Endy:Notebook/Wetware IDE

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
(Project Description)
(Use Cases, Requirements, Comments)
Line 36: Line 36:
==Use Cases, Requirements, Comments==
==Use Cases, Requirements, Comments==
-
Primary requirements:
+
*Physical building of standard biological 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 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]
-
*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]
+

Revision as of 17:57, 9 March 2010

Search this Project

Customize your entry pages

Project Description

  • We are in pursuit of 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

  • 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



Personal tools