title: Web-based software tool for constraint-based design specification of synthetic biological systems.
abstract: miniEugene provides computational support for solving combinatorial design problems, enabling users to specify and enumerate designs for novel biological systems based on sets of biological constraints. This technical note presents a brief tutorial for biologists and software engineers in the field of synthetic biology on how to use miniEugene. After reading this technical note, users should know which biological constraints are available in miniEugene, understand the syntax and semantics of these constraints, and be able to follow a step-by-step guide to specify the design of a classical synthetic biological system-the genetic toggle switch.1 We also provide links and references to more information on the miniEugene web application and the integration of the miniEugene software library into sophisticated Computer-Aided Design (CAD) tools for synthetic biology ( www.eugenecad.org ).
authors.affiliation: †Department of Electrical and Computer Engineering and ‡Center of Synthetic Biology (CoSBi), Boston University, Boston, Massachusetts 02215, United States.
authors.forename: Ernst
authors.initials: E
authors.lastname: Oberortner
authors.affiliation: †Department of Electrical and Computer Engineering and ‡Center of Synthetic Biology (CoSBi), Boston University, Boston, Massachusetts 02215, United States.
authors.forename: Douglas
authors.initials: D
authors.lastname: Densmore
mesh_terms: D019295:Computational Biology; D017076:Computer-Aided Design; D020407:Internet; D014584:User-Computer Interface