Web-tools for Design and Analysis of Transcriptional Logic Circuits

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Aaron Adler, Jacob Beal, Fusun Yaman

BBN Technologies, United States

Recent synthetic biology projects at BBN Technologies have produced a number of new methods for computational design and analysis of transcriptional logic circuits. To facilitate use of these methods by our collaborators, and to disseminate them more widely through the synthetic biology community, we have implemented several of these methods as web-tools. These web-tools are free, publicly accessible (https://synbiotools.bbn.com), and allow practitioners to take advantage of complex analytics and data management technologies without needing to grapple with a software infrastructure that combines Octave, python, C++, GraphViz, XML, and MySQL. The web-tools keep users’ data private, provide access to the latest code updates, and include documentation. At present, three tools are available online: * The Color Model analysis tool uses flow cytometry control data to produce a non-linear color model that maps fluorescence values to standard units, following the methods described in [1]. * The Characterization Experiments tool provides detailed quantitative analysis of flow cytometry data for experiments such as input-output transfer curves and time series, following the methods described in [1]. * The Biocompiler tool transforms high-level program descriptions into GRNs following the methods described in [2]. Each tool produces both machine-readable and graphical results. Several laboratories are already using these tools, and we hope the web-tools help disseminate our results and seed many more productive collaborations. Our future work includes: simplifying data entry using experiment templates, improving the user interface per user feedback, supporting sharing of data within a group, and adding more tools. [1]: A Method for Fast, High-Precision Characterization of Synthetic Biology Devices, Jacob Beal, Ron Weiss, Fusun Yaman, Noah Davidsohn, and Aaron Adler, MIT CSAIL Tech Report 2012-008, April, 2012. [2]: Automatic Compilation from High-Level Biologically-Oriented Programming Language to Genetic Regulatory Networks, Jacob Beal, Ting Lu, Ron Weiss, PLoS ONE 6(8): e22490.