This Supporting Information document contains method detail for the paper "An End-to-End Workflow for Engineering of Biological Networks from High-Level Specifications." In particular, it details:• The computational tools used and how they were executed.• Protocols used for DNA preparation and assembly• Protocols used for cell culture and FACS• Details of optical microscopy• Methods for analysis of FACS data
Computational ToolsThe compilation process used a standard Release 6 installation of the Proto p2b stand-alone compiler, 1 configured with neocompiler option. The Proto BioCompiler 2 was coded in C++ as a Proto plug-in. Both were executed on a standard MacBook laptop, with negligible execution time ( 1 second). The compilation process was executed using input configurations stored in Proto code files and invoked for each platform via command-line arguments. Intermediate models were recorded by means of standard Proto logging facilities. The final Proto BioCompiler AGRN output was encoded in a custom XML format based on SBOL 1.0. 3 MatchMaker was coded in Java as a stand-alone application, and also wrapped to produce a Clotho 4 application, for Clotho 2.0 ("tasbe"). The Clotho application version has interfaces to initialize feature, signal and part databases from Clotho databases. The algorithms and mathematical formulation of the feature matching, signal matching and part matching steps explained in detail in a stand-alone paper which is currently under review for publication. 5 MatchMaker was executed on a standard MacBook laptop, with negligible running time (under 1 second).
Dependence analysis is useful f o r software maintenance because it indicates the possible effects of a software modification on the rest of a program. This helps the software maintainer evaluate the appropriateness of a software modification, drive regression testing, and determine the vulnerability of critical sections of code. This paper presents a definition of interprocedural dependence analysis and its implementation in a prototype tool that supports software maintenance.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.