Team:USTC-Software

From 2013.igem.org

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         <h2>[NAME]</h2>
         <h2>[NAME]</h2>
             <div id="description_l">
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             <h3>[BASIC FUNCTION]</h3>
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             <h3>Map</h3>
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             <!--p>Our application aims to simulate genetic networks. The application analyzes the stability of genetic networks after introduction of exogenous genes. Meanwhile, given the specific purposes of the original network, the application traces the regulative process back and gives possible regulative patterns of new gene.</p-->
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             <p>Map is a simple and easy software to visualize your experimental data. Click to import the data and you will get exactly what you want.</p>
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             <div id="description_r">
             <div id="description_r">
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             <h3>[APPROACH & METHODOLOGY]</h3>
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             <h3>Genetic Regulatory Networks</h3>
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             <!--p> The software is comprised of several modules as shown below: Introduction of modules:</p-->
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             <p>Genetic Regulatory Network(GRN) has been a major subject in recent researches of synthetic biology, and the modulation of a GRN gives rise to a variety of exciting works among iGEM programs as well as softwares assisting synthetic biology researches. Traditionally, researches of GRNs have been focused on either connecting GRNs with real parts in the registry or with experimental data. Therefore, we want to completely connect these three factors.</p>
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             <div id="description_l">
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             <h3>[PURPOSE & BACKGROUND]</h3>
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             <h3>Report</h3>
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             <!--p>Synthetic biology has been working on transforming target organisms, which usually means integrating new genes with an available network to achieve a high expression level of certain compounds. Nevertheless, the new-integrated genes are always not the original parts of the target metabolic network, so it is hard to predict how the new genes will affect the network. In some cases, new genes may even lead the network to a breakdown unexpected by wet lab experimenter.
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             <p>Report organizes all output information in folders. You can review the simulation result while looking at the behaviors of certain genes or proteins. In addition, Report creates a web page where you can review the results on the go.</p>
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On the other hand, some wet lab experimenters also expect that target organisms could increase some original gene’s expression. As a reference to those experiment, our software put a virtual gene into the network and figure out its best regulation. To achieve wet lab’s purpose, experimenter could find a specific gene based on our prediction regulation.
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    Lots of simulations of metabolic networks have been done with various methods. Most of them concentrate on the network itself and some of them analyze those network’s stability, robustness and Flux Balance Analysis (FBA).</p-->
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             <div id="description_l">
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             <h3>[SIGNIFICANCE & INNOVATION]</h3>
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             <h3>Reverse Engineering</h3>
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             <!--p> The software provides a great model as a reference before wet lab experiments. It provides suggestions on both specific practicality and input of exogenous gene. Meanwhile, the software is comprised of separate modules, which can be customized for different database and optimized as the amount of users grows.
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             <p> Reverse Engineering is the process of discovering the inner technological or scientific principles of a device, object or system. Synthetic biology is a combination of biology and engineering, and with the engineering process gets more and more complicated, often it is impossible to easily understand the inside, which is the biological part of the system. Reverse engineering serves perfectly for the purpose to bring back the biological essence.</p>
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    Previously, we could not find any specific work on the simulation and analysis of the newly introduced genes’ impact on regulation networks, and also those softwares were unavailable, which makes our software an innovation in the field. Algorithmically, the software aims to complete the simulation based on a small amount of lab data as possible.</p-->
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             </div>  
             </div>  

Revision as of 13:46, 16 August 2013

Slide

Take a gNAP before wearing your gloves! Genetic Network Analyze and Predict
The sketch and final GUI of gNAP!
We compare the result of our software with gene expression profile in literature.
We are USTC-Software!

USTC-Software Home

Welcome to our wiki!

USTC-Software —— The unicorn consists "USTC".
Having discussion with iGEM Software co-head judge, Gil Alterovitz.
Team members were working.
What's your opinion?
Come to see this ! ~

Description

Synthetic biology has been working on transforming target organisms, which usually means integrating new genes with an available network to achieve a high expression level of certain compounds. Nevertheless, the new-integrated genes are always not the original parts of the target metabolic network, so it is hard to predict how the new genes will affect the network.

Our application aims to simulate genetic networks. The application analyzes the stability of genetic networks after introduction of exogenous genes. Meanwhile, given the original network and specific purposes, the application traces the regulative process back and gives possible regulative patterns.

[NAME]

Map

Map is a simple and easy software to visualize your experimental data. Click to import the data and you will get exactly what you want.

Genetic Regulatory Networks

Genetic Regulatory Network(GRN) has been a major subject in recent researches of synthetic biology, and the modulation of a GRN gives rise to a variety of exciting works among iGEM programs as well as softwares assisting synthetic biology researches. Traditionally, researches of GRNs have been focused on either connecting GRNs with real parts in the registry or with experimental data. Therefore, we want to completely connect these three factors.

Report

Report organizes all output information in folders. You can review the simulation result while looking at the behaviors of certain genes or proteins. In addition, Report creates a web page where you can review the results on the go.

Reverse Engineering

Reverse Engineering is the process of discovering the inner technological or scientific principles of a device, object or system. Synthetic biology is a combination of biology and engineering, and with the engineering process gets more and more complicated, often it is impossible to easily understand the inside, which is the biological part of the system. Reverse engineering serves perfectly for the purpose to bring back the biological essence.

Console

Console is where you manage heavy computing and complex tasks. With different buttons controlling each parameter, you can optimize the behaviors of the software. We applied evolution algorithm and machine learning techniques in the network inferences to provide the best simulation of your data.

Sand Box

SandBox displays the Genetic Regulatory Networks in a clean and interactive way, with clear connection and 3-D interaction, you will get better understanding of how genes and proteins regulating each other.

Sponsors

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