Team:USTC Software/Project

From 2009.igem.org

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!align="center"|[[Team:USTC_Software|Home]]
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!align="center"|[[Team:USTC_Software/Team|The Team]]
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!align="center"|[[Team:USTC_Software/Project|The Project]]
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<!---!align="center"|[[Team:USTC_Software/Parts|Parts Submitted to the Registry]]--->
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!align="center"|[[Team:USTC_Software/Modeling|Modeling]]
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|We hold in hands the same motivation to adventure, unfold and appreciate the secret of life via the way of virtual evolution and simulation. The seven of us major from automation to engineering, mathematics to physics, grading from freshman to PhD candidates. Though there had been hard times, we have a faith. More hopefully, we’d express our gratitude to the kind support from the School of Life Science of USTC, which makes all impossible possible.
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From the one-month brainstorm we collected our first proposal – construct virtual bacteria. Yet, for some practical reasons we then shifted to a second proposal, which narrowed to molecular level simulation and later on turned out to be the prototype of our present project.
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|[[Image:USTC_Software_templogo.png|200px|right]]
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What do we desire to realize? In short, just tell us what you want your bio-device to behave, and we will return you with a list of eligible formation strategies for your design, of course, with bio-bricks.
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Turgidly as the idea might appear to be, this is basically an adoption of the gist of reverse engineering and evolution. By intake the custom-designated behaviors, we search, sometimes traverse, the solution space formed by nearly-inexhaustible combination of Biobricks. In order to make the simulative process applicable and practical, we employed a couple of algorithms widely used in computational sciences like Metropolis method and Dijkstra Algorithm to cut down the time cost and optimize the final result. Analysis on sensitivity and robustness has also been carried out to escort a reliable output of the final list of Biobrick combinations.
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<font size = "5">A First Introduction - Dr. Ding's One Summer</font>
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|align="center"|[[Team:USTC_Software | USTC_Software]]
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:*Do you want to enjoy more sunshine rather than fail and fail again in lab?
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:*Do you want to design a biological system with computers rather than by thinking day and night? 
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:*Do you want to have more reasonable plans rather than an uncertain one for your experiments?
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:*Follow [https://2007.igem.org/USTC/DingBo Dr. Ding], our ABCD will try to make your dreams come true.
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:*Wait!It would be much more efficient to get some general ideas about our ABCD firstly: [https://2009.igem.org/Team:USTC_Software/hoWMMD Mathematical Model], [https://2009.igem.org/Team:USTC_Software/hoWDesign#Design_Level Design Level], [https://2009.igem.org/Team:USTC_Software/hoWDesign#Design_Type_.28Sub_Level.29 Design Type].
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<!---(''Or you can choose different headings.  But you must have a team page, a project page, and a notebook page.'')--->
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:*Now, tell ABCD what you want. There are different ways for you to [https://2009.igem.org/Team:USTC_Software/hoWIO Input] your desired dynamics to ABCD.
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:*Are there any [https://2009.igem.org/Team:USTC_Software/hoWRestriction restrictions] on this biological network that happen to meet your needs? Good news! Dr. Ding will tell you how to complete this in ABCD.
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:*Our ABCD engine starts working. The state of art [https://2009.igem.org/Team:USTC_Software/hoWAlgorithm algorithms] we implement in ABCD will make design process automatically and different feasible solutions will be generated.   
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:*How can you find real components to construct the system. Thanks to [http://partsregistry.org/Main_Page BioBricks]. Our [https://2009.igem.org/Team:USTC_Software/hoWDatabase database] makes it possible to retrieve them while some new standards should be proposed.
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:*Also, if our memory serves right, there are quite a few brilliant software packages specified at BioBrick organizing and related management, for example, [https://2008.igem.org/Team:UC_Berkeley_Tools Clotho] from Berkeley's dry team, 2008. If combined with these softwares, the construction will be even more applicable.
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== '''Overall project''' ==
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Your abstract
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:*Now, you may feel happy to realize a function such as [https://2009.igem.org/Team:USTC_Software/WhatDemo#Example_1._Synthetic_Oscillator oscillation], [https://2009.igem.org/Team:USTC_Software/WhatDemo#Example_2:_Perfect_Adaptation perfect adaptation] or [https://2009.igem.org/Team:USTC_Software/WhatDemo#Example_3._Bistable_Toggle_Switch bistability] following our solutions. But we still hold earnest expectations. Is it possible to complete the fabrication automatically in the [https://2009.igem.org/Team:USTC_Software/When future]?
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== Project Details==
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===Input===
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The input mainly consists of three parts. A targeted curve depicting the desired time dependent behavior of the device, a user designated choice of interaction forms represented in the mathematical factors of corresponding ODEs, and an optional curve which indicates the weighs (how much you care about a specific behavior on the targeted behavior curve) exerted along the first curve. Users just need to draw those curvatures by rough sketches in a conventional GUI resembling that of a painting tablet.
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[[Image:DBChe6.png|350x350px]]
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===System Reconstruction===
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After deciding the formation of the ODE array that bears the information of the bio-system, a search in the parameter space dimensioned by all equation coefficients is set off. Generally speaking, we divide the parameter space into pieces, start parallel searching in each region, and single out ‘regional best’s by means of simulated annealing or Metropolis sampling method. The ODE array is solved by self-adaptive fourth-order Runge Kutta method.
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{{USTCSW_Foot}}
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===Sensitivity Analysis===
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An application calls for robustness and universality to be truly applicable. As non-linear ODE array is well notorious for its instability, we realize the significance to test how sensitive the identification process relies on minor environmental perturbations existing in the coefficient matrix and initializations.
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……
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……
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===Output and GUI===
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===Highlights===
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== Simulation Results ==
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Latest revision as of 16:04, 21 October 2009


About Team and People Project Standard Notebook Demo Safety External Links


A First Introduction - Dr. Ding's One Summer

DBChe1.png

  • Do you want to enjoy more sunshine rather than fail and fail again in lab?
  • Do you want to design a biological system with computers rather than by thinking day and night?
  • Do you want to have more reasonable plans rather than an uncertain one for your experiments?

  • Follow Dr. Ding, our ABCD will try to make your dreams come true.
  • Now, tell ABCD what you want. There are different ways for you to Input your desired dynamics to ABCD.

DBChe2.png

DBChe3.png

  • Are there any restrictions on this biological network that happen to meet your needs? Good news! Dr. Ding will tell you how to complete this in ABCD.

  • Our ABCD engine starts working. The state of art algorithms we implement in ABCD will make design process automatically and different feasible solutions will be generated.

DBChe4.png

DBChe5.png

  • How can you find real components to construct the system. Thanks to [http://partsregistry.org/Main_Page BioBricks]. Our database makes it possible to retrieve them while some new standards should be proposed.
  • Also, if our memory serves right, there are quite a few brilliant software packages specified at BioBrick organizing and related management, for example, Clotho from Berkeley's dry team, 2008. If combined with these softwares, the construction will be even more applicable.

  • Now, you may feel happy to realize a function such as oscillation, perfect adaptation or bistability following our solutions. But we still hold earnest expectations. Is it possible to complete the fabrication automatically in the future?

DBChe6.png

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