Applications

If you are a synthetic biologist, you may not be aware that there are already many software tools available that support different aspects of the synthetic biology workflow, such as optimizing DNA assembly or simulating gene networks. Each of the software tools listed here supports exchange of genetic designs in the SBOL file format (SBOL core) or supports display of genetic designs using standard SBOL Visual glyphs.

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Graphviz

a package of open-source tools initiated by AT&T Labs Research for drawing graphs specified in DOT language scripts.

iBioSim

iBioSim has been developed for the modeling, analysis, and design of genetic circuits.

ICE

Physical and Informatic repository and associated tools for plant seeds, microbial strains, DNA and protein sequences.

j5

DNA assembly design automation

MoSeC

Automated derivation of genetic circuit designs from computational models.

Parts & Pools

A graphical, drag and drop design of synthetic gene circuit with Standard Biological Parts.

Pigeon Visualizer

A tool for creating SBOL Visual diagrams from a concise textual representation.

Pinecone

Serotiny’s web-based protein design software aimed at researchers doing R&D for therapeutics, materials, as well as those in basic research.

Pool Designer

Designing Multiplexed Pools for Assembling Library Constructs

Proto BioCompiler

Proto BioCompiler generates optimized genetic regulatory network designs from specifications written in a high-level programming language, producing both SBOL specifications, visualization, and ODE models.