Team:USTC-Software

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    <title >  Home  USTC-Software</title>
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            <p class="h2">Map</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><a href="https://2012.igem.org/Team:USTC-Software/software.html#map" class="da-link">Read More</a>
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            <div class="da-img"><img src="https://static.igem.org/mediawiki/2012/3/37/USTC-Software-images-1.png" width="480px" height="330"/></div>
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            <p class="h2">Console</p>
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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><a href="https://2012.igem.org/Team:USTC-Software/software.html#console" class="da-link">Read More</a>
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            <p class="h2">SandBox</p>
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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><a href="https://2012.igem.org/Team:USTC-Software/software.html#sandbox" class="da-link">Read More</a>
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            <p class="h2">Report</p>
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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><a href="https://2012.igem.org/Team:USTC-Software/software.html#report" class="da-link">Read More</a>
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                    <p class="h2">Reverse Engineering</p>
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<div id = "description_title">Project Description</div>
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<div id = "description_team_name">USTC-Software 2012</div>
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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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<p/>This summer, USTC-Software team is going to combine experiment data, genetic circuits and mathematical models into a single software, one that not only enables us to better understand Genetic Regulatory Networks (GRNs), but also provide researchers with complete workflows.
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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 on a plasmid or with experimental data, but complete work that combines the three factors have not been paid enough attention to. Here we propose a project that aims to fully connect them with a software that enables us to study GRNs in a much more efficient way.
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                    <p><a href="https://2012.igem.org/Team:USTC-Software/project.html#reverse-engineering">Read More</a></p>
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<p/>The project starts from using experimental data to generate proper ordinary differential equations (ODEs) that describe the behavior of the given data. With ODEs, we can abstract the possible GRNs and use the Parts available in registry to generate plasmid models that can be used in experiments. In this way, we combine mathematics, biology and experiments, the three main areas supporting a complete iGEM project, in a single software.  
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<div id="safety_title">Safety</div>
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<p>This century saw the increasing popularity of synthetic biology, which is a combination of biology, chemistry, physics, mathematics, computer science, etc. Greater importance comes with greater concern about the safety and security issues. As a software team, we are not facing the same issues that may caused by bacteria, chemicals and contaminating materials. Still, we are concerned with the possibility of safety problems maybe in or caused our project. We have listed the answers to the safety questions as follows.</p>
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<p class="question">1.Q: Would any of your project ideas raise safety issues in terms of : </p>
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                    <p class="h2">Genetic Regulatory Networks</p>
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<p class="question">Researcher safety,</p>
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<p class="question">Public safety, or</p>
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<p class="question">Environmental safety?</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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<p class="answer">A: No. Our project serves to help researchers design the feasible biological circuits with certain behavior, and thus relieve them from heavy experimental work in the lab. And all parts that we suggest are coming from natural E. Coli that have been fully sequenced and understood. So plans generated from our software simulate the behavior researchers want with things that can be found in nature. Therefore, our project will not raise safety issues in terms of researchers, public and environments.</p>
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                    <p><a href="https://2012.igem.org/Team:USTC-Software/project.html#grn">Read More</a></p>
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<p class="question">2.Q: Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues? If yes,</p>
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<p class="question">did you document these issues in the Registry?</p>
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<p class="question">how did you manage to handle the safety issue?</p>
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<p class="question">How could other teams learn from your experience?</p>
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<p class="answer">A: No. As a software team, we will not submit any BioBrick parts or devices. The parts we use in this project encodes non-hazardous genes and the data are from the registry and other databases that are widely recognized.</p>
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<p class="question">3.Q: Is there a local biosafety group, committee, or review board at your institution?</p>
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<p class="question">If yes, what does your local biosafety group think about your project?</p>
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<p class="question">If no, which specific biosafety rules or guidelines do you have to consider in your country?</p>
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                    <p class="h2">All-in-one Software</p>
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<p class="answer">A: Yes. The project in under the instruction of School of Life Sciences in University of Science and Technology of China. And with the supervision of our instructors and advisors, we are sure that our software development project will not raise any kind of issues in terms of researcher safety, public safety and environmental safety.</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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<p class="question">4.Q: Do you have any other ideas how to deal with safety issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering?</p>
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<p class="answer">A: Yes. (1) We suggest the registry of standard biological parts should have a dedicated safety page of every part to ensure that users would not raise any safety issue when using them. (2) In addition to safety usage of single part, a database should be setup to store the possible safety issue when using several parts together. (3) With the safety page and database, team of the software development track can write softwares that help researchers search safety issues that may be caused by their experiments.</p>
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                    <p><a href="https://2012.igem.org/Team:USTC-Software/software.html#software_intro">Read More</a></p>
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                    <p class="h2">Machine Learning</p>
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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><a href="https://2012.igem.org/Team:USTC-Software/project.html#machine-learning">Read More</a></p>
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{{Team:USTC-Software/global_footer}}

Latest revision as of 09:15, 9 August 2013

global_header

igem
Home USTC-Software

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.

Read More

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.

Read More

SandBox

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.

Read More

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.

Read More

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.

Read More

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.

Read More

All-in-one Software

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.

Read More

Machine Learning

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.

Read More

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