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Team:USTC-Software/overview
From 2011.igem.org
USTC-Software
Overview
The endeavor to build a user’s friendly powerful software tool for synthetic biology has passed on to the2011USTC software team.
“The programming talents needed to make great software need nuturing” Over the past 3 three years, the USTC softwares hasformed series.And we are going to develop more in the future, hoping that the USTC software series, with rounds of refinement, could stand out in the world to do something for synthetic biologist.
Under the care of many elder IGEMers, instructors, faculty members, ustc2011 software team devote themselves to a more professional and committedpractice both in technique and biology reality.
We named our project Lachesisand believe that our software will provide the user with a uniform platform to use their intelligence in synthetic biology as well as a coachfellow to novice.
On this platform, users arefree to fetch parts they want from the registry, build their assembly and visualize the network, and look at the design from different aspects.
Design and automatic modeling
We inherited the traditional way to demonstrate a design with an assembly view, which allow users to drag parts to form an assembly.The following step is to generate the network associated with the assembly.Here, we used an rule based modeling approachto build the network.On simulating the dynamics of the network, the ode modeling approach is adapted.
The biological system is complex, and sometimes the mathematical models trying to describe that is far from accurate.How do you know which substance or which ode equation plays a more vital role in the total performance?And it’s hard for modeler to tell the software all the possible combinations by listing all the reactions, all the substances that make sense.Based on these considerations, we use rule based modeling approach to depict a more comprehensive and elaborate profile of the gene circuit.That is, we first list out almost all the possible species and then decide which is more important.Anetwork generated with such an approach is immune to incompetent or too simplified modeling of the system.And it’s the software’s duty to analyze which ode can be omitted, which parameter is crucial.
Visualization
Traditional synthetic biology software tools try to illustrate the outcome of a circuit with a time course demonstration. The method is not so intuitive. To help novice to understand how the circuit work. We provide a new way to visualize the network.Putting the species and reactions on one map as nodes and show their relationships with lines connecting each other.If we have time , we will also make it possible to show how a network is generated in a dynamic visualized way.
Parameter tune and sensitivity analysis
In order to establish a workable circuit, biologist has to spend a lot of time on fine tuning the network, balancing on increase one promoter’s strength or decreasing another activator’s binding affinity. The process is a sweat, and sometimes there are just too much to consider and how can a novice know which parameter to tune to adjust to a better performance circuit? Our software will suggest the user a local direction of where to go when they are tracked in a plaetu, boggling what to do.
Assessment
Topology is more important than parameters, once you got a bad design, it’s hard to realize the anticipated behavior in a wide range of parameters, and our software can help to assess whether a designated network can work under parameter variations.
