Software

Scientists currently enjoy unprecedented access to custom genetic constructs through synthetic biology. The cost of gene synthesis falls while efficiency rises – circumstances that have encouraged researchers to move beyond gene and pathway synthesis towards whole genome synthesis. A chemically synthesized genome has the benefit of being customizable, offering designers a chance to test otherwise intractable hypotheses about chromosome structure, function, and evolution. However, while tools for the design of synthetic genes abound, the larger-scale problem of computer-assisted chromosome design remains unaddressed. Practitioners currently either edit sequence by hand or press smaller design tools into awkward service. An optimal genome design framework allows a team of designers to make coordinated modifications to sequence at both the base pair and the genome scale, to track changes, and to roll back changes at multiple scales. We have developed several software packages and frameworks, all with permissive open source licenses, to permit groups throughout academia, government, and industry to make faster progress.

BioPartsBuilder: Combinatorial assembly of biological parts

Publication: Yang et al 2016 Bioinformatics
Software: GitHub repository

BioPartsDB: Synthetic biology workflow

Publication: Stracquadanio et al 2016 Bioinformatics Software: GitHub repository

BioStudio: Design and visualization of synthetic genomes

Publication: Richardson et al 2017 Science
Software: MetaCPAN repository
Update to installation notes: BioStudio Update

CloneQC: Sequence verification for synthetic biology

Publication: Lee at al 2010 Nucleic Acids Research
Software: GitHub repository

GeneDesign: Design of synthetic genes

Publication: Richardson et al 2010 Nucleic Acids Research Sofware: MetaCPAN repository

SCRaMbLE reconstruction: Reconstruction of SCRaMbLE’d synthetic genomes

Publication: Shen, Stracquadanio et al 2016 Genome Research
Software: GitHub repository

Software

BioStudio

Update for 2023 We recommend installing as an AWS EC2 instance using our AMI ami-dcb8f4b6 as described in our supplement from Richardson et al 2017 Science. Most of the notes below are standard procedures for launching an AWS EMI. The BioStudio-specific notes are highlighted as BioStudio-specific. Amazon provides a guide to launching an EC2 instance. We recommend an instance with resources equivalent to m5.xlarge or larger and configuring to accept SSH, HTTPS, and HTTP.