Standard Virtual Parts

Project Description

Although synthetic biological systems can be designed manually, complex and large-scale projects require computational design and simulation. Computational modelling enables synthetic biologists to develop reliable and predictable novel genetic circuits. Therefore, in addition to cataloguing genetic parts, models of these parts should also be available in order to model the behaviour of synthetic biological systems.

Standard Virtual Parts (SVPs) is a formalism developed for the modelling of genetic elements. Virtual parts are modular, reusable models of physical biological parts such as promoters and RBSs, and can be composed based on the exchange of commonly accepted biological signals such as PoPS and RiPS. These models link the nucleotide sequences of parts to their dynamic behaviour. Therefore, the behaviour of biological systems constructed using physical biological parts can be modelled and simulated using SVPs.

SVPs

In order to construct models of biological systems, information about how parts interact and regulate each other must be available. This information can then be combined with kinetic parameters in order to create simulateable models. BacillOndex already provides information about biological parts and their interactions, integrated from various bioinformatics databases. This integrated knowledge base was therefore used to create SVPs for Bacillus subtilis.

The catalogue, called Virtual Parts, currently holds around 3000 SVPs for promoters, CDSs, RBSs, terminators and shims, and can be accessed via a website. Using the website, SVPs can be browsed manually or computationally via the REST-based interface. A Java API that handles the communication to the website and provides utility methods to contruct simulateable models is also available. Models are currently available in standard SBML format. In addition, sequence-based descriptions of parts can be accessed in SBOL format.

Funding

This project is funded by the EPSRC/NSF via grant EP/H019162/1.