Qath - a programming language for synthetic biology
Qath is a formal language for designing engineered genomes. Its syntax and data model is similar to mainstream programming languages like Java and C#.
Cell-based therapies for chronic diseases
The intended use of the Qath language is to design engineered genomes for cell-based therapies like adoptive immune cells against cancer, or cells that migrate into damaged tissue and heal / replace it.
The Qath genome compiler
Please check here the status of the Qath compiler software and planned release date.
Human somatic-cell chassis
A 'chassis' in synthetic biology means the cell into which enginereed genes are introduced. The chassis is expected to provide the 'runtime' environment that executes the genetic program: expressing and translating the new genes, and performing the intended functionality.
Synthetic biologists mostly use bacterial chassis, like E. coli.
Here, I try to sketch the genome for a chassis that is based on human somatic cells, that can be safely introduced into the human body as a therapeutic agent, without triggering immune response, and can be quickly removed when necessary. It is meant to be safe, stable, immortalized, easy to culture, resistant to viruses, free from transposable elements, and extendable through usual transformation techniques.
The Qath language
- an overview of the language ;
- A tutorial that explains that Qath language while guiding through a simple but real genome design example;
- the detailed language specification and reference .
The Qath gene network simulator
The Qath compiler includes a simple simulator for gene reguratory networks (GRN) , based on boolean networks. This allows some in-silico verification of genome designs.