Endy:Notebook/Wetware IDE

(Difference between revisions)

Revision as of 23:34, 8 December 2009

BioBrick Studio is an integrated development environment (IDE) that supports review, annotatation, design, and implemention of standard biological parts
Our core goals are to develop programming languages, information models, communication/computational architectures that support the development and responsible use of standard biological parts.
BioBrick Studio Mobile is an application on the Apple iPhone/iPod Touch computing platform that complements BioBrick Studio
The tools support communication between members of the synthetic biology community and industry affiliates
The tools are components of the BioBuilder Educational Toolkit which are tools for project-based learning of biological science and engineering at the high school level.

Czar MJ, et al. Gene synthesis demystified. Trends in Biotechnology 27(2):63-72. (2009) Link
Goler JA, et al. Genetic design: rising above the sequence. Trends in Biotechnology 26(10):538-44. (2008) Link
Peccoud J, et al. Targeted development of registries of biological parts PLoS ONE 3(7):e2671. (2008) Link
Cai, et al. A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts. Bioinformatics 23(20): 2760-2767. (2007) Link
Villalobos, et al. Gene Designer: a synthetic biology tool for constructing artificial DNA segments. BMC Bioinformatics 2006 7:285. Link

Primary requirements: Physical building of standard biological parts.

primers design for part cloning (including prefix and suffix. see:Ginkgo)
primers design for mutagenize the restriction sites present in the original sequence to fit to the BBS designed one. A very good program here: stratagene

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 ==Use Cases, Requirements, Comments==
 Primary requirements:
-Physical building of parts
+Physical building of standard biological parts.
 *primers design for part cloning (including prefix and suffix. see:[http://ginkgobioworks.com/cgi/primer.cgi Ginkgo])
 *primers design for mutagenize the restriction sites present in the original sequence to fit to the BBS designed one. A very good program here: [http://www.stratagene.com/sdmdesigner/default.aspx stratagene]