Endy:Notebook/Wetware IDE

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(Design)
(BioBrick Studio Source Code)
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== Implementation ==
== Implementation ==
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====[http://code.google.com/p/biobrickstudio/ BioBrick Studio Source Code]====
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====[http://code.google.com/p/wetwarestudio/ Source Code]====
====[https://sourceforge.net/projects/synbiolib/ SynBioLib]====
====[https://sourceforge.net/projects/synbiolib/ SynBioLib]====

Revision as of 17:52, 9 March 2010

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Project Description

  • We are interested in an integrated development environment (IDE) that supports review, 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.

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 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


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

Design

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

Source Code

SynBioLib

Maintenance

Notes


Recent changes



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