptimusPrimer directories have a single zipped file archive containing the source code for these applications. The zipped archive contains source files in the form of a Netbeans module. To compile and build these applications, you will need to install Java and the latest version of Netbeans, and obtain a copy of the Clotho Core. For instructions on how to do this, please visit our help page located at http://wiki.bu.edu/ece-clotho/index.php/DeveloperSetupNew. Once you have built the Clotho Core successfully, unzip and untar the archives for our applications and add them to the Netbeans Clotho module. Be sure to check and refresh their dependency on the Clotho Core, and then build them. Finally, use Netbeans' ``Package As'' feature to build an executable. The executable will appear in the ClothoProject/dist directory as a zipped file. To execute it, unzip the file and execute the script file ``clotho'' or ``clotho.exe'' depending on your operating system. The G-nome Surfer Pro directory contains the source code required to build our G-nome Surfer application for the Microsoft Surface. Please refer to the README file in that directory for instructions on how to build that application. Please visit our iGEM wiki located at http://2011.igem.org/Team:BU_Wellesley_Software to learn more about our projects. There, you will find video tutorials, descriptions, and other details on how our tools create and complement the synthetic biology workflow. Links to video tutorials are also included below: G-nome Surfer Pro : http://bit.ly/odWmBL Optimus Primer : http://bit.ly/qh3m5h Trumpet : http://bit.ly/nTCE0r PuppetShow and E-Lab Notebook : http://bit.ly/pAIqMb We hope that you will try out our software tools. If you have questions, please email us at firstname.lastname@example.org. The BU-Wellesley iGEM Team September 28th, 2011