Dynamic Modeling of Cellular Populations within iBioSim

Abstract

As the complexity of synthetic genetic circuits increases, modeling is becoming a necessary first step to inform subsequent experimental efforts. In recent years, the design automation community has developed a wealth of computational tools for assisting experimentalists in designing and analyzing new genetic circuits at several scales. However, existing software primarily caters to either the DNA- or single-cell level, with little support for the multicellular level. To address this need, the iBioSim software package has been enhanced to provide support for modeling, simulating, and visualizing dynamic cellular populations in a two-dimensional space. This capacity is fully integrated into the software, capitalizing on iBioSim's strengths in modeling, simulating, and analyzing single-celled systems.

A Versatile Microfluidic Device for Automating Synthetic Biology

“…We used our device to design two sets of 16 plasmids: one set of plasmids for Golden Gate and Gibson assembly, which contains a p15A origin of replication gene and kanamycin selection marker for bacteria, and one set of plasmids for yeast assembly, which contains both a 2 micron origin of replication gene with a tryptophan selection marker for yeast and an F1 origin of replication gene with an ampicillin selection marker for bacteria. Both sets of plasmids have two common sets of DNA inserts: four promoter (Prom) variants (1,2,9,11) and four bicistronic design (BCD) variants (1,2,20,21) coupled with a gf p gene. Prior to DNA assembly, these fragments for each assembly method are digested with DpnI (as well as BsaI for Golden Gate assembly) and gel purified (Figure 3a−c).…”

Plant synthetic biology for molecular engineering of signalling and development

“…When combined with high-fidelity genomic engineering 86,87 , higher efficiency transformation 88 , high-throughput phenotyping platforms 89 and improved in silico tools for pathway design and testing 90–94 , the scale of reasonable plant engineering projects expands dramatically. Detailed knowledge of a genome, specifically the genotype-to-phenotype map, is essential for targeting and rapidly prototyping the optimal candidates for engineering.…”

Guidelines for Reproducibly Building and Simulating Systems Biology Models

“…In particular, simulation software programs should be expanded to support the Arrays, Distributions, Flux Balance Constraints, Hierarchical Model Composition, and Multistate and Multicomponent Species SBML packages. Several simulation software programs, including BioUML [25] and iBioSim [26], have already begun to support these packages. Unfortunately, most simulation software developers have insufficient funding to implement every package.…”