DIVA bioCAD

DIVA bioCAD

Overview:

DIVA is a software platform that brings together a tool-chain that enables the design of (combinatorial) DNA libraries and automates the generation of protocols to construct them. It brings together a tool-chain of DNA component repositories and visualization tools (e.g., ICE/VectorEditor), visual design tools (e.g., DeviceEditor), DNA construction optimization tools (e.g., BOOST, j5), and biosecurity screening tools (e.g., BLiSS), and researcher DNA construction request consolidation and tracking (DIVA). It enables the DIVA DNA construction and DIVA DNA sequence validation capabilities, integrates downstream with the Experiment Data Depot, and importantly captures design intent (of great importance to downstream statistical and mechanistic learning/modeling approaches). Digital DNA sequence sources may be constrained by supported data formats (e.g., FASTA, Genbank, SBOL v1.1 and v2.0 are supported) and sequence length (portions of the tool-chain may not yet well support genome-scale sequences). DIVA is available to ABF researchers, as well as to ABF CRADA projects. Some components (e.g., ICE, VectorEditor, BOOST, j5) are accessible externally to the ABF (potentially through licensing or through commercially-available offerings).

References and Additional Information: 

Oberortner E, Cheng JF, Hillson NJ, and Deutsch S. (2016) Streamlining the Design-to-Build transition with Build-Optimization Software Tools (BOOST) ACS Synth. Biol.,DOI: 10.1021/acssynbio.6b00200

Ham, T.S., Dmytriv, Z. Plahar, H., Chen, J., Hillson, N.J., and Keasling, J.D. (2012) Design, Implementation and Practice of JBEI-ICE: An Open Source Biological Part Registry Platform and Tools. Nucleic Acids Research 40 (18):e141.

Chen, J., Densmore, D., Ham, T.S., Keasling, J.D. and Hillson, N.J. (2012) DeviceEditor visual biological CAD canvas. Journal of Biological Engineering 6:1.

Hillson, N.J.*, Rosengarten, R.D., and Keasling, J.D. (2012) j5 DNA Assembly Design Automation Software. ACS Synthetic Biology 1 (1), 14-21.

https://public-registry.jbei.org

https://boost.jgi.doe.gov

https://j5.jbei.org

Labs:

Lawrence Berkeley National Laboratory

Categories: Design