The ultimate aim of the TEBio project is to develop a design framework (including associated algorithms and software) for designing circuits at the population level.
Several aspects of the project are focused on solving visualisation and human-computer interaction problems that arise when trying to do this.
Synthetic Biology is defined as the "engineering of biology". It aims to apply engineering design principles and approaches in order to construct biological circuits, devices and systems for a particular purpose and application.
One major area of synthetic biology is the genetic engineering of cells, in order to create synthetic genetic circuits with some desired function, meeting a specification. This is reminiscent of the design of electrical circuits, where capacitors, inductors, resistors etc are linked together to form a circuit with a particular behaviour (e.g. a filter). Examples of Synthetic Biology circuits that have been designed to date include switches, oscillators or simple feedback control loops. Most of these circuit designs operate within a single cell, with the circuit within each cell being isolated from the others.
Cells have evolved several mechanisms to communicate and affect each other, e.g. through so-called quorum sensing molecules. Previous work has shown that it is possible to create population-level behaviours, but there are several unanswered questions on what type of circuits is achievable and when a circuit should be built across populations, rather than being implemented within a single cell.
The problem of automatically designing genetic circuits is broad, and so we have identified a series of problems, which we are addressing in parallel.
In so doing, we are creating a suite of software tools that we are releasing under a free-software license (the BSD license).
To be able to rationally engineer systems, we need mathematical models of them. A widely-used standard for modelling systems of (bio)molecular reaction systems is the Systems Biology Markup Language (SBML). sbml-diff is a tool that can draw a range of diagrams illustrating the structure of a single model, or comparing two or more models.
TEBio-fit is a tool for visualizing the results of parameter fitting and model comparison using Approximate Bayesian Computation. It visualises the results of the ABC-SysBio tool.
Before we can create a system that will design circuits to do 'what we want', we need a precise way to specify exactly what it is that we want the circuit to do. One promising approach is to express specifications using Signal Temporal Logic. However, when written as strings of mathematical symbols these are difficult to interpret, so we have developed a visual editor for viewing and editing specifications - TimeRails.
Laboratory robots offer the promise of increasing laboratory throughput, freeing up researchers to think rather than pipette, and potentially increase reproducibility. However, existing interfaces for telling the robot what to do are verbose. Lists of Liquids is a novel user interface designed to be faster and easier to use.
