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
- Synthetic Biology
- Systems Biology
- Molecular Biology
- NUPACK,BioCocoa,ApE,EnzymeX,Four Peaks,Genome Browser,CLC Genomics Workbench,MacGDE,CLC DNA WorkbenchCLC Protein Workbench,CLC RNA Workbench,CLC Sequence Viewer,KoriBlast,Geneious,MacVector,Novocraft aligner package for the Illumina Genome Analyzer,Mac Sequence, Molegro Molecular Viewer,AlleleID, Beacon Designer,PrimerPlex,OligoChecker X,PhyloCoco,OligoFaktory,GelEval,Serial Cloner,Central Dogma,OnScreen DNA Lite,A/G BLAST
- Software Engineering IDE
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
Implementation
Maintenance
Notes
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