Motivation

CAD tools in the field of electronic engineering has become a necessity, it saves the engineer a lot of time from simple trial and error.

Design in silicon is flexible, and one can manage the complexity of a framework, and analyze the result easily.

But in silicon design of gene circuit is far from mature. Pursuant to the goal of a user friendly tool, which can really give synthetic biologist some aids in designing gene circuit, the USTC SOFTWARE oriented in the following points:

• Free user from the chores of blind trial and error.

• Software prediction attests to model validity at the current state of synthetic biology development.

• Predictive behavior in silicon

• Combine rational design and directed evolution with an assessment tool of the robustness of the circuit.

• Various criteria to access a design: robustness to parameter variation and stochastic noise.

What is Lachesis?

The project Lachesis aims at providing an integrated, easy-using and extensible CAD environment for the general purpose of Synthetic Biology.

To achieve this goal, Lachesis adopts plug-ins based structure. We provide the following three kinds of plug-ins:

• Document parsers that handles various types of files, such as SBML and MoDeL.
• Models that each represents a specific kind of synthetic biological model.
• Views that present graphical user interface for users to work with biological models.

Available Features for Now

We have developed several useful plug-ins to justify our motivation as well as make Lachesis a powerful tool for designing and simulating Synthetic Biology models. Lachesis is coded with C++ and Qt. We welcome everyone to develop more helpful plug-ins for Lachesis.

Documents parsers

Currently, we provide support for .sbml file, .model file and various kinds of other file types.

Models

• Reaction Network Model represents an biological reaction network,e.g. read from an .sbml file,
• MoDeL model represents an model for the software MoDeL, which is an refactored and superior version of our last year's project iGaME.

Views

• Assembly View provides an easy-using graphical interface for working with MoDeL,
• Network View provides an graphical interface for editing biological reaction network,
• Parameter fitting view(still under construction) can analysis synthetic biology models' behavior with respect to parameter changing, and tune parameters to give the desired behavior.

Technology & Algorithms

Chen Liao refactored iGaME to form the new software package MoDeL, which is a rule-based modeling approach for synthetic biology.

Xudong Sun designed an algorithm for parameter analyzing for biological reaction network. We currently working on re-implementing the algorithm to provide an efficient graphical interface and free users from mathematical details.

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• Technology & Algorithm
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