Endy:Notebook/Wetware IDE

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(Use Cases, Requirements, Comments)
(Use Cases, Requirements, Comments)
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Primary requirements:
Primary requirements:
Physical building of parts
Physical building of parts
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*primers design for part cloning (including prefix and suffix. see:[http://ginkgobioworks.com/cgi/primer.cgi Ginkgo]
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*primers design for part cloning (including prefix and suffix. see:[http://ginkgobioworks.com/cgi/primer.cgi Ginkgo])
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*primers design for mutagenizing the restricition sites present in the original sequence to fit to the BBS designed one.
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*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]
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a very good prgram here: [http://www.stratagene.com/sdmdesigner/default.aspx stratagene]
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Revision as of 23:34, 8 December 2009

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Project Description

  • 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.

Review

Existing Software Tools

Peer-Reviewed Literature

  • 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

Use Cases, Requirements, Comments

Primary requirements: Physical building of 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


Click here to read the ongoing discussions... You are highly encouraged to contribute!

Design

Big Picture

Image:overall_architecture.png

General

  • Use a studio motif
    • Foyer - Entry point for the application
    • Library - Area to study natural or non-standard DNA sequences, basic and composite parts
    • Palette - Developers personal collection of DNA sequences, basic and composite parts
    • Canvas - Design environment DNA sequence refinement, basic and composite part development
    • Services - Area to explore the availability and cost of implementation services

Icons for BioBrick Studio iPhone

DNA Sequence Refinement Notebook

Implementation

BioBrick Studio Source Code

SynBioLib

Maintenance

Notes


Recent changes



Personal tools