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Team:USTC-Software/project
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<p>Xudong Sun designed an algorithm for parameter analyzing for biological reaction network. We currently working on re-implementing | <p>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.</p> | the algorithm to provide an efficient graphical interface and free users from mathematical details.</p> | ||
| + | |||
| + | <h2>Overview</h2> | ||
| + | |||
| + | <p>The endeavor to build a user’s friendly powerful software tool for synthetic biology has passed on to the2011USTC software team.</p> | ||
| + | |||
| + | <p>“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.</p> | ||
| + | |||
| + | <p>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.</p> | ||
| + | |||
| + | <p>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.</p> | ||
| + | <p>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.</p> | ||
| + | |||
| + | <h3>Design and automatic modeling</h3> | ||
| + | |||
| + | <p>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.</p> | ||
| + | |||
| + | <p>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.</p> | ||
| + | |||
| + | |||
| + | <h3>Visualization</h3> | ||
| + | |||
| + | <p>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.</p> | ||
| + | |||
| + | |||
| + | <h3>Parameter tune and sensitivity analysis</h3> | ||
| + | |||
| + | <p>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.</p> | ||
| + | |||
| + | |||
| + | <h3>Assessment</h3> | ||
| + | |||
| + | <p>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.</p> | ||
| + | |||
<h2>Continue reading:</h2> | <h2>Continue reading:</h2> | ||
Revision as of 07:45, 3 October 2011
USTC-Software
Project Lachesis
Introduction
What is Lachesis?
The project Lachesis aims at providing and 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 categories 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.
Currently, we provide support for .sbml file, .model file and various kinds of other file types.
- 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.
- 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.
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.
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.
