Team:UCSF/lily2

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    <title> USTC-Software Home</title>
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    <meta name="Description" content="Our teammates have designed a software to help the synthetic biologists work more efficiently
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in the summer holiday.we enjoyed igem ,we enjoyed the competition ">
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Thanks a lot to the 2011 Brown-Stanford and 2012 Lethbridge iGEM teams for snippets of their code!
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Check out their wikis at:
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https://2011.igem.org/Team:Brown-Stanford
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https://2012.igem.org/Team:Lethbridge
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***/
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            <div class="camera_caption fadeFromBottom"> <em>USTC-Software —— The unicorn consists "USTC".</em> </div>
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            <div class="camera_caption fadeFromBottom"><em>Having discussion with iGEM Software co-head judge, Gil Alterovitz.</em></div>
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        <h1>Description</h1>
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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. </p>
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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 original network and specific purposes, the application traces the regulative process back and gives possible regulative patterns.</p>
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            <h3>Map</h3>
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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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            <h3>Genetic Regulatory Networks</h3>
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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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            <h3>Report</h3>
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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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            <h3>Reverse Engineering</h3>
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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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            <h3>Machine Learning</h3>
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            <p>Machine learning is a branch of artificial intelligence that is widely used in many disciplines such as software engineering, computer vision, finance, Neuroscience and bioinformatics. During reverse engineering, we use many machine learning techniques and algorithms to help optimize the process so that the process is faster and more accurate.</p>
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            <p>In order to fully combine biological networks, experimental data and mathematical models, we build a suite of applications that serves to solve different tasks and make them work seamlessly together. With the all-in-one software suite, you can display experimental data, extract mathematical models, understand the genetic regulatory networks and get a well-designed report of the results. We designed the user interfaces to be fun to interact with and easy to use.</p>
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<h2><center>Operation CRISPR: Deploying precision guided tools to target unique species in a complex microbiome</h2></center>
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<p>In microbial communities, bacterial populations are commonly controlled using indiscriminate, broad range antibiotics. There are few ways to target specific strains effectively without disrupting the entire microbiome and local environment. The goal of our project is to take advantage of a natural horizontal gene transfer mechanism in bacteria to precisely affect gene expression in selected strains. We combine bacterial conjugation with CRISPRi, an RNAi-like repression system developed from bacteria, to regulate gene expression in targeted strains within a complex microbial community. One possible application is to selectively repress pathogenic genes in a microbiome, leaving the community makeup unaffected. In addition, we use CRISPRi to lay the groundwork for transferring large circuits that enable complex functionality and decision-making in cells. </p>
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            <div id="ash_container"><h3>Console</h3>
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                  <p>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.</p>
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                              <div><span><a href=" ">Read More</a></span></div>
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            <div id="ash_container"><h3>Sand Box</h3>
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                        <p>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.</p>
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                              <div><span><a href="">Read More</a></span></div>
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                    <div><a href="https://2013.igem.org/Team:UCSF/About_Us">
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                    <a href="https://2013.igem.org/Team:UCSF/About_Us"><h3>Team</h3></a>
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                    <p>Meet our dedicated team of under-graduates who conceived of, planned, and carried out the whole project.</p></a>
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              <a href="https://2013.igem.org/Team:UCSF/Project/Background"><img src="https://static.igem.org/mediawiki/2013/c/c2/UCSF2013_MainBox_Project-1.jpg" class="blur"></a>
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              <a href="https://2013.igem.org/Team:UCSF/Project/Background"><h3>Project</h3></a>
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                    <p>Discover our precision guided tools to target unique species in a complex microbiome and our groundwork for transferring large circuits that enable complex functionality and decision-making in cells.</p>           
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                    <a href="https://2013.igem.org/Team:UCSF/Modeling">
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                    <a href="https://2013.igem.org/Team:UCSF/Modeling"><h3>Modeling</h3></a>
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                    <p>Take a look at how we use mathematical modeling to facilitate the design and construct of our project.                    </p>
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              <a href="https://2013.igem.org/Team:UCSF/Exploratorium"><img src="https://static.igem.org/mediawiki/2013/7/7c/UCSF2013_MainBox_HP.jpg" class="blur"</a>
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              <a href="https://2013.igem.org/Team:UCSF/Exploratorium"><h3>Human Practice</h3></a>
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                    <p>Examine how we teach Synthetic Biology to the general public through night event at Exploratorium and to high school students through a collaboration with Lincoln High School.</p>
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<h2>Sponsors</h2>
 
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Latest revision as of 19:15, 27 September 2013

UCSF Home

UCSF iGEM 2013 Group Photo
Brainstorming project ideas during our second week of Bootcamp
Presenting a poster at the UCSF Center for Systems and Synthetic Biology retreat
Having a skype meeting with one of our mentors!
Human Practices: Speaking about Synthetic Biology at the SF Exploratorium
Having fun outside of the lab making ice cream with dry ice

Operation CRISPR: Deploying precision guided tools to target unique species in a complex microbiome

In microbial communities, bacterial populations are commonly controlled using indiscriminate, broad range antibiotics. There are few ways to target specific strains effectively without disrupting the entire microbiome and local environment. The goal of our project is to take advantage of a natural horizontal gene transfer mechanism in bacteria to precisely affect gene expression in selected strains. We combine bacterial conjugation with CRISPRi, an RNAi-like repression system developed from bacteria, to regulate gene expression in targeted strains within a complex microbial community. One possible application is to selectively repress pathogenic genes in a microbiome, leaving the community makeup unaffected. In addition, we use CRISPRi to lay the groundwork for transferring large circuits that enable complex functionality and decision-making in cells.

Team

Meet our dedicated team of under-graduates who conceived of, planned, and carried out the whole project.

Project

Discover our precision guided tools to target unique species in a complex microbiome and our groundwork for transferring large circuits that enable complex functionality and decision-making in cells.

Modeling

Take a look at how we use mathematical modeling to facilitate the design and construct of our project.

Human Practice

Examine how we teach Synthetic Biology to the general public through night event at Exploratorium and to high school students through a collaboration with Lincoln High School.

Special Thanks to Our 2013 iGEM Team Sponsors!


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