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Team:USTC-Software/software.html
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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.
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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.
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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.
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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.
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REBORN: synthetic biology tools for hackers
Are you those are curious about the fundamental principles of everything? Or those are itching to know what is inside a "black box"? Or even willing to share the joy and fun of discovering something new? If yes, you are a hacker. Synthetic biology needs hackers; it needs those who want to discover the mysterious yet beautiful side of biological system. And we, USTC-Software, provide tools for them. It is time to REBORN.
REBORN, Reverse Engineering for BiolOgical Regulatory Networks, is an application suite to reversely engineer a biological system and get a better understanding of the basic structures of the system.
To combine experimental data, biological networks, and mathematical networks into one integrated software, we build a suite of applications for the convenience of both common users and biological researchers. Therefore, the all-in-one software has powerful functions including displaying output results, reverse engineering the system, viewing 3D graph of GRNs and guiding further experiments.
Map
Map is a simple tool to input experimental data and display it on a beautiful map. Click each time sequence and you can see a brief summary on the right. Map works great with other tools in the suite. Click the GO TO CONSOLE button to jump to the Console and we stores the data in right format for further calculation and manipulation.
Console
To do the reverse engineering work, you really need a place to do heavy computing and simulation, and that is what Console are built for. Console is a dedicated tool to reversely engineer the input behavior to get the possible structures of a biological system. You can manipulate lots of parameters in the Console to get different desired results. Since the process may tack some time, we integrated email and ftp service in the tool to automatically upload results on to a server and email you with a link. So no matter where you are, you can check out the latest results.
Sandbox
Sandbox is an immersive 3-D tool to view the structure of a genetic regulatory network. You can drag, scroll to change the viewpoint and camera angle of the 3-D scene to get a better understanding of the whole structure.
Report
Last, when Console have done all the heavy computation, it will generate results and automatically make it a well-designed report. The report includes the simulated behavior of the system and reverse-engineered structure that best resemble the behavior. With the Report tool you can show others clearly what may be inside the "black box".
As to experimental data, this all-in-one software uses time courses as its input. The convenience and user friendly input interface let users feel comfortable and easy to interact. In generating possible biological network candidates, genetic algorithm, which is a commonly used algorithm in computer science, is also used for shorter calculation time and smaller computational space. The mathematical models accounts for the most important part in this all-in-one software. In our program, ODE model is used to analyze the reaction network of the GRN. Other mathematical models including Dynamic Baysian Network or Boolean Network have been discussed by both mathematicians and biological researchers.
To develop an all-in-one software is indeed a very smart idea for people who are interested in synthetic biology. Also we believe our software can make a difference to help this group of people.
The software is now host on GitHub:
Regulon Lib: a Clotho App
To better assist synthetic biological researchers and other iGEM programmers, we integrate our database and recursion algorithm into one independent application on Clotho platform(Clotho is a java based platform for both software users and developers). Our clotho app, with the name “Regulon Lib”, mainly aims at finding proper regulators and regulatees in the two matrices. To make our app more user friendly, we optimize the GUI of our app and write a detailed user manual for ordinary users. It has two main features: serving two modes for users to implement GRN regulatory matrix, aiding users to find vivo valid regulators and regulatees for their experiments.
1) Main Page: Library of regulations.
The only inputs are your regulatory matrix size and elements of the matrix. The picture takes 4 positive regulations for example. Right below the input table, two buttons respectively named ”mode 1” and “mode 2” mean the database you will search in. To say in a more specific way, by clicking “mode 1” operon-operon matrix is used and by clicking “mode 2” gene-promoter matrix is employed. The output results of using these two modes are pasted below:

The possible regulatory network candidates are shown in the text field. Users can either save it or clear it by clicking right.
2) Search Page: Library of regulons.
By clicking “Search” in the menu bar, two kinds of search page is for users to choose. The example presented here only takes account of “Search In Operon-Operon”.

The table on the right side includes all the regulators and the left side the regulatees. These are choice pools for user to select one. As for the two tables in the middle, the right side is called “regulatee candidates table”, in which all the regulatees corresponding to a certain regulator will be presented here including the regulation type. It is the same for the left table by exchanging the terminology “regulator” and “regulatee”.
For more information about how to use this app to find right regulons, you can refer to user manual of this app.
The software is now host on GitHub:
