Team:USTC-Software/project

From 2011.igem.org

Revision as of 12:49, 4 October 2011 by Gamegame151 (Talk | contribs)


Team:USTC-Software - 2011.igem.org/project

Motivation

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 an plug-in 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.

Continue reading: