Computer-Aided Design (CAD) tools are software packages which are created to help in designing and engineering new systems. In traditional engineering fields, these programs have long been used to aid in optimizing production processes, modeling chemical reactions, and creating new products. Graphical User Interfaces (GUIs) act as the human-readable visualization of computer languages which are designed to assemble components into useful products or devices. Many of these programs include capabilities for simulating the outcome of a given assembled device as well as automating the assembly with a specific goal in mind. The field of synthetic biology is advancing to the point where high throughput automated design of synthetic biological devices will be necessary to realize the potential of the discipline.
Synthetic Biology CAD Tools
Synthetic Biology CAD tools are programs which help to create novel biological constructs. At the most basic, these programs are essentially enhanced DNA editors which provide a user interface to facilitate easier manipulation of the basic “parts” which comprise biological devices. Some of the more advanced programs have a variety of functions including visualization, asserting validity of constructs, and simulations of metabolic networks. In general, CAD programs for synthetic biology should comply with SBOL to facilitate use with the Parts Registry and sharing of parts with other researchers.
Representing Synthetic Biology Designs
The Synthetic Biology Open Language is an open-source standard for representing designs consisting of both DNA sequence information and higher level annotation of parts with defined roles and behaviors . The core specification of this system has been developed as an RFC . Several different synthetic biology CAD software programs use this format. Representation at this higher level of parts can be visualized and simulated in some of these systems (e.g., TinkerCell).
The Eugene Language is an open-source human-readable language designed to facilitate automatic creation of new devices from a collection of parts. Eugene includes a standardized format for specifying devices and parts as well as constraints on how they can be assembled into higher level devices (i.e. genetic toggle switch). Eugene also features functions for automatic generation of functional assemblies into complex devices. Eugene does not support visualization of constructs.
iGEM Software Tools Development
The iGEM competition for development of software tools is designed to promote creation of publicly available CAD programs for synthetic biology. Similar to the Registry for Standard Biological Parts, the software tools entered into the competition must adhere to certain standards of interoperability and data format in order to facilitate reuse and ease of collaboration among researchers. There are several categories developers can pursue, including specific modular CAD frameworks (i.e. Clotho) as well as sharing data and interfacing with the Parts Registry. iGEM hosts a repository of these open source software packages from past competitions, which is freely available.
- Chandran D, Bergmann FT, and Sauro HM. TinkerCell: modular CAD tool for synthetic biology. J Biol Eng. 2009 Oct 29;3:19. DOI:10.1186/1754-1611-3-19 |
TinkerCell: modular CAD tool for synthetic biology
- Weeding E, Houle J, and Kaznessis YN. SynBioSS designer: a web-based tool for the automated generation of kinetic models for synthetic biological constructs. Brief Bioinform. 2010 Jul;11(4):394-402. DOI:10.1093/bib/bbq002 |
SynBioSS designer: a web-based tool for the automated generation of kinetic models for synthetic biological constructs
- Ham TS, Dmytriv Z, Plahar H, Chen J, Hillson NJ, and Keasling JD. Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools. Nucleic Acids Res. 2012 Oct;40(18):e141. DOI:10.1093/nar/gks531 |
Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools.
- Villalobos A, Ness JE, Gustafsson C, Minshull J, and Govindarajan S. Gene Designer: a synthetic biology tool for constructing artificial DNA segments. BMC Bioinformatics. 2006 Jun 6;7:285. DOI:10.1186/1471-2105-7-285 |
Gene Designer:a synthetic biology tool for constructing artificial DNA segments
- Galdzicki M, Rodriguez C, Chandran D, Sauro HM, and Gennari JH. Standard biological parts knowledgebase. PLoS One. 2011 Feb 24;6(2):e17005. DOI:10.1371/journal.pone.0017005 |
Standard biological parts knowledgebase
Synthetic Biology Open Language (SBOL) Version 1.0.0
- Bilitchenko L, Liu A, Cheung S, Weeding E, Xia B, Leguia M, Anderson JC, and Densmore D. Eugene--a domain specific language for specifying and constraining synthetic biological parts, devices, and systems. PLoS One. 2011 Apr 29;6(4):e18882. DOI:10.1371/journal.pone.0018882 |
Eugene--a domain specific language for specifying and constraining synthetic biological parts, devices, and systems